ORCID Profile
0000-0002-4562-9131
Current Organisations
Christian Medical College Vellore
,
Murdoch University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Crop and Pasture Production | Plant Physiology | Crop and Pasture Nutrition | Crop and pasture improvement (incl. selection and breeding) | Crop and Pasture Biochemistry and Physiology | Plant Biochemistry And Physiology | Plant Improvement (Selection, Breeding And Genetic Engineering) | Plant biology | Genomics | Plant pathology
ANZSRC Socio-Economic Objective (SEO)
Environmentally Sustainable Plant Production not elsewhere classified | Grain legumes | Grain Legumes | Expanding Knowledge in the Agricultural and Veterinary Sciences |
Related Links
Publications
Characterization and mapping of Dt1 locus which co-segregates with CcTFL1 for growth habit in pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 24-05-2017
Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses
Publisher: Springer Science and Business Media LLC
Date: 28-01-2015
Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding
Publisher: Public Library of Science (PLoS)
Date: 10-06-2014
Evidence of a unique inter-allelic epistatic interaction for seed coat color in pigeonpea [Cajanus cajan (L.) Millspaugh]
Publisher: Springer Science and Business Media LLC
Date: 04-01-2012
Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea
Publisher: Wiley
Date: 30-04-2023
DOI: 10.1002/TPG2.20333
Abstract: Terminal drought is one of the major constraints to crop production in chickpea ( Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi‐parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013–14 and 2014–15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high‐density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome‐wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity‐by‐descent (IBD)‐based mixed model approach was used to map quantitative trait loci (QTLs). The IBD‐based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker‐trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas.
Impact of Genomic Technologies on Chickpea Breeding Strategies
Publisher: MDPI AG
Date: 23-08-2012
A simple hybridization-based strategy for the generation of non-redundant EST collections - A case study in barley (Hordeum vulgare L.)
Publisher: Elsevier BV
Date: 09-2004
Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids
Publisher: Oxford University Press (OUP)
Date: 07-2018
Abstract: Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors’ investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl millet. Despite the fact that 6× more sequencing data were generated per s le for RAD-seq than for tGBS, tGBS yielded more than 2× as many informative SNPs (defined as those having MAF & 0.05) than RAD-seq. A genomic prediction scheme utilizing only data from hybrids generated prediction accuracies (median) ranging from 0.73-0.74 (1000-grain weight), 0.87-0.89 (days to flowering time), 0.48-0.51 (grain yield) and 0.72-0.73 (plant height). For traits with little to no heterosis, hybrid only and hybrid/inbred prediction schemes performed almost equivalently. For traits with significant mid-parent heterosis, the direct inclusion of phenotypic data from inbred lines significantly (P & 0.05) reduced prediction accuracy when all lines were analyzed together. However, when inbreds and hybrid trait values were both scored relative to the mean trait values for the respective populations, the inclusion of inbred phenotypic datasets moderately improved genomic predictions of the hybrid genomic estimated breeding values. Here we show that modern approaches to genotyping by sequencing can enable genomic selection in pearl millet. While historical pearl millet breeding records include a wealth of phenotypic data from inbred lines, we demonstrate that the naive incorporation of this data into a hybrid breeding program can reduce prediction accuracy, while controlling for the effects of heterosis per se allowed inbred genotype and trait data to improve the accuracy of genomic estimated breeding values for pearl millet hybrids.
Can omics deliver temperature resilient ready-to-grow crops?
Publisher: Informa UK Limited
Date: 07-04-2021
Identification of dominant and recessive genes for resistance to Fusarium wilt in pigeonpea and their implication in breeding hybrids
Publisher: Springer Science and Business Media LLC
Date: 29-04-2012
Trehalose: A sugar molecule involved in temperature stress management in plants
Publisher: Elsevier BV
Date: 10-2023
Molecular mapping of dry root rot resistance genes in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 27-05-2021
Smart reprograming of plants against salinity stress using modern biotechnological tools
Publisher: Informa UK Limited
Date: 15-08-2023
DOI: 10.1080/07388551.2022.2093695
Abstract: Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.
Cereal Genomics: Excitements, Challenges and Opportunities
Publisher: Springer Netherlands
Date: 2013
Integrated multi‐omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.)
Publisher: Wiley
Date: 10-05-2023
DOI: 10.1002/TPG2.20337
Abstract: Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought‐responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought‐tolerant), and ICC 1882 (drought‐sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4′‐O‐methyltransferase, UDP‐ d ‐glucose/UDP‐ d ‐galactose 4‐epimerase, and delta‐1‐pyrroline‐5‐carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root‐omics data also revealed some key candidate genes underlying the drought‐responsive “QTL‐hotspot” region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.
Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and ‘Crack-Entry’ Legume Groundnut (Arachis hypogaea L.)
Publisher: MDPI AG
Date: 20-02-2020
Abstract: Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis (RNS) with nitrogen-fixing soil bacteria which are collectively called rhizobia. This mutualistic association is highly specific, and each rhizobia species/strain interacts with only a specific group of legumes, and vice versa. Nodulation involves multiple phases of interactions ranging from initial bacterial attachment and infection establishment to late nodule development, characterized by a complex molecular signalling between plants and rhizobia. Characteristically, legumes like groundnut display a bacterial invasion strategy popularly known as “crack-entry’’ mechanism, which is reported approximately in 25% of all legumes. This article accommodates critical discussions on the bacterial infection mode, dynamics of nodulation, components of symbiotic signalling pathway, and also the effects of abiotic stresses and phytohormone homeostasis related to the root nodule symbiosis of groundnut and Bradyrhizobium. These parameters can help to understand how groundnut RNS is programmed to recognize and establish symbiotic relationships with rhizobia, adjusting gene expression in response to various regulations. This review further attempts to emphasize the current understanding of advancements regarding RNS research in the groundnut and speculates on prospective improvement possibilities in addition to ways for expanding it to other crops towards achieving sustainable agriculture and overcoming environmental challenges.
The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.)
Publisher: Springer Science and Business Media LLC
Date: 11-03-2010
Abstract: Pigeonpea ( Cajanus cajan (L.) Millsp) is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [ Fusarium wilt (FW), sterility mosaic disease (SMD), etc.] are serious challenges for sustainable crop production. Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance. Availability of limited genomic resources, however, is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses. With an objective of enhancing genomic resources in pigeonpea, this study reports generation and analysis of comprehensive resource of FW- and SMD- responsive expressed sequence tags (ESTs). A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ('ICPL 20102' and 'ICP 2376') and SMD ('ICP 7035' and 'TTB 7') and a total of 9,888 (9,468 high quality) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231. Clustering and assembly analyses of these ESTs resulted into 4,557 unique sequences (unigenes) including 697 contigs and 3,860 singletons. BLASTN analysis of 4,557 unigenes showed a significant identity with ESTs of different legumes (23.2-60.3%), rice (28.3%), Arabidopsis (33.7%) and poplar (35.4%). As expected, pigeonpea ESTs are more closely related to soybean (60.3%) and cowpea ESTs (43.6%) than other plant ESTs. Similarly, BLASTX similarity results showed that only 1,603 (35.1%) out of 4,557 total unigenes correspond to known proteins in the UniProt database (≤ 1E-08). Functional categorization of the annotated unigenes sequences showed that 153 (3.3%) genes were assigned to cellular component category, 132 (2.8%) to biological process, and 132 (2.8%) in molecular function. Further, 19 genes were identified differentially expressed between FW- responsive genotypes and 20 between SMD- responsive genotypes. Generated ESTs were compiled together with 908 ESTs available in public domain, at the time of analysis, and a set of 5,085 unigenes were defined that were used for identification of molecular markers in pigeonpea. For instance, 3,583 simple sequence repeat (SSR) motifs were identified in 1,365 unigenes and 383 primer pairs were designed. Assessment of a set of 84 primer pairs on 40 elite pigeonpea lines showed polymorphism with 15 (28.8%) markers with an average of four alleles per marker and an average polymorphic information content (PIC) value of 0.40. Similarly, in silico mining of 133 contigs with ≥ 5 sequences detected 102 single nucleotide polymorphisms (SNPs) in 37 contigs. As an ex le, a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments. Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable licons were generated. PCR licons were not obtained in case of 4 contigs. Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved lified polymorphic sequences (CAPS) assay. The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance. Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes. Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding.
A systematic dissection in oilseed rape provides insights into the genetic architecture and molecular mechanism of yield heterosis
Publisher: Wiley
Date: 11-05-2023
DOI: 10.1111/PBI.14054
Abstract: Heterosis refers to the better performance of cross progeny compared with inbred parents, and its utilization contributes greatly to agricultural production. Several hypotheses have been proposed to explain heterosis mainly including dominance, over‐dominance (or pseudo‐overdominance) and epistasis. However, systematic dissection and verification of these hypotheses are rarely documented. Here, comparison of heterosis level across different traits showed that the strong heterosis of composite traits (such as yield) could be attributed to the multiplicative effects of moderate heterosis of component traits, whether at the genome or locus level. Yield heterosis was regulated by a complex trait‐QTL network that was characterized by obvious centre‐periphery structure, hub QTL, complex up/downstream and positive/negative feedback relationships. More importantly, we showed that better‐parent heterosis on yield could be produced in a cross of two near‐isogenic lines by the pyramiding and complementation of two major heterotic QTL showing partial‐dominance on yield components. The causal gene ( BnaA9.CYP78A9 ) of QC14 was identified, and its heterotic effect results from the heterozygous status of a CACTA‐like transposable element in its upstream regulatory region, which led to partial dominance at expression and auxin levels, thus resulting in non‐additive expression of downstream responsive genes involved in cell cycle and proliferation, eventually leading to the heterosis of cell number. Taken together, the results at the phenotypic, genetic and molecular levels were highly consistent, which demonstrated that the pyramiding effect of heterotic QTL and the multiplicative effect of in idual component traits could well explain substantial parts of yield heterosis in oilseed rape. These results provide in‐depth insights into the genetic architecture and molecular mechanism of yield heterosis.
Whole‐genome scanning for mapping determinacy in Pigeonpea (Cajanus spp.)
Publisher: Wiley
Date: 30-08-2012
A SSR kit to study genetic diversity in chickpea (Cicer arietinum L.)
Publisher: Cambridge University Press (CUP)
Date: 07-2014
DOI: 10.1017/S1479262114000392
Abstract: A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of lification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic ersity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.
Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]
Publisher: Springer Science and Business Media LLC
Date: 20-01-2011
Abstract: Pigeonpea [ Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic ersity analysis and mapping. In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent lification in eight erse pigeonpea varieties 71 were found to be polymorphic on agarose gel electrophoresis. Genetic ersity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus . A comprehensive set of genic-SSR markers was developed as an important genomic resource for ersity analysis and genetic mapping in pigeonpea.
Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains
Publisher: Wiley
Date: 15-02-2019
DOI: 10.1111/PBI.13087
Transcriptome profiling reveals the expression and regulation of genes associated with Fusarium wilt resistance in chickpea (Cicer arietinum L.)
Publisher: Wiley
Date: 21-05-2023
DOI: 10.1002/TPG2.20340
Abstract: Fusarium wilt (FW) is one of the most significant biotic stresses limiting chickpea production worldwide. To dissect the molecular mechanism of FW resistance in chickpea, comparative transcriptome analyses of contrasting resistance sources of chickpea genotypes under control and Fusarium oxysporum f. sp. ciceris ( Foc ) inoculated conditions were performed. The high‐throughput transcriptome sequencing generated about 1137 million sequencing reads from 24 s les representing two resistant genotypes, two susceptible genotypes, and two near‐isogenic lines under control and stress conditions at two‐time points (7th‐ and 12th‐day post‐inoculation). The analysis identified 5182 differentially expressed genes (DEGs) between different combinations of chickpea genotypes. Functional annotation of these genes indicated their involvement in various biological processes such as defense response, cell wall biogenesis, secondary metabolism, and disease resistance. A significant number (382) of transcription factor encoding genes exhibited differential expression patterns under stress. Further, a considerable number of the identified DEGs (287) co‐localized with previously reported quantitative trait locus for FW resistance. Several resistance/susceptibility‐related genes, such as SERINE/THREONINE PROTEIN KINASE , DIRIGENT , and MLO exhibiting contrasting expression patterns in resistant and susceptible genotypes upon Foc inoculation, were identified. The results presented in the study provide valuable insights into the transcriptional dynamics associated with FW stress response in chickpea and provide candidate genes for the development of disease‐resistant chickpea cultivars.
Comprehensive Transcriptome Profiling Uncovers Molecular Mechanisms and Potential Candidate Genes Associated with Heat Stress Response in Chickpea
Publisher: MDPI AG
Date: 10-01-2023
DOI: 10.3390/IJMS24021369
Abstract: Chickpea (Cicer arietinum L.) production is highly susceptible to heat stress (day/night temperatures above 32/20 °C). Identifying the molecular mechanisms and potential candidate genes underlying heat stress response is important for increasing chickpea productivity. Here, we used an RNA-seq approach to investigate the transcriptome dynamics of 48 s les which include the leaf and root tissues of six contrasting heat stress responsive chickpea genotypes at the vegetative and reproductive stages of plant development. A total of 14,544 unique, differentially expressed genes (DEGs) were identified across different combinations studied. These DEGs were mainly involved in metabolic processes, cell wall remodeling, calcium signaling, and photosynthesis. Pathway analysis revealed the enrichment of metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction, under heat stress conditions. Furthermore, heat-responsive genes encoding bHLH, ERF, WRKY, and MYB transcription factors were differentially regulated in response to heat stress, and candidate genes underlying the quantitative trait loci (QTLs) for heat tolerance component traits, which showed differential gene expression across tolerant and sensitive genotypes, were identified. Our study provides an important resource for dissecting the role of candidate genes associated with heat stress response and also paves the way for developing climate-resilient chickpea varieties for the future.
Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits
Publisher: Springer Science and Business Media LLC
Date: 20-05-2021
DOI: 10.1007/S00122-021-03847-6
Abstract: Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance ( σ 2 g ) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic ersity. Selection intensity ( i ) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability ( h 2 ). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ 2 g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time ( t ), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.
Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement
Publisher: Springer Science and Business Media LLC
Date: 07-2009
DOI: 10.1007/BF03263311
Large‐scale development of cost‐effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes
Publisher: Wiley
Date: 16-06-2012
Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection
Publisher: Springer Science and Business Media LLC
Date: 27-12-2013
A comparative assessment of genetic diversity in cultivated barley collected in different decades of the last century in Austria, Albania and India by using genomic and genic simple sequence repeat (SSR) markers
Publisher: Cambridge University Press (CUP)
Date: 08-2006
DOI: 10.1079/PGR2006109
Abstract: Molecular investigations of qualitative and quantitative changes in the genetic ersity of cultivated crops are useful for plant breeding and the management of crop genetic resources. A genotyping study, based on 28 genomic (g-SSR) and 13 expressed sequence tag-derived (e-SSR) microsatellite markers uniformly distributed across the barley genome, was conducted on s les of cultivated barley ( Hordeum vulgare L.) collected at intervals of 40–50 years in three comparable geographical regions in Austria, Albania and India. The analysis indicated an absence of any significant differences either in the total number of alleles per locus or in g-SSR and e-SSR polymorphic information content (PIC) values from the Indian and Austrian materials. However, a slight reduction in genetic ersity was noted among the materials collected in Albania. The trend in numbers of collection mission-specific SSR alleles suggests significant allele flow over the time interval s led. The g-SSRs yielded a higher mean number of alleles per locus and a superior PIC than the e-SSR markers. We conclude that a qualitative, rather than a quantitative shift in ersity has taken place over time, and that g-SSR markers detect more ersity than do e-SSR markers.
Assessment of ICCV 2 × JG 62 chickpea progenies shows sensitivity of reproduction to salt stress and reveals QTL for seed yield and yield components
Publisher: Springer Science and Business Media LLC
Date: 17-06-2012
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
Publisher: Wiley
Date: 24-06-2022
DOI: 10.1002/TPG2.20109
Abstract: The gene content of plants varies between in iduals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic ersity). Here we have assembled and analyzed a soybean ( Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic ersity, we found a significant reduction in the average number of protein‐coding genes per in idual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.
Multiple Resistant and Nutritionally Dense Germplasm Identified from Mini Core Collection in Peanut
Publisher: Wiley
Date: 03-2014
Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut
Publisher: American Peanut Research and Education Society
Date: 07-2013
DOI: 10.3146/PS13-03.1
Abstract: The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic ersity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are ex les of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.
CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea
Publisher: Oxford University Press (OUP)
Date: 2015
Yield is negatively correlated with nucleotide-binding leucine-rich repeat gene content in soybean
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2021
DOI: 10.1101/2021.12.12.472330
Abstract: The availability of increasing quantities of crop pangenome data permits the detailed association of gene content with agronomic traits. Here, we investigate disease resistance gene content of erse soybean cultivars and report a significant negative correlation between the number of NLR resistance ( R ) genes and yield. We find no association between R- genes with seed weight, oil or protein content, and we find no correlation between yield and the number of RLK, RLP genes, or the total number of genes. These results suggest that recent yield improvement in soybean may be partially associated with the selective loss of NLR genes. Three quarters of soybean NLR genes do not show presence/absence variation, limiting the ability to select for their absence, and so the deletion or disabling of select NLR genes may support future yield improvement.
Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity
Publisher: Springer Science and Business Media LLC
Date: 09-07-2021
DOI: 10.1007/S00374-021-01578-W
Abstract: Roots secrete a vast array of low molecular weight compounds into the soil broadly referred to as root exudates. It is a key mechanism by which plants and soil microbes interact in the rhizosphere. The effect of drought stress on the exudation process and composition is rarely studied, especially in cereal crops. This study focuses on comparative metabolic profiling of the exudates from sensitive and tolerant genotypes of pearl millet after a period of drought stress. We employed a combined platform of gas and liquid chromatography coupled to mass spectrometry to cover both primary and secondary metabolites. The results obtained demonstrate that both genotype and drought stress have a significant impact on the concentration and composition of root exudates. The complexity and function of these differential root exudates are discussed. To reveal the potential effect of root exudates on the soil microbial community after a period of drought stress, we also tested for biological nitrification inhibition (BNI) activity. The analysis revealed a genotype-dependent enhancement of BNI activity after a defined period of drought stress. In parallel, we observed a genotype-specific relation of elongated root growth and root exudation under drought stress. These data suggest that the drought stress-dependent change in root exudation can manipulate the microbial soil communities to adapt and survive under harsh conditions.
Genomics for greater efficiency in pigeonpea hybrid breeding
Publisher: Frontiers Media SA
Date: 10-2015
Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement
Publisher: Elsevier BV
Date: 07-2019
DOI: 10.1016/J.MOLP.2019.03.005
Abstract: Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.
Introduction to Root Genomics
Publisher: Springer Berlin Heidelberg
Date: 15-09-2010
ICPH 2671 - the world's first commercial food legume hybrid
Publisher: Wiley
Date: 11-03-2013
DOI: 10.1111/PBR.12045
Editorial
Publisher: Springer Science and Business Media LLC
Date: 24-10-2012
Legume biology: The basis for crop improvement
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/FPV40N12_FO
Abstract: Legumes represent the most valued food sources in agriculture after cereals. Despite the advances made in breeding food legumes, there is a need to develop and further improve legume productivity to meet increasing food demand worldwide. Several biotic and abiotic stresses affect legume crop productivity throughout the world. The study of legume genetics, genomics and biology are all important in order to understand the limitations of yield of legume crops and to support our legume breeding programs. With the advent of huge genomic resources and modern technologies, legume research can be directed towards precise understanding of the target genes responsible for controlling important traits for yield potential, and for resistance to abiotic and biotic stresses. Programmed and systematic research will lead to developing high yielding, stress tolerant and early maturing varieties. This issue of Functional Plant Biology is dedicated to ‘Legume Biology’ research covering part of the work presented at VI International Conference on Legume Genetics and Genomics held at Hyderabad, India, in 2012. The 13 contributions cover recent advances in legume research in the context of plant architecture and trait mapping, functional genomics, biotic stress and abiotic stress.
Pearl millet [Pennisetum glaucum(L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs
Publisher: Springer Science and Business Media LLC
Date: 09-03-2013
Abstract: Pearl millet [ Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics and sub-tropics of Africa, South Asia and the Americas. It is considered an orphan crop with relatively few genomic and genetic resources. This study was undertaken to increase the EST-based microsatellite marker and genetic resources for this crop to facilitate marker-assisted breeding. Newly developed EST-SSR markers (99), along with previously mapped EST-SSR (17), genomic SSR (53) and STS (2) markers, were used to construct linkage maps of four F 7 recombinant inbred populations (RIP) based on crosses ICMB 841-P3 × 863B-P2 (RIP A), H 77/833-2 × PRLT 2/89-33 (RIP B), 81B-P6 × ICMP 451-P8 (RIP C) and PT 732B-P2 × P1449-2-P1 (RIP D). Mapped loci numbers were greatest for RIP A (104), followed by RIP B (78), RIP C (64) and RIP D (59). Total map lengths (Haldane) were 615 cM, 690 cM, 428 cM and 276 cM, respectively. A total of 176 loci detected by 171 primer pairs were mapped among the four crosses. A consensus map of 174 loci (899 cM) detected by 169 primer pairs was constructed using MergeMap to integrate the in idual linkage maps. Locus order in the consensus map was well conserved for nearly all linkage groups. Eighty-nine EST-SSR marker loci from this consensus map had significant BLAST hits (top hits with e -value ≤ 1E-10) on the genome sequences of rice, foxtail millet, sorghum, maize and Brachypodium with 35, 88, 58, 48 and 38 loci, respectively. The consensus map developed in the present study contains the largest set of mapped SSRs reported to date for pearl millet, and represents a major consolidation of existing pearl millet genetic mapping information. This study increased numbers of mapped pearl millet SSR markers by %, filling important gaps in previously published SSR-based linkage maps for this species and will greatly facilitate SSR-based QTL mapping and applied marker-assisted selection programs.
More genomic resources for less-studied crops
Publisher: Elsevier BV
Date: 09-2010
DOI: 10.1016/J.TIBTECH.2010.06.007
Abstract: Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and ersity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic ersity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries.
Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 08-01-2018
Improving crop performance under drought – cross-fertilization of disciplines
Publisher: Oxford University Press (OUP)
Date: 18-02-2017
DOI: 10.1093/JXB/ERX042
Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea)
Publisher: Wiley
Date: 10-11-2011
Characterization of ASR gene and its role in drought tolerance in chickpea (Cicer arietinum L.)
Publisher: Public Library of Science (PLoS)
Date: 14-07-2020
Model Plants and Crop Improvement
Publisher: CRC Press
Date: 29-09-2006
Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World
Publisher: Public Library of Science (PLoS)
Date: 20-08-2014
Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat
Publisher: Wiley
Date: 02-06-2023
DOI: 10.1002/TPG2.20358
Abstract: Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints—acidity (pH 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH 8.5)—are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high‐throughput genomics technologies have identified functional alleles in gene‐rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.
Characterization of heterosis and genomic prediction‐based establishment of heterotic patterns for developing better hybrids in pigeonpea
Publisher: Wiley
Date: 08-2021
DOI: 10.1002/TPG2.20125
Abstract: Whole‐genome resequencing (WGRS) of 396 lines, consisting of 104 hybrid parental lines and 292 germplasm lines, were used to study the molecular basis of mid‐parent heterosis (MPH) and to identify complementary heterotic patterns in pigeonpea [ Cajanus cajan (L.) Millsp.] hybrids. The lines and hybrids were assessed for yield and yield‐related traits in multiple environments. Our analysis showed positive MPH values in 78.6% of hybrids, confirming the potential of hybrid breeding in pigeonpea. By using genome‐wide prediction and association mapping approaches, we identified 129 single nucleotide polymorphisms and 52 copy number variations with significant heterotic effects and also established a high‐yielding heterotic pattern in pigeonpea. In summary, our study highlights the role of WGRS data in the study and use of heterosis in crops where hybrid breeding is expected to boost selection gain in order to ensure global food security.
Designing Future Crops: Genomics-Assisted Breeding Comes of Age
Publisher: Elsevier BV
Date: 06-2021
DOI: 10.1016/J.TPLANTS.2021.03.010
Abstract: Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel ersity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.
Genetic mapping identified major main‐effect and three co‐localized quantitative trait loci controlling high iron and zinc content in groundnut
Publisher: Wiley
Date: 05-07-2023
DOI: 10.1002/TPG2.20361
Abstract: Malnutrition is a major challenge globally, and groundnut is a highly nutritious self‐pollinated legume crop blessed with le genomic resources, including the routine deployment of genomic‐assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040 ). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single‐nucleotide polymorphism loci 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main‐effect QTLs for Fe content. These QTLs exhibited log‐of‐odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% ( qFe‐Ah01 ) to 30.0% ( qFe‐Ah14 ). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% ( qZn‐Ah01 ) to 32.8% ( qZn‐Ah08 ). Interestingly, three co‐localized major and main effect QTLs ( qFe‐Ah01, qZn‐Ah03, and qFe‐Ah11 ) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor , and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds . The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
Dissection of the barley 2L1.0 region carrying the 'Laevigatum' quantitative resistance gene to leaf rust using near-isogenic lines (NIL) and subNIL
Publisher: Scientific Societies
Date: 12-2007
Abstract: Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance h ers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 × ‘Vada’ mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei.
Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas
Publisher: Public Library of Science (PLoS)
Date: 02-2018
Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects
Publisher: Frontiers Media SA
Date: 11-08-2015
Safety and utility of kidney biopsy in patients with estimated glomerular filtration rate < 30 ml/min/1.73 m2
Publisher: Wiley
Date: 14-04-2021
DOI: 10.1111/NEP.13879
Abstract: Kidney biopsy (KBx) is the gold standard for evaluation of kidney disease, but is associated with a higher risk of complications in patients with reduced glomerular filtration rate (GFR). We studied the safety and utility of KBx in patients with eGFR ml/min/1.73 m 2 . Consecutive adult patients with eGFR ml/min/1.73 m 2 , who were planned for a KBx and consented to participate were prospectively enrolled. Patients with solitary/transplant kidney or acute kidney injury were excluded. Haemoglobin was checked on the day of KBx and repeated 18–24 h later along with a screening ultrasound. Post‐KBx complications were noted and their risk‐factors analysed. The utility of the KBx was graded as effecting significant, some, or no change to subsequent management. Of the 126 patients included, 75% were male, 27.7% were diabetic, and the median eGFR was 13.5 ml/min/1.73m 2 . Major complications occurred in 5.6%. Peri‐renal haematomas were detected in 37.3%, and haematomas ≥2 cm were significantly more frequent in those with eGFR ml/min/1.73 m 2 (29.2% vs. 13%, p = .032). Dialysis was a risk factor, while pre KBx blood transfusion, diabetes and higher serum albumin were protective against any complication. KBx was more likely to make a significant difference in management in those with eGFR 15–29 ml/min/1.73m 2 (44.1% vs. 11.1%, p .001). Increasing age, lower serum creatinine and albumin were independently associated with KBx utility. KBx is relatively safe in severe kidney disease but its risk to benefit balance needs to be carefully considered when eGFR is ml/min/1.73m 2 .
A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.)
Publisher: Frontiers Media SA
Date: 25-04-2017
Molecular Mapping of QTLs for Heat Tolerance in Chickpea
Publisher: MDPI AG
Date: 25-07-2018
DOI: 10.3390/IJMS19082166
Abstract: Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.
Translational Chickpea Genomics Consortium to Accelerate Genetic Gains in Chickpea (Cicer arietinum L.)
Publisher: MDPI AG
Date: 25-11-2021
Abstract: The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.
Inheritance of protein content and its relationships with seed size, grain yield and other traits in chickpea
Publisher: Springer Science and Business Media LLC
Date: 15-03-2016
Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost‐Effective Kompetitive Allele Specific Polymerase Chain React
Publisher: Wiley
Date: 11-2013
A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction
Publisher: Wiley
Date: 03-2020
DOI: 10.1002/TPG2.20009
Comparing the effect of different loading doses of phenobarbitone on serum phenobarbitone levels in babies with neonatal seizures and effect of therapeutic hypothermia on phenobarbitone levels
Publisher: Oxford University Press (OUP)
Date: 04-08-2022
Abstract: With current recommendation for phenobarbitone dosing, we have noted that babies are extremely sedated with elevated serum phenobarbitone levels. We postulate that asphyxiated neonates with hypoxic liver injury have impaired drug metabolism and renal injury affects drug elimination, thus elevating serum drug levels. Therapeutic hypothermia (TH) could further affect the drug levels. To determine the serum levels of the phenobarbitone in babies receiving different loading doses of phenobarbitone for neonatal seizures and to study the effect of asphyxia and TH on drug levels. Prospective observational cohort study. Term neonates with seizures of any cause were given phenobarbitone up to a maximum loading of 40 mg/kg followed by maintenance dose of 5 mg/kg/day. Serum phenobarbitone levels were assessed after 4 h of the initial loading dose and subsequently at 24, 48 and 72 h from the time after maximum loading dose. Babies were ided into three groups Group 1 (HIE + TH—hypoxic ischemic encephalopathy undergoing TH), Group 2 (HIE − TH—hypoxic ischemic encephalopathy without TH) and Group 3 (non-HIE group). A total of 47 babies completed the study. Twenty-three (49%) received 20 mg/kg, 14 (30%) received 30 mg/kg and 10 (21%) received 40 mg per kg of phenobarbitone as loading dose. HIE was the major cause of seizures 28 (59%) followed by hypoglycemia 7 (14%), cerebral malformations 4 (8%), inborn errors of metabolism 2 (4%) and hypocalcemia 1 (2%) while the cause of seizures was not known in 6 (13%). Median (IQR) Phenobarbitone levels at 72 h in babies who received 20 mg/kg loading dose of phenobarbitone was 46.72 (44.02–50.49) mcg/ml in HIE + TH group, 40.53 (28.66–65.09) mcg/ml in HIE − TH group and 49 (37–65) mcg/ml in non-HIE group. After a loading dose of 30 mg/kg, phenobarbitone level was 63.76 (59.5–65.94) mcg/ml in HIE + TH group, 42.5 (34.75–48.75) mcg/ml in HIE − TH group and 42.07 (40–49.05) mcg/ml in non-HIE group. After 40 mg/kg loading dose, it was 62.3 (60.2–64.9) mcg/ml in HIE + TH group, 57.0 (49.8–60.2) mcg/ml in HIE − TH group and 48.15 (40.8–50.97) mcg/ml in non-HIE group. In babies who received & mg/kg loading dose, 100% of HIE + TH, 80% of HIE − TH and 60% of non-HIE had supratherapeutic levels of phenobarbitone. At higher loading doses of 30 and 40 mg/kg, steady state concentration of serum phenobarbitone is higher in babies with hypoxic ischemic encephalopathy who underwent TH than in babies with non-HIE causes of seizures. Loading dose beyond 20 mg/kg should be used with close monitoring of serum drug level
Maize and heat stress: Physiological, genetic, and molecular insights
Publisher: Wiley
Date: 16-08-2023
DOI: 10.1002/TPG2.20378
Abstract: Global mean temperature is increasing at a rapid pace due to the rapid emission of greenhouse gases majorly from anthropogenic practices and predicted to rise up to 1.5°C above the pre‐industrial level by the year 2050. The warming climate is affecting global crop production by altering biochemical, physiological, and metabolic processes resulting in poor growth, development, and reduced yield. Maize is susceptible to heat stress, particularly at the reproductive and early grain filling stages. Interestingly, heat stress impact on crops is closely regulated by associated environmental covariables such as humidity, vapor pressure deficit, soil moisture content, and solar radiation. Therefore, heat stress tolerance is considered as a complex trait, which requires multiple levels of regulations in plants. Exploring genetic ersity from landraces and wild accessions of maize is a promising approach to identify novel donors, traits, quantitative trait loci (QTLs), and genes, which can be introgressed into the elite cultivars. Indeed, genome wide association studies (GWAS) for mining of potential QTL(s) and dominant gene(s) is a major route of crop improvement. Conversely, mutation breeding is being utilized for generating variation in existing populations with narrow genetic background. Besides breeding approaches, augmented production of heat shock factors (HSFs) and heat shock proteins (HSPs) have been reported in transgenic maize to provide heat stress tolerance. Recent advancements in molecular techniques including clustered regularly interspaced short palindromic repeats (CRISPR) would expedite the process for developing thermotolerant maize genotypes.
Mapping and identification of a Cicer arietinum NSP2 gene involved in nodulation pathway
Publisher: Springer Science and Business Media LLC
Date: 19-11-2013
DOI: 10.1007/S00122-013-2233-3
Abstract: For the first time the putative NSP2 gene in chickpea has been identified using pairs of NILs differing for the Rn1 / rn1 nodulation gene that was located in LG5 of chickpea genetic map. An intraspecific cross between the mutant non-nodulating genotype PM233, carrying the recessive gene rn1, and the wild-type CA2139 was used to develop two pairs of near-isogenic lines (NILs) for nodulation in chickpea. These pairs of NILs were characterized using sequence tagged microsatellite site (STMS) markers distributed across different linkage groups (LGs) of the chickpea genetic map leading to the detection of polymorphic markers located in LG5. Using this information, together with the genome annotation in Medicago truncatula, a candidate gene (NSP2) known to be involved in nodulation pathway was selected for mapping in chickpea. The full length sequence obtained in chickpea wild-type (CaNSP2) was 1,503 bp. Linkage analysis in an F3 population of 118 plants derived from the cross between the pair of NILS NIL7-2A (nod) × NIL7-2B (non-nod) revealed a co-localization between CaNSP2 and Rn1 gene. These data implicate the CaNSP2 gene as a candidate for identity to Rn1, and suggest that it could act in the nodulation signaling transduction pathway similarly to that in other legumes species.
The conservation of gene models can support genome annotation
Publisher: Wiley
Date: 21-08-2023
DOI: 10.1002/TPG2.20377
Abstract: Many genome annotations include false‐positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from 12 legume assemblies that can be used to support genome annotations for other legumes.
Global gene expression analysis of pigeonpea with male sterility conditioned by A2 cytoplasm
Publisher: Wiley
Date: 08-09-2021
DOI: 10.1002/TPG2.20132
Abstract: Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [ Cajanus cajan (L.) Huth], nine types of sterility‐inducing cytoplasm have been reported, of which A 2 and A 4 have been successfully deployed in hybrid breeding. Unfortunately, molecular mechanism of the CMS trait is poorly understood because of limited research invested. More recently, an association between a mitochondrial gene ( nad7 ) and A 4 ‐CMS has been demonstrated in pigeonpea however, the mechanism underlying A 2 ‐CMS still remains obscure. The current investigation aimed to analyze the differences in A 2 ‐CMS line (ICPL 88039A) and its isogenic maintainer line (ICPL 88039B) at transcriptome level using next‐generation sequencing. Gene expression profiling uncovered a set of 505 genes that showed altered expression in response to CMS, of which, 412 genes were upregulated while 93 were downregulated in the fertile maintainer line vs. the CMS line. Further, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses revealed association of CMS in pigeonpea with four major pathways: glucose and lipid metabolism, ATP production, pollen development and pollen tube growth, and reactive oxygen species (ROS) scavenging. Patterns of digital gene expression were confirmed by quantitative real‐time polymerase chain reaction (qRT‐PCR) of six candidate genes. This study elucidates candidate genes and metabolic pathways having potential associations with pollen development and male sterility in pigeonpea A 2 ‐CMS. New insights on molecular mechanism of CMS trait in pigeonpea will be helpful to accelerate heterosis utilization for enhancing productivity gains in pigeonpea.
Prospects for developing allergen‐depleted food crops
Publisher: Wiley
Date: 28-08-2023
DOI: 10.1002/TPG2.20375
Abstract: In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio‐molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentially life‐threatening consequences. The relentless working lifestyles of the modern era often incorporate poor eating habits that include readymade prepackaged and processed foods, which contain additives such as peanuts, tree nuts, wheat, and soy‐based products, rather than traditional home cooking. Of the predominant allergenic foods (soybean, wheat, fish, peanut, shellfish, tree nuts, eggs, and milk), peanuts ( Arachis hypogaea ) are the best characterized source of allergens, followed by tree nuts ( Juglans regia , Prunus amygdalus , Corylus avellana , Carya illinoinensis , Anacardium occidentale , Pistacia vera , Bertholletia excels ), wheat ( Triticum aestivum ), soybeans ( Glycine max ), and kidney beans ( Phaseolus vulgaris ). The prevalence of food allergies has risen significantly in recent years including chance of accidental exposure to such foods. In contrast, the standards of detection, diagnosis, and cure have not kept pace and unfortunately are often suboptimal. In this review, we mainly focus on the prevalence of allergies associated with peanut, tree nuts, wheat, soybean, and kidney bean, highlighting their physiological properties and functions as well as considering research directions for tailoring allergen gene expression. In particular, we discuss how recent advances in molecular breeding, genetic engineering, and genome editing can be used to develop potential low allergen food crops that protect consumer health.
Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea
Publisher: Springer Science and Business Media LLC
Date: 2016
A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 2009
Molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea (Cajanus cajan (L.) Millsp.)
Publisher: Springer Science and Business Media LLC
Date: 28-04-2018
Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 03-2014
Pigeonpea breeding in eastern and southern Africa: challenges and opportunities
Publisher: Wiley
Date: 02-2016
DOI: 10.1111/PBR.12340
Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing
Publisher: Frontiers Media SA
Date: 07-06-2017
Profile of incident chronic kidney disease related-mineral bone disorders in chronic kidney disease Stage 4 and 5: A hospital based cross-sectional survey
Publisher: Medknow
Date: 2014
Mini core collection as a resource to identify new sources of variation
Publisher: Wiley
Date: 11-2013
Oxidative stress and carbon metabolism influence Aspergillus flavus transcriptome composition and secondary metabolite production
Publisher: Springer Science and Business Media LLC
Date: 12-12-2016
DOI: 10.1038/SREP38747
Abstract: Contamination of crops with aflatoxin is a serious global threat to food safety. Aflatoxin production by Aspergillus flavus is exacerbated by drought stress in the field and by oxidative stress in vitro. We examined transcriptomes of three toxigenic and three atoxigenic isolates of A. flavus in aflatoxin conducive and non-conducive media with varying levels of H 2 O 2 to investigate the relationship of secondary metabolite production, carbon source, and oxidative stress. We found that toxigenic and atoxigenic isolates employ distinct mechanisms to remediate oxidative damage, and that carbon source affected the isolates’ expression profiles. Iron metabolism, monooxygenases, and secondary metabolism appeared to participate in isolate oxidative responses. The results suggest that aflatoxin and aflatrem biosynthesis may remediate oxidative stress by consuming excess oxygen and that kojic acid production may limit iron-mediated, non-enzymatic generation of reactive oxygen species. Together, secondary metabolite production may enhance A. flavus stress tolerance, and may be reduced by enhancing host plant tissue antioxidant capacity though genetic improvement by breeding selection.
Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches
Publisher: Public Library of Science (PLoS)
Date: 06-05-2014
Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 21-06-2013
DOI: 10.1007/S10681-013-0959-2
Abstract: Fusarium wilt (FW) and Ascochyta blight (AB) are two important diseases of chickpea which cause 100 % yield losses under favorable conditions. With an objective to validate and/or to identify novel quantitative trait loci (QTLs) for resistance to race 1 of FW caused by Fusarium oxysporum f. sp. ciceris and AB caused by Ascochyta rabiei in chickpea, two new mapping populations (F 2:3 ) namely ‘C 214’ (FW susceptible) × ‘WR 315’ (FW resistant) and ‘C 214’ (AB susceptible) × ‘ILC 3279’ (AB resistant) were developed. After screening 371 SSR markers on parental lines and genotyping the mapping populations with polymorphic markers, two new genetic maps comprising 57 (C 214 × WR 315) and 58 (C 214 × ILC 3279) loci were developed. Analysis of genotyping data together with phenotyping data collected on mapping population for resistance to FW in field conditions identified two novel QTLs which explained 10.4–18.8 % of phenotypic variation. Similarly, analysis of phenotyping data for resistance to seedling resistance and adult plant resistance for AB under controlled and field conditions together with genotyping data identified a total of 6 QTLs explaining up to 31.9 % of phenotypic variation. One major QTL, explaining 31.9 % phenotypic variation for AB resistance was identified in both field and controlled conditions and was also reported from different resistant lines in many earlier studies. This major QTL for AB resistance and two novel QTLs identified for FW resistance are the most promising QTLs for molecular breeding separately or pyramiding for resistance to FW and AB for chickpea improvement.
Cloning, Expression Pattern Analysis and Subcellular Localization of Resveratrol Synthase Gene in Peanut (<i>Arachis hypogaea</i> L.)
Publisher: Scientific Research Publishing, Inc.
Date: 2014
A chickpea genetic variation map based on the sequencing of 3,366 genomes
Publisher: Springer Science and Business Media LLC
Date: 10-11-2021
DOI: 10.1038/S41586-021-04066-1
Abstract: Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources 1 . So far, few chickpea ( Cicer arietinum ) germplasm accessions have been characterized at the genome sequence level 2 . Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic ersity across cultivated chickpea and its wild progenitor accessions. A ergence tree using genes present in around 80% of in iduals in one species allowed us to estimate the ergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic ersity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic ersity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.
Global Transcriptome Profiling Identified Transcription Factors, Biological Process, and Associated Pathways for Pre-Harvest Aflatoxin Contamination in Groundnut
Publisher: MDPI AG
Date: 26-05-2021
DOI: 10.3390/JOF7060413
Abstract: Pre-harvest aflatoxin contamination (PAC) in groundnut is a serious quality concern globally, and drought stress before harvest further exacerbate its intensity, leading to the deterioration of produce quality. Understanding the host–pathogen interaction and identifying the candidate genes responsible for resistance to PAC will provide insights into the defense mechanism of the groundnut. In this context, about 971.63 million reads have been generated from 16 RNA s les under controlled and Aspergillus flavus infected conditions, from one susceptible and seven resistant genotypes. The RNA-seq analysis identified 45,336 genome-wide transcripts under control and infected conditions. This study identified 57 transcription factor (TF) families with major contributions from 6570 genes coding for bHLH (719), MYB-related (479), NAC (437), FAR1 family protein (320), and a few other families. In the host (groundnut), defense-related genes such as senescence-associated proteins, resveratrol synthase, seed linoleate, pathogenesis-related proteins, peroxidases, glutathione-S-transferases, chalcone synthase, ABA-responsive gene, and chitinases were found to be differentially expressed among resistant genotypes as compared to susceptible genotypes. This study also indicated the vital role of ABA-responsive ABR17, which co-regulates the genes of ABA responsive elements during drought stress, while providing resistance against A. flavus infection. It belongs to the PR-10 class and is also present in several plant–pathogen interactions.
Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes
Publisher: Springer Science and Business Media LLC
Date: 25-03-2022
The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data
Publisher: Springer Science and Business Media LLC
Date: 13-10-2021
DOI: 10.1007/S00122-021-03954-4
Abstract: QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in erse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple ersity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two ersity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1-FTa2-FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and ersity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the ersity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology.
Future Prospects of Molecular Markers in Plants
Publisher: Wiley
Date: 10-10-2012
Comprehensive tissue-specific proteome analysis of drought stress responses in Pennisetum glaucum (L.) R. Br. (Pearl millet)
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.JPROT.2016.02.032
Abstract: Pearl millet is the fifth most important cereal crop worldwide and cultivated especially by small holder farmers in arid and semi-arid regions because of its drought and salt tolerance. The molecular mechanisms of drought stress tolerance in Pennisetum remain elusive. We have used a shotgun proteomics approach to investigate protein signatures from different tissues under drought and control conditions. Drought stressed plants showed significant changes in stomatal conductance and increased root growth compared to the control plants. Root, leaf and seed tissues were harvested and 2281 proteins were identified and quantified in total. Leaf tissue showed the largest number of significant changes (120), followed by roots (25) and seeds (10). Increased levels of root proteins involved in cell wall-, lipid-, secondary- and signaling metabolism and the concomitantly observed increased root length point to an impaired shoot-root communication under drought stress. The harvest index (HI) showed a significant reduction under drought stress. Proteins with a high correlation to the HI were identified using sparse partial least square (sPLS) analysis. Considering the importance of Pearl millet as a stress tolerant food crop, this study provides a first reference data set for future investigations of the underlying molecular mechanisms. Drought stress is the most limiting factor for plant growth and crop production worldwide. At the same time drought susceptible cereal crops are among the largest producers worldwide. In contrast, Pearl millet is a drought and salt tolerant cereal crop especially used in arid and semi-arid regions by small farmers. The multifactorial molecular mechanisms of this unique drought tolerance are not known. Here, we employ shotgun proteomics for a first characterization of the Pearl millet drought stress proteome. The experimental setup and the data set generated from this study reveal comprehensive physiological and proteomic responses of the drought stressed Pearl millet plants. Our study reveals statistically significant tissue-specific protein signatures during the adaptation to drought conditions. Thus, the work provides a first reference study of the drought stress proteome and related drought responsive proteins (DRP's) in Pearl millet.
Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.
Publisher: Springer Science and Business Media LLC
Date: 22-11-2011
Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping
Publisher: Springer Netherlands
Date: 12-10-2009
Current state-of-art of sequencing technologies for plant genomics research
Publisher: Oxford University Press (OUP)
Date: 2012
DOI: 10.1093/BFGP/ELR045
Abstract: A number of next-generation sequencing (NGS) technologies such as Roche/454, Illumina and AB SOLiD have recently become available. These technologies are capable of generating hundreds of thousands or tens of millions of short DNA sequence reads at a relatively low cost. These NGS technologies, now referred as second-generation sequencing (SGS) technologies, are being utilized for de novo sequencing, genome re-sequencing, and whole genome and transcriptome analysis. Now, new generation of sequencers, based on the 'next-next' or third-generation sequencing (TGS) technologies like the Single-Molecule Real-Time (SMRT™) Sequencer, Heliscope™ Single Molecule Sequencer, and the Ion Personal Genome Machine™ are becoming available that are capable of generating longer sequence reads in a shorter time and at even lower costs per instrument run. Ever declining sequencing costs and increased data output and s le throughput for NGS and TGS sequencing technologies enable the plant genomics and breeding community to undertake genotyping-by-sequencing (GBS). Data analysis, storage and management of large-scale second or TGS projects, however, are essential. This article provides an overview of different sequencing technologies with an emphasis on forthcoming TGS technologies and bioinformatics tools required for the latest evolution of DNA sequencing platforms.
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Publisher: Springer Science and Business Media LLC
Date: 18-09-2017
DOI: 10.1038/NBT.3943
Abstract: Pearl millet [ Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1 -P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic ersity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.
Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut
Publisher: MDPI AG
Date: 30-12-2020
Abstract: A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases malate dehydrogenases microtubule-associated proteins and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.
A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics
Publisher: Springer Science and Business Media LLC
Date: 12-01-2007
DOI: 10.1007/S00122-006-0480-2
Abstract: An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven in idual barley linkage groups. The map covers 1118.3 cM with in idual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the ergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.
Whole‐genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut
Publisher: Wiley
Date: 07-12-2022
DOI: 10.1002/TPG2.20265
Abstract: Seed weight in groundnut ( Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed‐size improvement as one of the most important objectives of groundnut breeding programs globally. Marker‐based early generation selection can accelerate the process of breeding for developing large‐seeded varieties. In this context, we deployed the quantitative trait locus‐sequencing (QTL‐seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4–389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9–95.1% genome coverage and 8.34–9.29× average read depth. The analysis of sequencing data using QTL‐seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single‐nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large‐seeded groundnut varieties.
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research
Publisher: Wiley
Date: 25-09-2023
DOI: 10.1002/TPG2.20382
Advances in Arachis genomics for peanut improvement
Publisher: Elsevier BV
Date: 05-2012
DOI: 10.1016/J.BIOTECHADV.2011.11.001
Abstract: Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic ersity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely h ered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
Development of a new CMS system in pigeonpea utilizing crosses with Cajanus lanceolatus (WV Fitgz) van der Maesen
Publisher: Springer Science and Business Media LLC
Date: 07-01-2015
Foliar fungal disease‐resistant introgression lines of groundnut (Arachis hypogaea L.) record higher pod and haulm yield in multilocation testing
Publisher: Wiley
Date: 04-2016
DOI: 10.1111/PBR.12358
Development and use of molecular markers for crop improvement
Publisher: Wiley
Date: 10-2013
DOI: 10.1111/PBR.12110
Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 16-12-2016
DOI: 10.1038/SREP38636
Abstract: In order to understand the impact of breeding on genetic ersity and gain insights into temporal trends in ersity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced ersity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.
Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)
Publisher: Springer Science and Business Media LLC
Date: 29-03-2011
Abstract: Pigeonpea [ Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea. A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using Hin dIII (34,560 clones) and Bam HI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of K non-redundant sequences, comprising 35 Mbp or % of the pigeonpea genome. These sequences were analyzed to develop annotation lists and sub ide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme. In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.
Next generation breeding in pulses: Present status and future directions
Publisher: FapUNIFESP (SciELO)
Date: 2021
Molecular Mapping in Barley: Shifting from the Structural to the Functional Level
Publisher: Czech Academy of Agricultural Sciences
Date: 30-09-2005
DOI: 10.17221/3665-CJGPB
Identification of two major quantitative trait locus for fresh seed dormancy using the diversity arrays technology and diversity arrays technology‐seq based genetic map in Spanish‐type peanuts
Publisher: Wiley
Date: 12-04-2016
DOI: 10.1111/PBR.12360
Assessing genetic diversity, allelic richness and genetic relationship among races in ICRISAT foxtail millet core collection
Publisher: Cambridge University Press (CUP)
Date: 30-10-2012
DOI: 10.1017/S1479262112000287
Abstract: Foxtail millet ( Setaria italica (L.) P. Beauv.) is an ideal crop for changing climate and food habits of peoples due to its short duration, high photosynthetic efficiency, nutritional richness and fair resistance to pest and diseases. However, foxtail millet yields are low mainly due to the lack of effort for its improvement and the lack of proper utilization of existing genetic variability. To enhance the use of erse germplasm in breeding programmes, a core collection in foxtail millet consisting of 155 accessions was established. Core collection accessions were fingerprinted using 84 markers (81 simple sequence repeats (SSRs) and three Expressed Sequence Tag (EST)-SSRs). Our results showed the presence of greater molecular ersity in the foxtail millet core collection. The 84 markers detected a total of 1356 alleles with an average of 16.14 alleles (4–35) per locus. Of these, 368 were rare alleles, 906 common alleles and 82 the most frequent alleles. Sixty-one unique alleles that were specific to a particular accession and useful for germplasm identification were also detected. In this study, the genetic ersity of foxtail millet was fairly correlated well with racial classification, and the race Indica showed a greater genetic distance from the races Maxima and Moharia. The pairwise estimate of dissimilarity was .50 except in 123 out of 11,935 pairs which indicated a greater genetic variability. Two hundred and fifty pairs of genetically most erse accessions were identified. This large molecular variation observed in the core collection could be utilized effectively by breeders or researchers for the selection of erse parents for breeding cultivars and the development of mapping populations.
Mobilizing Crop Biodiversity
Publisher: Elsevier BV
Date: 10-2020
SSR and SNP diversity in a barley germplasm collection
Publisher: Cambridge University Press (CUP)
Date: 14-05-2008
DOI: 10.1017/S1479262108993187
Abstract: Sets of microsatellites extracted from both a genomic library (gSSRs) and from expressed sequence tag sequence (eSSRs), and single nucleotide polymorphisms (SNPs) were applied to assess the levels of genetic ersity in a s le of 70 barley accessions, originating from 28 countries in Asia, Africa, the Middle East and Europe. The eSSR assays detected a mean of 9.5 alleles per locus, and the gSSRs only 5.7 alleles per locus, but the polymorphism information content values for the two assay types were indistinguishable. Strong and statistically significant correlations were observed between the eSSR and gSSR ( r = 0.86, P & 0.05), the eSSR and SNP ( r = 0.74, P & 0.05) and the gSSR and SNP genotypes ( r = 0.67, P & 0.05). Accessions originating from the Middle East and Asia had the highest levels of genetic ersity. Pairwise genetic similarity ranged from 0.16 to 0.87 (mean 0.43), indicating that the s le was genetically erse. When clustered on the basis of genotype, Asian and African accessions tended to be grouped together, but those originating from the Middle East were not concentrated in any particular cluster.
Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes
Publisher: Wiley
Date: 14-12-2021
DOI: 10.1111/PPL.13287
Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species
Publisher: Elsevier BV
Date: 11-2009
A randomized controlled trial comparing the effect of fortification of human milk with an infant formula powder versus unfortified human milk on the growth of preterm very low birth weight infants
Publisher: Informa UK Limited
Date: 06-01-2019
High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.PLANTSCI.2015.03.002
Abstract: Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs hasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5' RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA-target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes.
Future Prospects
Publisher: Springer International Publishing
Date: 2017
Genome-Wide Identification and Analysis of Arabidopsis Sodium Proton Antiporter (NHX) and Human Sodium Proton Exchanger (NHE) Homologs in Sorghum bicolor
Publisher: MDPI AG
Date: 03-05-2018
DOI: 10.3390/GENES9050236
Multiomics approach unravels fertility transition in a pigeonpea line for a two‐line hybrid system
Publisher: Wiley
Date: 18-06-2020
DOI: 10.1002/TPG2.20028
Association of mid-reproductive stage canopy temperature depression with the molecular markers and grain yields of chickpea ( Cicer arietinum L.) germplasm under terminal drought
Publisher: Elsevier BV
Date: 03-2015
Draft genome of the peanut A-genome progenitor ( Arachis duranensis ) provides insights into geocarpy, oil biosynthesis, and allergens
Publisher: Proceedings of the National Academy of Sciences
Date: 31-05-2016
Abstract: We present a draft genome of the peanut A-genome progenitor, Arachis duranensis , providing details on total genes present in the genome. Genome analysis suggests that the peanut lineage was affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion since their formation by human hands. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants. This study also provides millions of structural variations that can be used as genetic markers for the development of improved peanut varieties through genomics-assisted breeding.
Developing drought‐smart, ready‐to‐grow future crops
Publisher: Wiley
Date: 10-11-2023
DOI: 10.1002/TPG2.20279
Abstract: Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS‐associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought‐smart future crops. In short, we recommend incorporating several approaches, such as multi‐omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought‐smart cultivars to achieve the ‘zero hunger’ goal.
Assessing the prospects of Streptomyces sp. RP1A-12 in managing groundnut stem rot disease caused by Sclerotium rolfsii Sacc
Publisher: Springer Science and Business Media LLC
Date: 18-01-2016
Next-generation sequencing technologies: Opportunities and obligations in plant genomics
Publisher: Oxford University Press (OUP)
Date: 2012
DOI: 10.1093/BFGP/ELS001
Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
Publisher: Wiley
Date: 26-10-2021
DOI: 10.1002/TPG2.20156
Abstract: Common bean ( Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two‐stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome‐wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (−0.57 ± 0.21), and CKT and Zn (−0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high‐yielding, biofortified, and rapid cooking African common bean cultivars.
Genetics of ascochyta blight resistance in chickpea
Publisher: Springer Science and Business Media LLC
Date: 03-09-2009
Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome
Publisher: Springer Science and Business Media LLC
Date: 23-01-2010
A Multi-Model Based Stability Analysis Employing Multi-Environmental Trials (METs) Data for Discerning Heat Tolerance in Chickpea (Cicer arietinum L.) Landraces
Publisher: MDPI AG
Date: 26-10-2023
The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies
Publisher: Oxford University Press (OUP)
Date: 17-06-2022
DOI: 10.1093/PCP/PCAC086
Abstract: Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic ersity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, ersification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
Analysis of Genetic Diversity in Pongamia [Pongamia pinnata (L) Pierrre] using AFLP Markers
Publisher: Springer Science and Business Media LLC
Date: 07-2010
DOI: 10.1007/BF03263342
Simple sequence repeat-based diversity in elite pigeonpea genotypes for developing mapping populations to map resistance to Fusarium wilt and sterility mosaic disease
Publisher: Wiley
Date: 04-2010
In silico development of simple sequence repeat markers within the aeschynomenoid/dalbergoid and genistoid clades of the Leguminosae family and their transferability to Arachis hypogaea, groundnut
Publisher: Elsevier BV
Date: 2008
Coverage-based consensus calling (CBCC) of short sequence reads and comparison of CBCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
Publisher: Wiley
Date: 02-2012
DOI: 10.3732/AJB.1100419
Abstract: Next-generation sequencing (NGS) technologies are frequently used for resequencing and mining of single nucleotide polymorphisms (SNPs) by comparison to a reference genome. In crop species such as chickpea (Cicer arietinum) that lack a reference genome sequence, NGS-based SNP discovery is a challenge. Therefore, unlike probability-based statistical approaches for consensus calling and by comparison with a reference sequence, a coverage-based consensus calling (CbCC) approach was applied and two genotypes were compared for SNP identification. A CbCC approach is used in this study with four commonly used short read alignment tools (Maq, Bowtie, Novoalign, and SOAP2) and 15.7 and 22.1 million Illumina reads for chickpea genotypes ICC4958 and ICC1882, together with the chickpea trancriptome assembly (CaTA). A nonredundant set of 4543 SNPs was identified between two chickpea genotypes. Experimental validation of 224 randomly selected SNPs showed superiority of Maq among in idual tools, as 50.0% of SNPs predicted by Maq were true SNPs. For combinations of two tools, greatest accuracy (55.7%) was reported for Maq and Bowtie, with a combination of Bowtie, Maq, and Novoalign identifying 61.5% true SNPs. SNP prediction accuracy generally increased with increasing reads depth. This study provides a benchmark comparison of tools as well as read depths for four commonly used tools for NGS SNP discovery in a crop species without a reference genome sequence. In addition, a large number of SNPs have been identified in chickpea that would be useful for molecular breeding.
Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives
Publisher: MDPI AG
Date: 27-03-2022
Abstract: Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species ersity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic ersity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.
Overexpression of a Plasma Membrane Bound Na+/H+ Antiporter-Like Protein (SbNHXLP) Confers Salt Tolerance and Improves Fruit Yield in Tomato by Maintaining Ion Homeostasis
Publisher: Frontiers Media SA
Date: 06-01-2017
MAGIC lines in chickpea: development and exploitation of genetic diversity
Publisher: Springer Science and Business Media LLC
Date: 07-06-2021
Development of NIL s from heterogeneous inbred families for validating the rust resistance QTL in peanut (A rachis hypogaea L.)
Publisher: Wiley
Date: 06-12-2013
DOI: 10.1111/PBR.12130
The Chickpea Genome
Publisher: Springer International Publishing
Date: 2017
Meet the PCP Editor—Rajeev K. Varshney FRS
Publisher: Oxford University Press (OUP)
Date: 20-06-2023
DOI: 10.1093/PCP/PCAD064
Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects
Publisher: Springer Science and Business Media LLC
Date: 08-04-2014
Assessment of proline function in higher plants under extreme temperatures
Publisher: Wiley
Date: 27-02-2023
DOI: 10.1111/PLB.13510
Abstract: Climate change and abiotic stress factors are key players in crop losses worldwide. Among which, extreme temperatures (heat and cold) disturb plant growth and development, reduce productivity and, in severe cases, lead to plant death. Plants have developed numerous strategies to mitigate the detrimental impact of temperature stress. Exposure to stress leads to the accumulation of various metabolites, e.g. sugars, sugar alcohols, organic acids and amino acids. Plants accumulate the amino acid ‘proline’ in response to several abiotic stresses, including temperature stress. Proline abundance may result from de novo synthesis, hydrolysis of proteins, reduced utilization or degradation. Proline also leads to stress tolerance by maintaining the osmotic balance (still controversial), cell turgidity and indirectly modulating metabolism of reactive oxygen species. Furthermore, the crosstalk of proline with other osmoprotectants and signalling molecules, e.g. glycine betaine, abscisic acid, nitric oxide, hydrogen sulfide, soluble sugars, helps to strengthen protective mechanisms in stressful environments. Development of less temperature‐responsive cultivars can be achieved by manipulating the biosynthesis of proline through genetic engineering. This review presents an overview of plant responses to extreme temperatures and an outline of proline metabolism under such temperatures. The exogenous application of proline as a protective molecule under extreme temperatures is also presented. Proline crosstalk and interaction with other molecules is also discussed. Finally, the potential of genetic engineering of proline‐related genes is explained to develop ‘temperature‐smart’ plants. In short, exogenous application of proline and genetic engineering of proline genes promise ways forward for developing ‘temperature‐smart’ future crop plants.
Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 2016
Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.)
Publisher: Springer Science and Business Media LLC
Date: 06-05-2011
Genomic signatures of barley breeding for environmental adaptation to the new continents
Publisher: Wiley
Date: 27-07-2023
DOI: 10.1111/PBI.14077
Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant
Publisher: Springer Science and Business Media LLC
Date: 15-04-2020
DOI: 10.1186/S12870-020-02383-7
Abstract: Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil. An integrative analysis of transcriptomes, metabolomes and histocytology was performed on wsc mutant and its wild type to investigate the regulatory mechanisms underlying color pigmentation. Metabolomes revealed flavonoids were redirected in wsc , while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the TCA cycle and amino acid metabolism. The mutation also enhanced plant hormones synthesis and signaling. Further, co-expression analysis showed that FLS genes co-expressed with MBW complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common DEGs for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3 , Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype . WSC might be regulated expression competition between FLS and DFR by controlling hormone synthesis and signaling as well as the MBW complex. The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality.
The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor
Publisher: Springer Science and Business Media LLC
Date: 02-10-2014
DOI: 10.1007/S10142-014-0399-7
Abstract: The AP2/ERF family is one of the largest transcription factor gene families that are involved in various plant processes, especially in response to biotic and abiotic stresses. Complete genome sequences of one of the world's most important pulse crops chickpea (Cicer arietinum L.), has provided an important opportunity to identify and characterize genome-wide ERF genes. In this study, we identified 120 putative ERF genes from chickpea. The genomic organization of the chickpea ERF genes suggested that the gene family might have been expanded through the segmental duplications. The 120 member ERF family was classified into eleven distinct groups (I-X and VI-L). Transcriptional factor CarERF116, which is differentially expressed between drought tolerant and susceptible chickpea cultivar under terminal drought stress has been identified and functionally characterized. The CarERF116 encodes a putative protein of 241 amino acids and classified into group IX of ERF family. An in vitro CarERF116 protein-DNA binding assay demonstrated that CarERF116 protein specifically interacts with GCC box. We demonstrate that CarERF116 is capable of transactivation activity of and show that the functional transcriptional domain lies at the C-terminal region of the CarERF116. In transgenic Arabidopsis plants overexpressing CarERF116, significant up-regulation of several stress related genes were observed. These plants also exhibit resistance to osmotic stress and reduced sensitivity to ABA during seed germination. Based on these findings, we conclude that CarERF116 is an abiotic stress responsive gene, which plays an important role in stress tolerance. In addition, the present study leads to genome-wide identification and evolutionary analyses of chickpea ERF gene family, which will facilitate further research on this important group of genes and provides valuable resources for comparative genomics among the grain legumes.
Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 22-11-2011
Features and applications of haplotypes in crop breeding
Publisher: Springer Science and Business Media LLC
Date: 04-11-2021
DOI: 10.1038/S42003-021-02782-Y
Abstract: Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives
Publisher: Public Library of Science (PLoS)
Date: 22-06-2012
Draft Genome Report of Bacillus altitudinis SORB11, Isolated from the Indian Sector of the Southern Ocean
Publisher: American Society for Microbiology
Date: 08-06-2017
Abstract: Here, we present the draft genome sequence of Bacillus altitudinis SORB11, which is tolerant to UV radiation. The strain was isolated from the Indian sector of the Southern Ocean at a depth of 3.8 km. The genome sequence information reported here for B. altitudinis SORB11 gives the basis of its UV resistance mechanism and provides data for further comparative studies with other bacteria resistant to UV radiation.
Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq
Publisher: Frontiers Media SA
Date: 19-07-2016
Sigma Factor Modulation for Cyanobacterial Metabolic Engineering
Publisher: Elsevier BV
Date: 03-2021
Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress
Publisher: Springer Science and Business Media LLC
Date: 22-04-2011
Abstract: Chickpea ( Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea. EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity ( E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay. Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.
Differential Physio-Biochemical and Metabolic Responses of Peanut (Arachis hypogaea L.) under Multiple Abiotic Stress Conditions
Publisher: MDPI AG
Date: 08-01-2022
DOI: 10.3390/IJMS23020660
Abstract: The frequency and severity of extreme climatic conditions such as drought, salinity, cold, and heat are increasing due to climate change. Moreover, in the field, plants are affected by multiple abiotic stresses simultaneously or sequentially. Thus, it is imperative to compare the effects of stress combinations on crop plants relative to in idual stresses. This study investigated the differential regulation of physio-biochemical and metabolomics parameters in peanut (Arachis hypogaea L.) under in idual (salt, drought, cold, and heat) and combined stress treatments using multivariate correlation analysis. The results showed that combined heat, salt, and drought stress compounds the stress effect of in idual stresses. Combined stresses that included heat had the highest electrolyte leakage and lowest relative water content. Lipid peroxidation and chlorophyll contents did not significantly change under combined stresses. Biochemical parameters, such as free amino acids, polyphenol, starch, and sugars, significantly changed under combined stresses compared to in idual stresses. Free amino acids increased under combined stresses that included heat starch, sugars, and polyphenols increased under combined stresses that included drought proline concentration increased under combined stresses that included salt. Metabolomics data that were obtained under different in idual and combined stresses can be used to identify molecular phenotypes that are involved in the acclimation response of plants under changing abiotic stress conditions. Peanut metabolomics identified 160 metabolites, including amino acids, sugars, sugar alcohols, organic acids, fatty acids, sugar acids, and other organic compounds. Pathway enrichment analysis revealed that abiotic stresses significantly affected amino acid, amino sugar, and sugar metabolism. The stress treatments affected the metabolites that were associated with the tricarboxylic acid (TCA) and urea cycles and associated amino acid biosynthesis pathway intermediates. Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and heatmap analysis identified potential marker metabolites (pinitol, malic acid, and xylopyranose) that were associated with abiotic stress combinations, which could be used in breeding efforts to develop peanut cultivars that are resilient to climate change. The study will also facilitate researchers to explore different stress indicators to identify resistant cultivars for future crop improvement programs.
Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Publisher: Oxford University Press (OUP)
Date: 23-02-2017
DOI: 10.1093/JXB/ERX010
Agricultural biotechnology for crop improvement in a variable climate: Hope or hype?
Publisher: Elsevier BV
Date: 07-2011
DOI: 10.1016/J.TPLANTS.2011.03.004
Abstract: Developing crops that are better adapted to abiotic stresses is important for food production in many parts of the world today. Anticipated changes in climate and its variability, particularly extreme temperatures and changes in rainfall, are expected to make crop improvement even more crucial for food production. Here, we review two key biotechnology approaches, molecular breeding and genetic engineering, and their integration with conventional breeding to develop crops that are more tolerant of abiotic stresses. In addition to a multidisciplinary approach, we also examine some constraints that need to be overcome to realize the full potential of agricultural biotechnology for sustainable crop production to meet the demands of a projected world population of nine billion in 2050.
Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines
Publisher: Springer Science and Business Media LLC
Date: 22-05-2015
Molecular and Genomic Characterization of PFAB2: A Non-virulent Bacillus anthracis Strain Isolated from an Indian Hot Spring
Publisher: Bentham Science Publishers Ltd.
Date: 2020
DOI: 10.2174/1389202920666191203121610
Abstract: Thermophilic bacilli in both aerobic or facultative anaerobic forms have been isolated for over a hundred years from different mesophilic or thermophilic environments as they are potential source of bioactive secondary metabolites. But the taxonomic resolution in the Bacillus genus at species or at strain level is very challenging for the insufficient ergence of the 16S rRNA genes. One such recurring problem is among Bacillus anthracis, B. cereus and B. thuringiensis. The disease-causing B. anthracis strains have their characteristic virulence factors coded in two wellknown plasmids, namely pXO1 (toxin genes) and pXO2 (capsule genes). The present study aimed at the molecular and genomic characterization of a recently reported thermophilic and environmental isolate of B. anthracis, strain PFAB2. We performed comparative genomics between the PFAB2 genome and different strains of B. anthracis, along with closely related B. cereus strains. The pangenomic analysis suggests that the PFAB2 genome harbors no complete prophage genes. Cluster analysis of Bray-Kurtis similarity resemblance matrix revealed that gene content of PFAB2 is more closely related to other environmental strains of B. anthracis. The secretome analysis and the in vitro and in vivo pathogenesis experiments corroborate the avirulent phenotype of this strain. The most probable explanation for this phenotype is the apparent absence of plasmids harboring genes for capsule biosynthesis and toxins secretion in the draft genome. Additional features of PFAB2 are good spore-forming and germinating capabilities and rapid replication ability. The high replication rate in a wide range of temperatures and culture media, the nonpathogenicity, the good spore forming capability and its genomic similarity to the Ames strain together make PFAB2 an interesting model strain for the study of the pathogenic evolution of B. anthracis.
Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea
Publisher: MDPI AG
Date: 17-07-2020
DOI: 10.3390/IJMS21145058
Abstract: Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.
Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research
Publisher: MDPI AG
Date: 17-06-2021
Abstract: The groundnut breeding program at International Crops Research Institute for the Semi-Arid Tropics routinely performs marker-based early generation selection (MEGS) in thousands of segregating populations. The existing MEGS includes planting of segregating populations in fields or glasshouses, label tagging, and s le collection using leaf-punch from 20–25 day old plants followed by genotyping with 10 single nucleotide polymorphisms based early generation selection marker panels in a high throughput genotyping (HTPG) platform. The entire process is laborious, time consuming, and costly. Therefore, in order to save the time of the breeder and to reduce the cost during MEGS, we optimized a single seed chipping (SSC) process based MEGS protocol and deployed on large scale by genotyping s les from ongoing groundnut breeding program. In SSC-based MEGS, we used a small portion of cotyledon by slicing-off the posterior end of the single seed and transferred to the 96-deep well plate for DNA isolation and genotyping at HTPG platform. The chipped seeds were placed in 96-well seed-box in the same order of 96-well DNA s ling plate to enable tracking back to the selected in idual seed. A high germination rate of 95–99% from the chipped seeds indicated that slicing of seeds from posterior end does not significantly affect germination percentage. In addition, we could successfully advance 3.5 generations in a year using a low-cost rapid generation turnover glass-house facility as compared to routine practice of two generations in field conditions. The integration of SSC based genotyping and rapid generation advancement (RGA) could significantly reduce the operational requirement of person-hours and expenses, and save a period of 6–8 months in groundnut genetics and breeding research.
Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.)
Publisher: Elsevier BV
Date: 02-2012
Molecular plant breeding: Methodology and achievements
Publisher: Humana Press
Date: 2009
DOI: 10.1007/978-1-59745-427-8_15
Abstract: The progress made in DNA marker technology has been remarkable and exciting in recent years. DNA markers have proved valuable tools in various analyses in plant breeding, for ex le, early generation selection, enrichment of complex F(1)s, choice of donor parent in backcrossing, recovery of recurrent parent genotype in backcrossing, linkage block analysis and selection. Other main areas of applications of molecular markers in plant breeding include germplasm characterization/fingerprinting, determining seed purity, systematic s ling of germplasm, and phylogenetic analysis. Molecular markers, thus, have proved powerful tools in replacing the bioassays and there are now many ex les available to show the efficacy of such markers. We have illustrated some basic concepts and methodology of applying molecular markers for enhancing the selection efficiency in plant breeding. Some successful ex les of product developments of molecular breeding have also been presented.
Breeding custom‐designed crops for improved drought adaptation
Publisher: Wiley
Date: 21-08-2021
DOI: 10.1002/GGN2.10052
Application of SSR markers for molecular characterization of hybrid parents and purity assessment of ICPH 2438 hybrid of pigeonpea [Cajanus cajan (L.) Millspaugh]
Publisher: Springer Science and Business Media LLC
Date: 26-05-2010
New eSSR and gSSR markers added to Australian barley maps
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/AR05384
Abstract: To enhance genetic maps of barley previously developed in Australia for identifying markers useable in molecular breeding, a new set of simple sequence repeat (SSR) and indel markers was added to the maps. These markers were developed through (i) database mining of barley expressed sequence tag (EST) sequences, (ii) comparative barley-rice genome analysis, and (iii) screening of a genomic library with SSR probes. The primer set selected for this study comprised 216 EST-SSR (eSSR) and 25 genomic SSR (gSSR) markers, which were screened for polymorphism on 4 doubled haploid (DH) or recombinant inbred line (RIL) populations. In total, 81 new markers were added to the maps, with good coverage on all 7 chromosomes, except 6H, which only had 2 new markers added. The marker order of previously published maps was re-evaluated by comparing recombination fractions calculated by 2 methods to discover the best position for each marker. The new SSR markers were then added to the updated maps. Several of these new markers are linked to important barley disease resistance genes such as those for cereal cyst nematode, spot form of net blotch, and leaf scald resistance, and are readily useable for marker-assisted barley breeding. The new maps are available on-line at www.genica.net.au.
Comparative transcriptome analysis of aerial and subterranean pods development provides insights into seed abortion in peanut
Publisher: Springer Science and Business Media LLC
Date: 05-05-2014
Evaluation of Streptomyces sp. obtained from herbal vermicompost for broad spectrum of plant growth-promoting activities in chickpea
Publisher: Springer Science and Business Media LLC
Date: 24-02-2015
Future Prospects for Peanut Improvement
Publisher: Springer International Publishing
Date: 2017
CicArMiSatDB: the chickpea microsatellite database
Publisher: Springer Science and Business Media LLC
Date: 21-06-2014
Identification of quantitative trait loci for protein content, oil content and oil quality for groundnut (Arachis hypogaea L.)
Publisher: Elsevier BV
Date: 04-2011
Challenges and Strategies for Next Generation Sequencing (NGS) Data Analysis
Publisher: OMICS Publishing Group
Date: 2010
DOI: 10.4172/JCSB.1000053
Development and evaluation of high‐density Axiom®CicerSNP Array for high‐resolution genetic mapping and breeding applications in chickpea
Publisher: Wiley
Date: 31-10-2017
DOI: 10.1111/PBI.12836
Characterisation of pathogenic and molecular diversity in Sclerospora graminicola, the causal agent of pearl millet downy mildew
Publisher: Informa UK Limited
Date: 04-2010
A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1093/MP/SSR111
Capturing genetic variability and selection of traits for heat tolerance in a chickpea recombinant inbred line (RIL) population under field conditions
Publisher: Springer Science and Business Media LLC
Date: 12-01-2018
Proline over-accumulation alleviates salt stress and protects photosynthetic and antioxidant enzyme activities in transgenic sorghum [Sorghum bicolor (L.) Moench]
Publisher: Elsevier BV
Date: 09-2015
DOI: 10.1016/J.PLAPHY.2015.05.014
Abstract: Shoot-tip derived callus cultures of Sorghum bicolor were transformed by Agrobacterium tumefaciens as well as by bombardment methods with the mutated pyrroline-5-carboxylate synthetase (P5CSF129A) gene encoding the key enzyme for proline biosynthesis from glutamate. The transgenics were selfed for three generations and T4 plants were examined for 100 mM NaCl stress tolerance in pot conditions. The effect of salt stress on chlorophyll and carotenoid contents, photosynthetic rate, stomatal conductance, internal carbon dioxide concentration, transpiration rates, intrinsic transpiration and water use efficiencies, proline content, MDA levels, and antioxidant enzyme activities were evaluated in 40-day-old transgenic lines and the results were compared with untransformed control plants. The results show that chlorophyll content declines by 65% in untransformed controls compared to 30-38% loss (significant at P < 0.05) in transgenics but not carotenoid levels. Photosynthetic rate (PSII activity) was reduced in untransformed controls almost completely, while it declined by 62-88% in different transgenic lines. Salinity induced ca 100% stomatal closure in untransformed plants, while stomatal conductance was decreased only by 64-81% in transgenics after 4 days. The intercellular CO2 decreased by ca 30% in in idual transgenic lines. Malondialdehyde (MDA) content was lower in transgenics compared to untransformed controls. The activities of superoxide dismutase (SOD EC 1.15.1.1), catalase (CAT EC 1.11.1.6) and glutathione reductase (GR EC1.8.1.7) were quantified in leaves exposed to 100 mM NaCl stress and found higher in transgenics. The results suggest that transgenic lines were able to cope better with salt stress than untransformed controls by protecting photosynthetic and antioxidant enzyme activities.
Genotypic variation in soil water use and root distribution and their implications for drought tolerance in chickpea
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/FP16154
Abstract: Chickpeas are often grown under receding soil moisture and suffer ~50% yield losses due to drought stress. The timing of soil water use is considered critical for the efficient use of water under drought and to reduce yield losses. Therefore the root growth and the soil water uptake of 12 chickpea genotypes known for contrasts in drought and rooting response were monitored throughout the growth period both under drought and optimal irrigation. Root distribution reduced in the surface and increased in the deep soil layers below 30 cm in response to drought. Soil water uptake was the maximum at 45–60 cm soil depth under drought whereas it was the maximum at shallower (15–30 and 30–45 cm) soil depths when irrigated. The total water uptake under drought was 1-fold less than optimal irrigation. The amount of water left unused remained the same across watering regimes. All the drought sensitive chickpea genotypes were inferior in root distribution and soil water uptake but the timing of water uptake varied among drought tolerant genotypes. Superiority in water uptake in most stages and the total water use determined the best adaptation. The water use at 15–30 cm soil depth ensured greater uptake from lower depths and the soil water use from 90–120 cm soil was critical for best drought adaptation. Root length density and the soil water uptake across soil depths were closely associated except at the surface or the ultimate soil depths of root presence.
Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops
Publisher: Research Square Platform LLC
Date: 16-11-2020
DOI: 10.21203/RS.3.RS-108241/V1
Abstract: Background: Chickpea, pigeonpea, and groundnut are the primary crop legumes of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. – Results: In this study, genome-wide NAC proteins – 72, 96, and 166 – have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana , Oryza sativa (rice), Medicago truncatula , and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). On exploring the available transcriptome data of each of these legumes, putative stress-responsive NACs at various developmental stages revealed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC ( Cicer arietinum - 14) , Cc_NAC ( Cajanus cajan - 15) , and Ah_NAC ( Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, 10/14 Ca_NACs ( Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186 ) 6/15 Cc_NACs ( Cc_26125 , Cc_43030 , Cc_43785 , Cc_43786 , Cc_22429 , and Cc_22430 ) 5/14 Ah_NACs ( Ah_ann1.G1V3KR.2 , Ah_ann1.MI72XM.2 , Ah_ann1.V0X4SV.1 , Ah_ann1.FU1JML.2 , and Ah_ann1.8AKD3R.1 ) were identified as potential drought stress-responsive candidate genes. Conclusion: In the present study, comprehensive genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. Based on the genome sequence, we analyzed phylogenetic association, structural characteristics, promoter analysis, gene interaction networks, and expression profiles of NAC genes among these three legumes. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. The identified candidate genes would serve as a useful resource for molecular breeding for developing drought-tolerant legume varieties with improved productivity.
A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction
Publisher: Cold Spring Harbor Laboratory
Date: 03-10-2019
DOI: 10.1101/775221
Abstract: Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of in iduals. We developed two PHGs in sorghum, one with 24 in iduals and another with 398 in iduals, that reflect the ersity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted licons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a erse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.
miRNAs for crop improvement
Publisher: Elsevier BV
Date: 08-2023
Wildsoydb DataHub: a platform for accessing soybean multiomic datasets across multiple reference genomes
Publisher: Oxford University Press (OUP)
Date: 05-09-2022
Abstract: The Wildsoydb DataHub is an integrated interface for biologists and breeders to access soybean genomic resources easily, allowing them to fully utilize the results of genomic research.
A high density barley microsatellite consensus map with 775 SSR loci
Publisher: Springer Science and Business Media LLC
Date: 08-03-2007
DOI: 10.1007/S00122-007-0503-7
Abstract: A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the in idual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more in idual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype ersity studies of barley.
Genome-Wide Association Analysis of Yield-Related Traits of Soybean Using Haplotype-Based Framework
Publisher: MDPI
Date: 02-12-2021
Harnessing Genetic Diversity of Wild Arachis Species for Genetic Enhancement of Cultivated Peanut
Publisher: Wiley
Date: 05-2017
Correction to: Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 06-2018
Genomics and Physiological Approaches for Root Trait Breeding to Improve Drought Tolerance in Chickpea (Cicer arietinum L.)
Publisher: Springer Berlin Heidelberg
Date: 15-09-2010
A QTL analysis of aluminium tolerance in barley, using gene-based markers
Publisher: Springer Science and Business Media LLC
Date: 12-2009
A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues
Publisher: Springer Science and Business Media LLC
Date: 18-11-2007
DOI: 10.1007/S00122-006-0448-2
Abstract: A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was ided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin.
Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 30-12-2010
An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations
Publisher: Springer Science and Business Media LLC
Date: 08-07-2012
Genetic and Physical Mapping of Genic Microsatellites in Barley (Hordeum vulgare L.)
Publisher: Czech Academy of Agricultural Sciences
Date: 31-12-2005
DOI: 10.17221/3661-CJGPB
Advances in Chickpea Genomics
Publisher: Springer New York
Date: 27-09-2013
Aggravated food insecurity in COVID-19 era: quality seed flow of adapted and nutrient-dense varieties is central to the recovery equation in the drylands
Publisher: PLUS COMMUNICATION CONSULTING SRL
Date: 23-06-2020
DOI: 10.47577/TECHNIUM.V2I5.1074
Abstract: The COVID-19 pandemic has disrupted every area of our daily activities and businesses. After the health crisis, the food crisis is the next battle to encounter, which will need to mobilize all energies to maintain social security and protect the citizens of the world. For sustained support and recovery of rural and urban populations, especially in the dryland areas of Sub-Saharan Africa, seed of the well-adapted, nutrient dense varieties should flow. The solution of quality seed flow equation is complex and involves several intervention areas, e.g., adapted and modern groundnut, chickpea, pigeonpea, sorghum and finger millet varieties, sustainable and long term approaches leveraging various seed production and delivery models, remote information and knowledge dissemination systems, digital seed production and delivery roadmaps, digitized variety release and promotion processes, smart food c aigns and trainings to promote good utilization of nutrient dense crops.
Construction and comparison of three reference‐quality genome assemblies for soybean
Publisher: Wiley
Date: 28-10-2019
DOI: 10.1111/TPJ.14500
Abstract: We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean ersity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
Advances in Pigeonpea Genomics
Publisher: Springer New York
Date: 27-09-2013
Genomics of plant genetic resources: a gateway to a new era of global food security
Publisher: Cambridge University Press (CUP)
Date: 07-2014
Genomics-Assisted Crop Improvement
Publisher: Springer Netherlands
Date: 2007
Identification of heterotic groups in South-Asian-bred hybrid parents of pearl millet
Publisher: Springer Science and Business Media LLC
Date: 02-01-2020
DOI: 10.1007/S00122-019-03512-Z
Abstract: Pearl millet breeding programs can use this heterotic group information on seed and restorer parents to generate new series of pearl millet hybrids having higher yields than the existing hybrids. Five hundred and eighty hybrid parents, 320 R- and 260 B-lines, derived from 6 pearl millet breeding programs in India, genotyped following RAD-GBS (about 0.9 million SNPs) clustered into 12 R- and 7 B-line groups. With few exceptions, hybrid parents of all the breeding programs were found distributed across all the marker-based groups suggesting good ersity in these programs. Three hundred and twenty hybrids generated using 37 (22 R and 15 B) representative parents, evaluated for grain yield at four locations in India, showed significant differences in yield, heterosis, and combining ability. Across all the hybrids, mean mid- and better-parent heterosis for grain yield was 84.0% and 60.5%, respectively. Groups G12 B × G12 R and G10 B × G12 R had highest heterosis of about 10% over best check hybrid Pioneer 86M86. The parents involved in heterotic hybrids were mainly from the groups G4R, G10B, G12B, G12R, and G13B. Based on the heterotic performance and combining ability of groups, 2 B-line (HGB-1 and HGB-2) and 2 R-line (HGR-1 and HGR-2) heterotic groups were identified. Hybrids from HGB-1 × HGR-1 and HGB-2 × HGR-1 showed grain yield heterosis of 10.6 and 9.3%, respectively, over best hybrid check. Results indicated that parental groups can be formed first by molecular markers, which may not predict the best hybrid combination, but it can reveal a practical value of assigning existing and new hybrid pearl millet parental lines into heterotic groups to develop high-yielding hybrids from the different heterotic groups.
Genetic molecular markers to accelerate genetic gains in crops
Publisher: Future Science Ltd
Date: 09-2020
Simultaneous Establishing Single-cell Transcriptome Atlas and Chromatin Accessibility Landscapes in Allotetraploid Leguminous Plant
Publisher: Research Square Platform LLC
Date: 29-09-2022
DOI: 10.21203/RS.3.RS-2082716/V1
Abstract: Plant cell proliferation associated with multiple layers of gene regulation, including modulation of transcriptome by changes in chromatin accessibility. However, cell proliferation is an asynchronous process precluding a temporal understanding of regulatory events leading to single-cell fate commitment. Here, a robust single nucleus RNA sequencing approach, where single nucleus employed for simultaneous investigation of transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same single-cell of Arachis hypogaea leaves. A total of 5,930 leaf cells with 10,793 expressed genes were used to construct development trajectory and characterized large-scale critical differentially expressed genes (DEGs). Additionally, uncovered extending insights of chromatin opening guided 5,315 DEGs expression involved biological pathway determines differentiation direction in distinct cell-types. But obtained members in each cell-clusters not exhibits obvious difference in distinct cell-cycling regulated genome duplication phases. Furthermore, snRNA-seq identified AT-hook transcription factor AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displays contrasting results to repress the leaf development by jasmonic acid pathway in ectopically expressed Arabidopsis . We concluded that, snRNA-seq combined with snATAC-seq is an extensible platform to explore association between the chromatin regulatory events and gene expression across ersity cell-types in peanut leaf, broadly application of this approach will enable significant advances in the functional research of tissues ontology in plant species.
Progress in the utilization of Cajanus platycarpus (Benth.) Maesen in pigeonpea improvement
Publisher: Wiley
Date: 31-05-2011
Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea
Publisher: Springer Science and Business Media LLC
Date: 19-03-2018
DOI: 10.1038/S41598-018-23116-9
Abstract: Salinity is a major constraint for intrinsically salt sensitive grain legume chickpea. Chickpea exhibits large genetic variation amongst cultivars, which show better yields in saline conditions but still need to be improved further for sustainable crop production. Based on previous multi-location physiological screening, JG 11 (salt tolerant) and ICCV 2 (salt sensitive) were subjected to salt stress to evaluate their physiological and transcriptional responses. A total of ~480 million RNA-Seq reads were sequenced from root tissues which resulted in identification of 3,053 differentially expressed genes (DEGs) in response to salt stress. Reproductive stage shows high number of DEGs suggesting major transcriptional reorganization in response to salt to enable tolerance. Importantly, cationic peroxidase, Aspartic ase, NRT1/PTR , phosphatidylinositol phosphate kinase, DREB1E and ERF genes were significantly up-regulated in tolerant genotype. In addition, we identified a suite of important genes involved in cell wall modification and root morphogenesis such as dirigent proteins, expansin and casparian strip membrane proteins that could potentially confer salt tolerance. Further, phytohormonal cross-talk between ERF and PIN-FORMED genes which modulate the root growth was observed. The gene set enrichment analysis and functional annotation of these genes suggests they may be utilised as potential candidates for improving chickpea salt tolerance.
Simultaneous Analysis of Single-nucleus Transcriptome and Chromatin Accessibility Unveils the Mechanisms of Leaf Cell Development in Arachis hypogaea L.
Publisher: Research Square Platform LLC
Date: 07-03-2023
DOI: 10.21203/RS.3.RS-2082716/V2
Abstract: Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of Arachis hypogaea . A total of 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. The developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insight for mesophyll and vascular cell development. Additionally, dual-omics described the epidermal progenitor cell development trajectory, primordium and palisade cells were able to convert into spongy cells, and bundle sheath cells developed earlier than other vascular-cells. Further cell-cycle analysis demonstrated that cytokinin biosynthesis promotes mesophyll cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified that the AT-hook transcription factor AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displaying contrasting results by repressing leaf development via the jasmonic acid pathway in ectopically expressed Arabidopsis . Conclusively, our study demonstrates that snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across erse cell types in peanut leaves. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species. Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of peanut. Totally 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. Developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insights for mesophyll and vascular cells development. Further ell-cycle demonstrated that cytokinin promotes mesophyll-cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 repressing leaf development via jasmonic acid pathway. Conclusively, snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across erse cell-types. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species.
High‐density genetic map using whole‐genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut
Publisher: Wiley
Date: 15-05-2018
DOI: 10.1111/PBI.12930
Single nucleotide polymorphisms in rye (Secale cereale L.): Discovery, frequency, and applications for genome mapping and diversity studies
Publisher: Springer Science and Business Media LLC
Date: 08-03-2007
DOI: 10.1007/S00122-007-0504-6
Abstract: To elucidate the potential of single nucleotide polymorphism (SNP) markers in rye, a set of 48 barley EST (expressed sequence tag) primer pairs was employed to lify from DNA prepared from five rye inbred lines. A total of 96 SNPs and 26 indels (insertion-deletions) were defined from the sequences of 14 of the resulting licons, giving an estimated frequency of 1 SNP per 58 bp and 1 indel per 214 bp in the rye transcriptome. A mean of 3.4 haplotypes per marker with a mean expected heterozygosity of 0.66 were observed. The nucleotide ersity index (pi) was estimated to be in the range 0.0059-0.0530. To improve assay cost-effectiveness, 12 of the 14 SNPs were converted to a cleaved lified polymorphic sequence (CAPS) format. The resulting 12 SNP loci mapped to chromosomes 1R, 3R, 4R, 5R, 6R, and 7R, at locations consistent with their known map positions in barley. SNP genotypic data were compared with genomic simple sequence repeat (SSR) and EST-derived SSR genotypic data collected from the same templates. This showed a broad equivalence with respect to genetic ersity between these different data types.
Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groun
Publisher: MDPI AG
Date: 16-12-2020
DOI: 10.3390/JOF6040370
Abstract: Aflatoxin-affected groundnut or peanut presents a major global health issue to both commercial and subsistence farming. Therefore, understanding the genetic and molecular mechanisms associated with resistance to aflatoxin production during host–pathogen interactions is crucial for breeding groundnut cultivars with minimal level of aflatoxin contamination. Here, we performed gene expression profiling to better understand the mechanisms involved in reduction and prevention of aflatoxin contamination resulting from Aspergillus flavus infection in groundnut seeds. RNA sequencing (RNA-Seq) of 16 s les from different time points during infection (24 h, 48 h, 72 h and the 7th day after inoculation) in U 4-7-5 (resistant) and JL 24 (susceptible) genotypes yielded 840.5 million raw reads with an average of 52.5 million reads per s le. A total of 1779 unique differentially expressed genes (DEGs) were identified. Furthermore, comprehensive analysis revealed several pathways, such as disease resistance, hormone biosynthetic signaling, flavonoid biosynthesis, reactive oxygen species (ROS) detoxifying, cell wall metabolism and catabolizing and seed germination. We also detected several highly upregulated transcription factors, such as ARF, DBB, MYB, NAC and C2H2 in the resistant genotype in comparison to the susceptible genotype after inoculation. Moreover, RNA-Seq analysis suggested the occurrence of coordinated control of key pathways controlling cellular physiology and metabolism upon A. flavus infection, resulting in reduced aflatoxin production.
Siphoning novel sources of seedling salinity tolerance from the diverse chickpea landraces
Publisher: CSIRO Publishing
Date: 14-03-2023
DOI: 10.1071/CP22319
QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 11-02-2016
Phase Changing Material: An Alternative Method for Cooling Babies with Hypoxic Ischaemic Encephalopathy
Publisher: S. Karger AG
Date: 2015
DOI: 10.1159/000375286
Abstract: b i Background: /i /b Therapeutic hypothermia for hypoxic ischaemic encephalopathy (HIE) has been proved effective. Standard equipment is expensive, while ice packs used in low resource settings are labour intensive and associated with wider temperature fluctuations. b i Objectives: /i /b To assess the feasibility of using phase changing material (PCM) as an alternative method for providing therapeutic hypothermia. b i Methods: /i /b We retrospectively analysed 41 babies with HIE who had been cooled with PCM (OM 32™ or HS 29™) to a target rectal temperature of 33-34°C. Rectal temperature was continuously monitored and recorded every hour. If the rectal temperature was .8°C, cool gel packs were applied, and if the temperature was .2°C, the baby was covered with sheets and the warmer output turned on till the temperature stabilized at 33.5°C. The unit's standard protocol for cooling was followed for monitoring and treatment. The outcome measures were stability and fluctuation of the rectal temperature and the need for interventions to maintain the target temperature. b i Results: /i /b The mean (±SD) temperature during the cooling phase was 33.45 ± 0.26°C. Throughout the cooling phase, the target temperature range was maintained in 96.2% of the time. There was no temperature reading °C. With HS 29, ice packs were not used in any baby, and the warmer was used for a median of 7 h (interquartile range 1.5-14). b i Conclusions: /i /b PCM provides a low cost and effective method to maintain therapeutic hypothermia. However, careful monitoring is required during induction and the rewarming phase to avoid hypothermia outside the therapeutic range.
Mapping QTL for resistance to botrytis grey mould in chickpea
Publisher: Springer Science and Business Media LLC
Date: 25-02-2011
The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers
Publisher: Springer Science and Business Media LLC
Date: 04-2011
DOI: 10.1007/S12041-011-0050-5
Abstract: With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 ersity arrays technology (DArT) markers showed polymorphism in a pigeon pea F(2) mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using ersity arrays technology.
Pan-genome for pearl millet that beats the heat
Publisher: Elsevier BV
Date: 08-2023
Improving protein content and nutrition quality.
Publisher: CABI
Date: 2011
Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress
Publisher: Springer Science and Business Media LLC
Date: 22-02-2019
DOI: 10.1038/S41598-019-39084-7
Abstract: Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL ( qDTY ) combinations in the genetic background of IR64, TDK1- Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1- Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.
Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping
Publisher: Wiley
Date: 16-05-2018
DOI: 10.1111/PBI.12929
Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives
Publisher: Elsevier BV
Date: 08-2017
DOI: 10.1016/J.MOLP.2017.06.008
Abstract: There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
SSR markers associated to early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut ( Arachis hypogaea L.)
Publisher: Elsevier BV
Date: 09-2017
Male-sterility systems in pigeonpea and their role in enhancing yield
Publisher: Wiley
Date: 04-2010
Reap the crop wild relatives for breeding future crops
Publisher: Elsevier BV
Date: 04-2022
DOI: 10.1016/J.TIBTECH.2021.08.009
Abstract: Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic ersity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
Partitioning coefficient-A trait that contributes to drought tolerance in chickpea
Publisher: Elsevier BV
Date: 08-2013
Identification of QTLs for resistance to Fusarium wilt and Ascochyta blight in a recombinant inbred population of chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 05-02-2018
Vitamin D Status and Adequacy of Standard Supplementation in Preterm Neonates From South India
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2014
Functional molecular markers in barley: Development and applications
Publisher: Czech Academy of Agricultural Sciences
Date: 31-12-2005
DOI: 10.17221/6152-CJGPB
Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Publisher: Wiley
Date: 23-01-2016
DOI: 10.1111/PBI.12520
Clinical presentation of type 1 and type 2 pyrethroid poisoning in humans
Publisher: Informa UK Limited
Date: 21-10-2021
DOI: 10.1080/15563650.2021.1994145
Abstract: It is unclear if the clinical presentation of poisoning with type 1 and type 2 pyrethroid compounds is different. This study was undertaken to detail the clinical profile and outcome of patients presenting with pyrethroid poisoning and to quantify serum pyrethroid levels. In this prospective study, patients were categorised as poisoning with type 1 pyrethroids or type 2 pyrethroids. Blood s les were sent for compound identification and quantification. Clinical features and outcomes were compared between the two groups. Factors associated with moderate and severe toxicity were explored using univariate logistic regression analysis and presented as odds ratio (OR) and 95% confidence intervals (CI). Type 1 pyrethroids were implicated in 16 patients and type 2 in 43 patients. The incidence of nausea and vomiting (81.2% vs. 81.3%) and tremor (37.5% vs. 32.6%) were similar in type 1 and type 2 poisoning paraesthesia (6.2% vs. 32.6%, Patients with pyrethroid poisoning present predominantly with mild to moderate symptoms. Paraesthesia and hypersalivation are more frequent in type 2 poisoning. A favourable outcome can be expected.
InDel markers: An extended marker resource for molecular breeding in chickpea
Publisher: Public Library of Science (PLoS)
Date: 18-03-2019
Enhancement of the use and impact of germplasm in crop improvement
Publisher: Cambridge University Press (CUP)
Date: 07-2014
DOI: 10.1017/S1479262114000458
Abstract: Plant genetic resources are raw materials and their use in breeding is one of the most sustainable ways to conserve bio ersity. The ICRISAT has over 120,000 accessions of its five mandate crops and six small millets. The management and utilization of such large ersity are greatest challenges to germplasm curators and crop breeders. New sources of variations have been discovered using core and minicore collections developed at the ICRISAT. About 1.4 million seed s les have been distributed some accessions with specific attributes have been requested more frequently. The advances in genomics have led researchers to dissect population structure and ersity and mine allelic variations associated with agronomically beneficial traits. Genome-wide association mapping in sorghum has revealed significant marker–trait associations for many agronomically beneficial traits. Wild relatives harbour genes for resistance to diseases and insect pests. Resistance to pod borer in chickpea and pigeonpea and resistance to rust and late leaf spot in groundnut have been successfully introgressed into a cultivated genetic background. Synthetics in groundnut are available to broaden the cultigen's gene pool. ICRISAT has notified the release of 266 varieties/cultivars, germplasm, and elite genetic stocks with unique traits, with some having a significant impact on breeding programs. Seventy-five germplasm lines have been directly released for cultivation in 39 countries.
Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops
Publisher: Springer Science and Business Media LLC
Date: 14-06-2012
Factors Influencing Preferences and Adoption of Improved Groundnut Varieties among Farmers in Tanzania
Publisher: MDPI AG
Date: 27-08-2020
Abstract: Access and use of seed of improved varieties of groundnut among farmers can improve farmers’ livelihoods and contribute to the potential of crop production in Tanzania. This paper analyzes factors underpinning the adoption of improved groundnut varieties among farmers to pave the way for upscaling quality seed used for increased production and commodity business in farming communities. A four-stage stratified s ling was used to collect data from 300 groundnut farmers in seven agro-ecological zones through in idual interviews. Secondary data were collected from the literature and the Tanzania Agricultural Research Institute at Naliendele centre (TARI–Naliendele). Descriptive statistics and Probit regression model were used for data analysis. The empirical results showed that Johari 1985, Pendo 1998, Naliendele 2009, Mnanje 2009, Mangaka 2009 and Nachi 2015, are the main six improved groundnut varieties used by farmers, with Pendo 1998 having the highest adoption rate (17.1%). In the grain market, four varieties, namely Pendo 1998, Mnanje 2009, Nachi 2015 and Johari 1985, were observed to be highly preferred by grain off-takers. Furthermore, among the adopted improved varieties, Nachi 2015, is observed to be the most consistent high yielding variety, ranging from 1100 kg/ha to 1500 kg/ha in all agro-ecological zones. A farmer’s decision to adopt new varieties is affected by age and gender, farmer group membership, availability of improved seed and seed cost. Overall, male farmers are more likely to adopt improved varieties of groundnut than female farmers. The implications of these findings are also discussed, in particular in the area of policy support.
Evaluation of Global Composite Collection Reveals Agronomically Superior Germplasm Accessions for Chickpea Improvement
Publisher: MDPI AG
Date: 26-08-2022
Abstract: The rich genetic ersity existing within exotic, indigenous, and erse germplasm lays the foundation for the continuous improvement of crop cultivars. The composite collection has been suggested as a gateway to identifying superior germplasm for use in crop improvement programs. Here, a chickpea global composite collection was evaluated at five locations in India over two years for five agronomic traits to identify agronomically superior accessions. The desi, kabuli, and intermediate types of chickpea accessions differed significantly for plant height (PLHT) and 100-seed weight (100 SW). In contrast, the intermediate type differed substantially from kabuli for days to maturity (DM). Several highly significant trait correlations were detected across different locations. The most stable and promising accessions from each of the five locations were prioritised based on their superior performance over the best-performing check cultivar. Accordingly, the selected germplasm accessions of desi type showed up to 176% higher seed yield (SY), 29% lower flowering time, 21% fewer maturity days, 64% increase in PLHT, and 183% larger seeds than the check cultivar JG11 or Annigeri. The prioritised kabuli accessions displayed up to 270% more yield, 13% less flowering time, 8% fewer maturity days, 111% increase in PLHT, and 41% larger seeds over the check cultivar KAK2. While the intermediate type accessions had up to 169% better yield, 1% early flowering, 3% early maturity, 54% taller plants, and 25% bigger seeds over the check cultivar JG 11 or KAK2. These accessions can be utilised in chickpea improvement programs to develop high-yielding, early flowering, short duration, taller, and large-seeded varieties with a broad genetic base.
The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
Publisher: Springer Science and Business Media LLC
Date: 22-02-2016
DOI: 10.1038/NG.3517
Abstract: Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
Large variation in salinity tolerance in chickpea is explained by differences in sensitivity at the reproductive stage
Publisher: Elsevier BV
Date: 10-2007
Monitoring Changes in the Cultivation of Pigeonpea and Groundnut in Malawi Using Time Series Satellite Imagery for Sustainable Food Systems
Publisher: MDPI AG
Date: 21-06-2019
DOI: 10.3390/RS11121475
Abstract: Malawi, in south-eastern Africa, is one of the poorest countries in the world. Food security in the country hinges on rainfed systems in which maize and sorghum are staple cereals and groundnut and pigeonpea are now major grain legume crops. While the country has experienced a considerable reduction in forest lands, population growth and demand for food production have seen an increase in the area dedicated to agricultural crops. From 2010, pigeonpea developed into a major export crop, and is commonly intercropped with cereals or grown in double-up legume systems. Information on the spatial extent of these crops is useful for estimating food supply, understanding export potential, and planning policy changes as ex les of various applications. Remote sensing analysis offers a number of efficient approaches to deliver spatial, reproducible data on land use and land cover (LULC) and changes therein. Moderate Resolution Imaging Spectroradiometer (MODIS) products (fortnightly and monthly) and derived phenological parameters assist in mapping cropland areas during the agricultural season, with explicit focus on redistributed farmland. Owing to its low revisit time and the availability of long-term period data, MODIS offers several advantages, e.g., the possibility of obtaining cloud-free Normalized Difference Vegetation Index (NDVI) profile and an analysis using one methodology applied to one sensor at regular acquisition dates, avoiding incomparable results. To assess the expansion of areas used in the production of pigeonpea and groundnut resulting from the release of new varieties, the spatial distribution of cropland areas was mapped using MODIS NDVI 16-day time-series products (MOD13Q1) at a spatial resolution of 250 m for the years 2010–2011 and 2016–2017. The resultant cropland extent map was validated using intensive ground survey data. Pigeonpea is mostly grown in the southern dry districts of Mulanje, Phalombe, Chiradzulu, Blantyre and Mwanza and parts of Balaka and Chikwawa as a groundnut-pigeonpea intercrop, and sorghum-pigeonpea intercrop in Mzimba district. By 2016, groundnut extent had increased in Mwanza, Mulanje, and Phalombe and fallen in Mzimba. The result indicates that the area planted with pigeonpea had increased by 29% (75,000 ha) from 2010–2011 to 2016–2017. Pigeonpea expansion in recent years has resulted from major export opportunities to Asian countries like India, and its consumption by Asian expatriates all over the world. This study provides useful information for policy changes and the prioritization of resources allocated to sustainable food production and to support smallholder farmers.
The extent of grain yield and plant growth enhancement by plant growth-promoting broad-spectrum Streptomyces sp. in chickpea
Publisher: Springer Science and Business Media LLC
Date: 23-01-2015
Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean
Publisher: Springer Science and Business Media LLC
Date: 31-05-2022
DOI: 10.1007/S00122-022-04120-0
Abstract: Plant height of soybean is associated with a haplotype block on chromosome 19, which classified 211 soybean accessions into five distinct groups showing significant differences for the target trait. Genetic variation is pivotal for crop improvement. Natural populations are precious genetic resources. However, efficient strategies for the targeted utilization of these resources for quantitative traits, such as plant height (PH), are scarce. Being an important agronomic trait associated with soybean yield and quality, it is imperative to unravel the genetic mechanisms underlying PH in soybean. Here, a genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with PH in a natural population of 211 cultivated soybeans, which was genotyped with NJAU 355 K Soy SNP Array and evaluated across six environments. A total of 128 SNPs distributed across 17 chromosomes were found to be significantly associated with PH across six environments and a combined environment. Three significant SNPs were consistently identified in at least three environments on Chr.02 (AX-93958260), Chr.17 (AX-94154834), and Chr.19 (AX-93897200). Genomic regions of ~ 130 kb flanking these three consistent SNPs were considered as stable QTLs, which included 169 genes. Of these, 22 genes (including Dt1) were prioritized and defined as putative candidates controlling PH. The genomic region flanking 12 most significant SNPs was in strong linkage disequilibrium (LD). These SNPs formed a single haplotype block containing five haplotypes for PH, namely Hap-A, Hap-B, Hap-C, Hap-D, and Hap-E. Deployment of such superior haplotypes in breeding programs will enable development of improved soybean varieties with desirable plant height.
Genome sequence of Jatropha curcas L., a non‐edible biodiesel plant, provides a resource to improve seed‐related traits
Publisher: Wiley
Date: 11-09-2018
DOI: 10.1111/PBI.12995
Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea
Publisher: Wiley
Date: 21-05-2022
DOI: 10.1111/PBI.13840
Abstract: Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of ‘ QTL‐hotspot ’, a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non‐synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in ‘ QTL‐hotspot ’ improves pre‐anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high‐yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF‐INTERACTING FACTOR1 ( GIF1 ), a transcriptional co‐activator of Growth‐Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on erse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
Widely targeted metabolomics characterizes the dynamic changes of chemical profile in postharvest peanut sprouts grown under the dark and light conditions
Publisher: Elsevier BV
Date: 12-2021
Developing future heat-resilient vegetable crops
Publisher: Springer Science and Business Media LLC
Date: 24-01-2023
DOI: 10.1007/S10142-023-00967-8
Abstract: Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants’ biochemical and molecular processes having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.
scRNA-seq Reveals the Mechanism of Fatty Acid Desaturase 2 Mutation to Repress Leaf Growth in Peanut (Arachis hypogaea L.)
Publisher: MDPI AG
Date: 19-09-2023
Genetic Mapping of QTLs Controlling Fatty Acids Provided Insights into the Genetic Control of Fatty Acid Synthesis Pathway in Peanut (Arachis hypogaea L.)
Publisher: Public Library of Science (PLoS)
Date: 07-04-2015
Fast-forward breeding for a food-secure world
Publisher: Elsevier BV
Date: 12-2021
DOI: 10.1016/J.TIG.2021.08.002
Abstract: Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms, leveraged by evolving machine learning tools, will help provide mechanistic explanations for complex plant traits. Targeted and rapid assembly of beneficial alleles using optimized breeding strategies and precise genome editing techniques could deliver ideal crops for the future. Realizing desired productivity gains in the field is imperative for securing an adequate future food supply for 10 billion people.
Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)
Publisher: Wiley
Date: 07-02-2023
DOI: 10.1002/TPG2.20307
Abstract: The grain‐filling stage in Triticum aestivum (wheat) is highly vulnerable to increasing temperature as terminal heat stress diminishes grain quality and yield. To examine the mechanism of terminal heat tolerance, we performed the biochemical and gene expression analyses using two heat‐tolerant (WH730 and WH1218) and two heat‐sensitive (WH711 and WH157) wheat genotypes. We observed a significant increase in total soluble sugar (25%–47%), proline (7%–15%), and glycine betaine (GB) (22%–34%) contents in flag leaf, whereas a decrease in grain‐filling duration, 1000‐kernel weight (8%–25%), and grain yield per plant (11%–23%) was observed under the late‐sown compared to the timely sown. The maximum content of osmolytes, including total soluble sugar, proline, and GB, was observed in heat‐tolerant genotypes compared to heat‐sensitive genotypes. The expression of 10 heat‐responsive genes associated with heat shock proteins ( sHsp‐1 , Hsp17 , and HsfA4 ), flavonoid biosynthesis ( F3′‐1 and PAL ), β‐glucan synthesis ( CslF6 and CslH ), and xyloglucan metabolism ( XTH1 , XTH2 , and XTH5 ) was studied in flag leaf exposed to different heat treatments (34, 36, 38, and 40°C) at 15 days after anthesis by quantitative real‐time polymerase chain reaction. A significant increase in the relative fold expression of these genes with increasing temperature indicated their involvement in providing heat‐stress tolerance. The high differential expression of most of the genes in heat‐tolerant genotype “WH730” followed by “WH1218” indicates the high adaptability of these genotypes to heat stress compared to heat‐sensitive wheat genotypes. Based on the previous results, “WH730” performed better in terms of maximum osmolyte accumulation, grain yield, and gene expression under heat stress.
Identification and Characterization of Toxigenic Fusaria Associated with Sorghum Grain Mold Complex in India
Publisher: Springer Science and Business Media LLC
Date: 10-08-2010
DOI: 10.1007/S11046-010-9354-X
Abstract: Fusarium species are dominant within the sorghum grain mold complex. Some species of Fusarium involved in grain mold complex produce mycotoxins, such as fumonisins. An attempt was made to identify Fusarium spp. associated with grain mold complex in major sorghum-growing areas in India through AFLP-based grouping of the isolates and to further confirm the species by sequencing part of α-Elongation factor gene and comparing the sequences with that available in the NCBI database. The dendrogram generated from the AFLP data clustered the isolates into 5 groups. Five species of Fusarium--F. proliferatum, F. thapsinum, F. equiseti, F. andiyazi and F. sacchari were identified based on sequence similarity of α-Elongation factor gene of the test isolates with those in the NCBI database. Fusarium thapsinum was identified as predominant species in Fusarium--grain mold complex in India and F. proliferatum as highly toxigenic for fumonisins production. Analysis of molecular variance (AMOVA) revealed 54% of the variation in the AFLP patterns of 63 isolates was due to the differences between Fusarium species, and 46% was due to differences between the strains within a species.
Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis
Publisher: Frontiers Media SA
Date: 19-12-2017
Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 11-12-2013
Can genomics boost productivity of orphan crops?
Publisher: Springer Science and Business Media LLC
Date: 12-2012
DOI: 10.1038/NBT.2440
Translational Pigeonpea Genomics Consortium for Accelerating Genetic Gains in Pigeonpea (Cajanus cajan L.)
Publisher: MDPI AG
Date: 31-08-2020
Abstract: Pigeonpea is one of the important pulse crops grown in many states of India and plays a major role in sustainable food and nutritional security for the smallholder farmers. In order to overcome the productivity barrier the Translational Pigeonpea Genomics Consortium (TPGC) was established, representing research institutes from six different states (Andhra Pradesh, Karnataka, Madhya Pradesh, Maharashtra, Telangana, and Uttar Pradesh) of India. To enhance pigeonpea productivity and production the team has been engaged in deploying modern genomics approaches in breeding and popularizing modern varieties in farmers’ fields. For instance, new genetic stock has been developed for trait mapping and molecular breeding initiated for enhancing resistance to fusarium wilt and sterility mosaic disease in 11 mega varieties of pigeonpea. In parallel, genomic segments associated with cleistogamous flower, shriveled seed, pods per plant, seeds per pod, 100 seed weight, and seed protein content have been identified. Furthermore, 100 improved lines were evaluated for yield and desirable traits in multi-location trials in different states. Furthermore, a total of 303 farmers’ participatory varietal selection (FPVS) trials have been conducted in 129 villages from 15 districts of six states with 16 released varieties/hybrids. Additionally, one line (GRG 152 or Bheema) from multi-location trials has been identified by the All India Coordinated Research Project on Pigeonpea (AICRP-Pigeonpea) and released for cultivation by the Central Variety Release Committee (CVRC). In summary, the collaborative efforts of several research groups through TPGC is accelerating genetics gains in breeding plots and is expected to deliver them to pigeonpea farmers to enhance their income and improve livelihood.
Genetic relationships among seven sections of genus Arachis studied by using SSR markers
Publisher: Springer Science and Business Media LLC
Date: 20-01-2010
Abstract: The genus Arachis , originated in South America, is ided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2 n = 2 x = 20) and the tetraploid species (2 n = 2 x = 40) are found in sections Arachis , Extranervosae and Rhizomatosae . Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis . The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 ( A. duranensis ) and the B-genome accession ICG 8206 ( A. ipaënsis ) were found most closely related to A. hypogaea . A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis , including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.
Peanut Seed Coat Acts as a Physical and Biochemical Barrier against Aspergillus flavus Infection
Publisher: MDPI AG
Date: 23-11-2021
DOI: 10.3390/JOF7121000
Abstract: Aflatoxin contamination is a global menace that adversely affects food crops and human health. Peanut seed coat is the outer layer protecting the cotyledon both at pre- and post-harvest stages from biotic and abiotic stresses. The aim of the present study is to investigate the role of seed coat against A. flavus infection. In-vitro seed colonization (IVSC) with and without seed coat showed that the seed coat acts as a physical barrier, and the developmental series of peanut seed coat showed the formation of a robust multilayered protective seed coat. Radial growth bioassay revealed that both insoluble and soluble seed coat extracts from 55-437 line (resistant) showed higher A. flavus inhibition compared to TMV-2 line (susceptible). Further analysis of seed coat biochemicals showed that hydroxycinnamic and hydroxybenzoic acid derivatives are the predominant phenolic compounds, and addition of these compounds to the media inhibited A. flavus growth. Gene expression analysis showed that genes involved in lignin monomer, proanthocyanidin, and flavonoid biosynthesis are highly abundant in 55-437 compared to TMV-2 seed coats. Overall, the present study showed that the seed coat acts as a physical and biochemical barrier against A. flavus infection and its potential use in mitigating the aflatoxin contamination.
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics
Publisher: Springer Science and Business Media LLC
Date: 22-09-2022
DOI: 10.1038/S41588-022-01172-2
Abstract: Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome ersity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum . Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem length ( Le/le ) and seed shape ( R/r ) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.
Key Plant and Grain Characteristics and Their Importance in Breeding and Adaptation of Pigeonpea Cultivars
Publisher: Springer International Publishing
Date: 2017
The Pigeonpea Genome: An Overview
Publisher: Springer International Publishing
Date: 2017
Wide Crossing Technology for Pigeonpea Improvement
Publisher: Springer International Publishing
Date: 2017
Botanical Description of Pigeonpea [Cajanus Cajan (L.) Millsp.]
Publisher: Springer International Publishing
Date: 2017
Molecular Mapping of Genes and QTLs in Pigeonpea
Publisher: Springer International Publishing
Date: 2017
Key Regulators of Sucrose Metabolism Identified through Comprehensive Comparative Transcriptome Analysis in Peanuts
Publisher: MDPI AG
Date: 06-07-2021
DOI: 10.3390/IJMS22147266
Abstract: Sucrose content is a crucial indicator of quality and flavor in peanut seed, and there is a lack of clarity on the molecular basis of sucrose metabolism in peanut seed. In this context, we performed a comprehensive comparative transcriptome study on the s les collected at seven seed development stages between a high-sucrose content variety (ICG 12625) and a low-sucrose content variety (Zhonghua 10). The transcriptome analysis identified a total of 8334 genes exhibiting significantly different abundances between the high- and low-sucrose varieties. We identified 28 differentially expressed genes (DEGs) involved in sucrose metabolism in peanut and 12 of these encoded sugars will eventually be exported transporters (SWEETs). The remaining 16 genes encoded enzymes, such as cell wall invertase (CWIN), vacuolar invertase (VIN), cytoplasmic invertase (CIN), cytosolic fructose-bisphosphate aldolase (FBA), cytosolic fructose-1,6-bisphosphate phosphatase (FBP), sucrose synthase (SUS), cytosolic phosphoglucose isomerase (PGI), hexokinase (HK), and sucrose-phosphate phosphatase (SPP). The weighted gene co-expression network analysis (WGCNA) identified seven genes encoding key enzymes (CIN, FBA, FBP, HK, and SPP), three SWEET genes, and 90 transcription factors (TFs) showing a high correlation with sucrose content. Furthermore, upon validation, six of these genes were successfully verified as exhibiting higher expression in high-sucrose recombinant inbred lines (RILs). Our study suggested the key roles of the high expression of SWEETs and enzymes in sucrose synthesis making the genotype ICG 12625 sucrose-rich. This study also provided insights into the molecular basis of sucrose metabolism during seed development and facilitated exploring key candidate genes and molecular breeding for sucrose content in peanuts.
Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits
Publisher: Springer Science and Business Media LLC
Date: 22-05-2017
DOI: 10.1038/NG.3872
Abstract: Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.
Sequencing Ancestor Diploid Genomes for Enhanced Genome Understanding and Peanut Improvement
Publisher: Springer International Publishing
Date: 2017
Development of a High‐Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping‐by‐Sequencing Markers
Publisher: Wiley
Date: 07-2016
DOI: 10.3835/PLANTGENOME2015.10.0106
Abstract: Pearl millet [ Pennisetum glaucum (L.) R. Br also Cenchrus americanus (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping‐by‐sequencing (GBS) markers can be used to build high‐density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines ‘Tift 99D 2 B 1 ’ and ‘Tift 454’. DNA from 186 RILs, the parents, and the F 1 was used for 96‐plex Ape KI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per in idual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High‐quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single‐nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to Pyricularia leaf spot [ Pyricularia grisea (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community.
Evaluation and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) Under Drought Stress Conditions
Publisher: Public Library of Science (PLoS)
Date: 07-04-2015
Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping
Publisher: Springer Science and Business Media LLC
Date: 02-05-2017
DOI: 10.1038/S41598-017-01211-7
Abstract: Soil salinity results in reduced productivity in chickpea. However, breeding for salinity tolerance is challenging because of limited knowledge of the key traits affecting performance under elevated salt and the difficulty of high-throughput phenotyping for large, erse germplasm collections. This study utilised image-based phenotyping to study genetic variation in chickpea for salinity tolerance in 245 erse accessions. On average salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the ersity panel with seed number being the major determinant for salinity tolerance measured as yield. This study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.
Agronomic Performance of Chickpea Affected by Drought Stress at Different Growth Stages
Publisher: MDPI AG
Date: 21-04-2022
Abstract: Susceptibility to drought stress has restrained chickpea productivity at a global level, and the development of drought-tolerant varieties is essential to maintain its productivity. Therefore, the present study was conducted to evaluate genetic ergence in selected genotypes of chickpea and their morpho-physiological responses under irrigated and stressed conditions to identify the traits that account for the better performance of these genotypes under stressed conditions, as well as genotypes with improved drought tolerance. The genotypes were evaluated for two years under irrigated and drought stressed conditions, and significant variation was found amongst the genotypes for different morpho-physiological and yield traits. The maximum reduction was observed for plant yield (33.23%) under stressed conditions. Principle component analysis (PCA)-based biplots and correlation studies established its strong positive correlation with relative water content (RWC), membrane stability index (MSI), chlorophyll index (CI), secondary branches (SB) and yield traits and negative correlations with drought susceptibility index (DSI), days to maturity (DM) and 100 seed weight (100 SW) under drought stress, suggesting their use in selecting drought-tolerant germplasm. Ten genotypes with high values of RWC, MSI, CI, SB, yield traits and lower DSI were identified as drought-tolerant and might serve as ideal donors in the forthcoming breeding of elite chickpea cultivars. The seed-filling stage began earlier in these genotypes, with significantly reduced days to maturity under stressed conditions. Our results indicate selection for earliness offers a promising strategy for the development of drought-tolerant chickpea cultivars.
Genomic Selection for Crop Improvement
Publisher: Springer International Publishing
Date: 2017
Genomics-Assisted Crop Improvement
Publisher: Springer Netherlands
Date: 2007
Association of nad7a Gene with Cytoplasmic Male Sterility in Pigeonpea
Publisher: Wiley
Date: 07-2015
Molecular and phenotypic diversity among chickpea (Cicer arietinum) genotypes as a function of drought tolerance
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/CP17284
Abstract: Diversity as a function of drought tolerance may be identified by morphological characters, and molecular tools used to find the most ergent genotypes for breeding programs for drought tolerance in future. The narrow genetic base of chickpea can be circumvented by using erse lines in breeding programs. Forty chickpea genotypes were studied for their morphological and molecular ersity with an objective of identifying the most erse drought-tolerant lines. In total, 90 alleles were detected with 3.6 alleles per locus. Polymorphism information content (PIC) values ranged from 0.155 to 0.782 with an average value of 0.4374 per locus. The size of lified products ranged from 160 bp to 390 bp. Primer TA136 with eight alleles showed the highest PIC value of 0.7825, indicating its ability to differentiate the genotypes at molecular level. DARwin neighbour-joining tree analysis based on dissimilarity estimates was done for the molecular data and sequential agglomerative hierarchical non-overlapping (SAHN) grouping for the morphological data. It could clearly discriminate the tolerance and the sensitivity of genotypes. Two-dimensional principal coordinates analysis (PCoA) plot indicated good ersity for drought tolerance. The genetic similarity coefficients ranged from 0.115 (genotypes BGD72 to ICCV 5308) to 0.828 (genotypes ICCV 10316 to ICCV 92337).
Diagnostics in Plant Breeding
Publisher: Springer Netherlands
Date: 2013
The Peanut Genome: An Introduction
Publisher: Springer International Publishing
Date: 2017
Structural variations in plant genomes
Publisher: Oxford University Press (OUP)
Date: 06-06-2014
DOI: 10.1093/BFGP/ELU016
Co-localization of major quantitative trait loci for pod size and weight to a 3.7 cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 09-01-2017
High resolution mapping of restoration of fertility (Rf) by combining large population and high density genetic map in pigeonpea [Cajanus cajan (L.) Millsp]
Publisher: Springer Science and Business Media LLC
Date: 03-07-2020
Genome-based trait prediction in multi- environment breeding trials in groundnut
Publisher: Springer Science and Business Media LLC
Date: 18-08-2020
DOI: 10.1007/S00122-020-03658-1
Abstract: Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K ‘Axiom_Arachis’ SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L) (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L (3) model 3 (M3 = E + L + G + GE), a naïve interaction model and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies ( 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400–0.600) were obtained for pods lant, shelling %, and total yield lant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut.
Metabolomics Intervention Towards Better Understanding of Plant Traits
Publisher: MDPI AG
Date: 07-02-2021
Abstract: The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other -omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)
Publisher: Springer Science and Business Media LLC
Date: 17-09-2009
Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)
Publisher: Frontiers Media SA
Date: 31-07-2018
Whole-Genome Sequencing of Pigeonpea: Requirement, Background History, Current Status and Future Prospects for Crop Improvement
Publisher: Springer International Publishing
Date: 2017
Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea
Publisher: Wiley
Date: 13-05-2022
DOI: 10.1111/PBI.13822
Abstract: Salinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post‐transcriptional levels is challenging. To address this, we deep sequenced 24 salt‐challenged flower transcriptomes from two parental genotypes of a RIL population that significantly differ in salt tolerance ability. The transcriptomes for the first time included 12 polyadenylated and 12 non‐polyadenylated RNA libraries to a sequencing depth of ~50 million reads. The ab initio transcriptome assembly comprised ~34 082 transcripts from three biological replicates of salt‐tolerant (JG11) and salt‐sensitive (ICCV2) flowers. A total of 9419 lncRNAs responding to salt stress were identified, 2345 of which were novel lncRNAs specific to chickpea. The expression of poly(A+) lncRNAs and naturally antisense transcribed RNAs suggest their role in post‐transcriptional modification and gene silencing. Notably, 178 differentially expressed lncRNAs were induced in the tolerant genotype but repressed in the sensitive genotype. Co‐expression network analysis revealed that the induced lncRNAs interacted with the FLOWERING LOCUS ( FLC ), chromatin remodelling and DNA methylation genes, thus inducing flowering during salt stress. Furthermore, 26 lncRNAs showed homology with reported lncRNAs such as COOLAIR , IPS1 and AT4 , thus confirming the role of chickpea lncRNAs in controlling flowering time as a crucial salt tolerance mechanism in tolerant chickpea genotype. These robust set of differentially expressed lncRNAs provide a deeper insight into the regulatory mechanisms controlled by lncRNAs under salt stress.
Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications
Publisher: Springer Science and Business Media LLC
Date: 04-09-2023
Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing
Publisher: Springer Science and Business Media LLC
Date: 08-02-2021
DOI: 10.1038/S41597-021-00834-W
Abstract: We report characteristics of soybean genetic ersity and structure from the resequencing of 481 erse soybean accessions, comprising 52 wild ( Glycine soja ) selections and 429 cultivated ( Glycine max ) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 02-12-2009
DOI: 10.1007/S00122-008-0933-X
Abstract: Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut or groundnut (Arachis hypogaea L.), an hidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these lified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2-5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5-14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety of applications.
Accessing genetic diversity for crop improvement
Publisher: Elsevier BV
Date: 04-2010
DOI: 10.1016/J.PBI.2010.01.004
Abstract: Vast germplasm collections are accessible but their use for crop improvement is limited-efficiently accessing genetic ersity is still a challenge. Molecular markers have clarified the structure of genetic ersity in a broad range of crops. Recent developments have made whole-genome surveys and gene-targeted surveys possible, shedding light on population dynamics and on the impact of selection during domestication. Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, or banana. The challenge now is to finely characterize all the facets of plant behavior in carefully chosen materials. We suggest broadening the use of 'core reference sets' so as to facilitate material sharing within the scientific community.
Genome-wide transcriptome analysis and physiological variation modulates gene regulatory networks acclimating salinity tolerance in chickpea
Publisher: Elsevier BV
Date: 07-2021
Comparative analysis of the grain proteome fraction in barley genotypes with contrasting salinity tolerance during germination
Publisher: Wiley
Date: 11-01-2010
Breeding custom‐designed crops for improved drought adaptation
Publisher: Wiley
Date: 09-2021
Abstract: The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high‐throughput identification of the genetic architecture of key drought‐adaptive traits and explore innovative genomic breeding strategies for designing future crops.
Mapping Quantitative Trait Loci of Resistance to Tomato Spotted Wilt Virus and Leaf Spots in a Recombinant Inbred Line Population of Peanut (Arachis hypogaea L.) from SunOleic 97R and NC94022
Publisher: Public Library of Science (PLoS)
Date: 18-07-2016
Features of SNP and SSR diversity in a set of ICARDA barley germplasm collection
Publisher: Springer Science and Business Media LLC
Date: 07-01-2010
The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat
Publisher: Springer Science and Business Media LLC
Date: 2000
Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 22-11-2018
DOI: 10.1007/S00438-018-1511-9
Abstract: Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of ersity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for ersifying the gene pool of cultivated groundnut.
Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 20-12-2016
DOI: 10.1038/SREP39478
Abstract: Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 in iduals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.
QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)
Publisher: Wiley
Date: 07-02-2017
DOI: 10.1111/PBI.12686
QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea
Publisher: Wiley
Date: 26-05-2016
DOI: 10.1111/PBI.12567
Adapting legume crops to climate change using genomic approaches
Publisher: Wiley
Date: 13-06-2018
DOI: 10.1111/PCE.13203
Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 16-12-2019
DOI: 10.1007/S00122-019-03504-Z
Abstract: This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12-21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11-29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP "S7_14185076" marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.
Single‐cell RNA‐seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.)
Publisher: Wiley
Date: 19-07-2021
DOI: 10.1111/PBI.13656
Abstract: Single‐cell RNA‐seq (scRNA‐seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single cells were ided into eight cell clusters based on reported marker genes by applying scRNA‐seq. Further, a pseudo‐time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re‐investigation of the primordium‐driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA‐seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA‐seq values. Additionally, peanut AHL23 ( AT‐HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23 ), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA‐seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea . We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.
Translational Genomics in Agriculture: Some Examples in Grain Legumes
Publisher: Informa UK Limited
Date: 24-10-2014
Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers
Publisher: Frontiers Media SA
Date: 05-06-2014
Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan)
Publisher: Wiley
Date: 09-02-2017
DOI: 10.1111/PBI.12685
Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process
Publisher: Wiley
Date: 08-2021
DOI: 10.1111/TPJ.15410
Abstract: Grain filling and grain development are essential biological processes in the plant’s life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat ( Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In‐gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule‐bound and soluble starch synthase, pyruvate phosphate dikinase, 14‐3‐3 proteins as well as sugar precursors undergo a major tissue‐dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/ ision and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue‐specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
Drought or/and Heat-Stress Effects on Seed Filling in Food Crops: Impacts on Functional Biochemistry, Seed Yields, and Nutritional Quality
Publisher: Frontiers Media SA
Date: 27-11-2018
Translational Genomics for Crop Breeding
Publisher: Wiley
Date: 11-10-2013
Multilocus variable number tandem repeat analysis as a tool to discern genetic relationships among strains of yersinia enterocolitica biovar 1A
Publisher: Oxford University Press (OUP)
Date: 09-2009
DOI: 10.1111/J.1365-2672.2009.04267.X
Abstract: To identify variable number tandem repeat (VNTR)-containing loci, and to use multilocus VNTR (MLVA) to discern genetic relationships among strains of Yersinia enterocolitica biovar 1A isolated from erse sources. The whole genome sequence of Y. enterocolitica 8081 was analysed and eight VNTR loci with repeat sizes between 4 and 9 bp, and each containing more than four repeat copies were selected for MLVA typing of 88 strains of Y. enterocolitica. Of these, four loci were polymorphic and generated 26 MLVA genotypes among 81 strains of Y. enterocolitica biovar 1A. MLVA was found to be quite discriminatory (DI = 0.87). Cluster analysis and population modelling using minimum spanning tree (MST) clearly clustered Y. enterocolitica biovar 1A into two major groups. The MLVA is easy to perform and can be used to discern clonal relationship among strains of Y. enterocolitica. Also the phylogenetic relationships obtained with MLVA genotypes were in good agreement with those established by other typing methods. The MLVA method reported is relatively more discriminatory than the other genotyping methods and has the potential to be used as an epidemiological tool for the study of strains of Y. enterocolitica biovar 1A.
Molecular breeding for introgression of fatty acid desaturase mutant alleles ( ahFAD2A and ahFAD2B ) enhances oil quality in high and low oil containing peanut genotypes
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.PLANTSCI.2015.08.013
Abstract: High oleate peanuts have two marketable benefits, health benefits to consumers and extended shelf life of peanut products. Two mutant alleles present on linkage group a09 (ahFAD2A) and b09 (ahFAD2B) control composition of three major fatty acids, oleic, linoleic and palmitic acids which together determine peanut oil quality. In conventional breeding, selection for fatty acid composition is delayed to advanced generations. However by using DNA markers, breeders can reject large number of plants in early generations and therefore can optimize time and resources. Here, two approaches of molecular breeding namely marker-assisted backcrossing (MABC) and marker-assisted selection (MAS) were employed to transfer two FAD2 mutant alleles from SunOleic 95R into the genetic background of ICGV 06110, ICGV 06142 and ICGV 06420. In summary, 82 MABC and 387 MAS derived introgression lines (ILs) were developed using DNA markers with elevated oleic acid varying from 62 to 83%. Oleic acid increased by 0.5-1.1 folds, with concomitant reduction of linoleic acid by 0.4-1.0 folds and palmitic acid by 0.1-0.6 folds among ILs compared to recurrent parents. Finally, high oleate ILs, 27 with high oil (53-58%), and 28 ILs with low oil content (42-50%) were selected that may be released for cultivation upon further evaluation.
STMS markers for grain protein content and their validation using near-isogenic lines in bread wheat
Publisher: Wiley
Date: 27-08-2001
Genomic tools and germplasm diversity for chickpea improvement
Publisher: Cambridge University Press (CUP)
Date: 14-01-2011
DOI: 10.1017/S1479262110000468
Abstract: Chickpea is the third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years, specialized germplasm subsets such as global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources such as molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), ersity arrays technology (DArT) and transcript sequences, e.g. expressed sequence tags, short transcript reads, have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that the use of genomic resources and specialized germplasm subsets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Advent of the next generation sequencing technologies coupled with advances in bioinformatics offers the possibility of undertaking large-scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.
Assessment of the Control of Allergic Rhinitis and Asthma Test (CARAT) using MASK-air
Publisher: Elsevier BV
Date: 2022
Scope for improvement of yield under drought through the root traits in chickpea (Cicer arietinum L.)
Publisher: Elsevier BV
Date: 2015
Regulatory non-coding RNAs: a new frontier in regulation of plant biology
Publisher: Springer Science and Business Media LLC
Date: 20-05-2021
DOI: 10.1007/S10142-021-00787-8
Abstract: Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.
Future burden of cardiovascular disease in Australia: impact on health and economic outcomes between 2020 and 2029.
Publisher: Oxford University Press (OUP)
Date: 04-03-2022
Abstract: To estimate the health and economic burden of new and established cardiovascular disease from 2020 to 2029 in Australia. A two-stage multistate dynamic model was developed to predict the burden of the incident and prevalent cardiovascular disease, for Australians 40-90 years old from 2020 to 2029. The model captured morbidity, mortality, years of life lived, quality-adjusted life years, healthcare costs, and productivity losses. Cardiovascular risk for the primary prevention population was derived using Australian demographic data and the Pooled Cohort Equation. Risk for the secondary prevention population was derived from the REACH registry. Input data for costs and utilities were extracted from published sources. All outcomes were annually discounted by 5%. A number of sensitivity analyses were undertaken to test the robustness of the study. Between 2020 and 2029, the model estimates 377 754 fatal and 991 375 non-fatal cardiovascular events. By 2029, 1 061 756 Australians will have prevalent cardiovascular disease (CVD). The population accrued 8 815 271 [95% uncertainty interval (UI) 8 805 083-8 841 432] years of life lived with CVD and 5 876 975 (5 551 484-6 226 045) QALYs. The total healthcare costs of CVD were projected to exceed Australian dollars (AUD) 61.89 (61.79-88.66) billion, and productivity losses will account for AUD 78.75 (49.40-295.25) billion, driving the total cost to surpass AUD 140.65 (123.13-370.23) billion. Cardiovascular disease in Australia has substantial impacts in terms of morbidity, mortality, and lost revenue to the healthcare system and the society. Our modelling provides important information for decision making in relation to the future burden of cardiovascular disease.
Translational Genomics for Crop Breeding
Publisher: Wiley
Date: 11-10-2013
Evaluation of Streptomyces strains isolated from herbal vermicompost for their plant growth-promotion traits in rice
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.MICRES.2013.09.008
Abstract: Six actinomycetes, CAI-13, CAI-85, CAI-93, CAI-140, CAI-155 and KAI-180, isolated from six different herbal vermi-composts were characterized for in vitro plant growth-promoting (PGP) properties and further evaluated in the field for PGP activity in rice. Of the six actinomycetes, CAI-13, CAI-85, CAI-93, CAI-140 and CAI-155 produced siderophores CAI-13, CAI-93, CAI-155 and KAI-180 produced chitinase CAI-13, CAI-140, CAI-155 and KAI-180 produced lipase CAI-13, CAI-93, CAI-155 and KAI-180 produced protease and CAI-13, CAI-85, CAI-140 and CAI-155 produced ß-1-3-glucanase whereas all the six actinomycetes produced cellulase, hydrocyanic acid and indole acetic acid (IAA). The actinomycetes were able to grow in NaCl concentrations of up to 8%, at pH values between 7 and 11, temperatures between 20 and 40 °C and compatible with fungicide bavistin at field application levels. In the rice field, the actinomycetes significantly enhanced tiller numbers, panicle numbers, filled grain numbers and weight, stover yield, grain yield, total dry matter, root length, volume and dry weight over the un-inoculated control. In the rhizosphere, the actinomycetes also significantly enhanced total nitrogen, available phosphorous, % organic carbon, microbial biomass carbon and nitrogen and dehydrogenase activity over the un-inoculated control. Sequences of 16S rDNA gene of the actinomycetes matched with different Streptomyces species in BLAST analysis. Of the six actinomycetes, CAI-85 and CAI-93 were found superior over other actinomycetes in terms of PGP properties, root development and crop productivity. qRT-PCR analysis on selected plant growth promoting genes of actinomycetes revealed the up-regulation of IAA genes only in CAI-85 and CAI-93.
Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat
Publisher: Authorea, Inc.
Date: 18-01-2023
DOI: 10.22541/ESSOAR.167407907.74195256/V1
Abstract: Climate influences on below-ground plant traits seldom receive due attention. Climate change is varying the availability of resources, soil physical properties, rainfall events, soil mineral weathering and leaching intensity which collectively determines soil physical and chemical properties. Soil constraints – acidity (pH ), salinity(pH≤8.5), sodicity and dispersion (pH .5) are major causes of wheat yield loss in arid and semi-arid cropping systems. To cope with changing environment, plants employ adaptive strategies such as phenotypic plasticity a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies are complex, determined by key functional traits and Genotype × Environment interactions. The understanding of molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies has identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms and in silico gene expression profiles at various growth developmental stages. Our review focuses on favourable alleles for enhanced gene expression, QTLs and epigenetic regulation of plant responses to soil constraints including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles, functional characterization of variants, followed by gene validation using advanced genomic tools and marker development for molecular breeding and genome editing. Also, the review highlights the progress of gene editing in wheat, multiplex gene editing and novel alleles for smart control of gene expression. Integration of these genomic technologies will be effective to enhance plasticity traits and stabilizing wheat yields on constrained soils in the face of climate change.
Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292
Publisher: Public Library of Science (PLoS)
Date: 09-08-2021
DOI: 10.1371/JOURNAL.PONE.0254957
Abstract: Heat stress during reproductive stages has been leading to significant yield losses in chickpea ( Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F 8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars.
Application of CRISPR-Cas9-Mediated Gene Editing for Abiotic Stress Management in Crop Plants
Publisher: MDPI AG
Date: 08-09-2022
DOI: 10.20944/PREPRINTS202209.0117.V1
Abstract: Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reduce global agricultural production. Approaches such as conventional breeding and transgenic breeding have been widely used to cope with these environmental stresses. The clustered regularly interspaced short palindromic repeat- Cas (CRISPR/Cas) based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has a great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the most recent findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas mediated gene-editing system towards enhanced tolerance to drought, salinity, cold, heat, and heavy metals stresses. Furthermore, in this review, we highlighted the recent advancements in prime editing and base editing tools for crop improvement.
Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits
Publisher: Springer Science and Business Media LLC
Date: 29-04-2019
DOI: 10.1038/S41588-019-0401-3
Abstract: We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines s led from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.
Marker-Assisted Selection for Biotic Stress Resistance in Peanut
Publisher: Wiley
Date: 11-10-2013
Identification of ERF genes in peanuts and functional analysis of AhERF008 and AhERF019 in abiotic stress response
Publisher: Springer Science and Business Media LLC
Date: 06-06-2014
DOI: 10.1007/S10142-014-0381-4
Abstract: Ethylene-responsive factor (ERF) play an important role in regulating gene expression in plant development and response to stresses. In peanuts (Arachis hypogaea L.), which produce flowers aerially and pods underground, only a few ERF genes have been identified so far. This study identifies 63 ERF unigenes from 247,313 peanut EST sequences available in the NCBI database. The phylogeny, gene structures, and putative conserved motifs in the peanut ERF proteins were analysed. Comparative analysis revealed the absence of two subgroups (A1 and A3) of the ERF family in peanuts only 10 subgroups were identified in peanuts compared to 12 subgroups in Arabidopsis and soybeans. AP2/ERF domains were found to be conserved among peanuts, Arabidopsis, and soybeans. Outside the AP2/ERF domain, many soybean-specific conserved motifs were also detected in peanuts. The expression analysis of ERF family genes representing each clade revealed differential expression patterns in response to biotic and abiotic stresses. Overexpression of AhERF008 influenced the root gravity of Arabidopsis, whereas overexpression of AhERF019 enhanced tolerance to drought, heat, and salt stresses in Arabidopsis. The information generated in this study will be helpful to further investigate the function of ERFs in plant development and stress response.
Differences between Cajanus cajan (L.) Millspaugh and C. cajanifolius (Haines) van der Maesen, the progenitor species of pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 19-04-2011
Translational Genomics in Crop Breeding for Biotic Stress Resistance: An Introduction
Publisher: Wiley
Date: 11-10-2013
EST-SSR based estimates on functional genetic variation in a barley (Hordeum vulgare L.) collection from Egypt
Publisher: Springer Science and Business Media LLC
Date: 15-10-2009
Modelling predicts that soybean is poised to dominate crop production across A frica
Publisher: Wiley
Date: 18-11-2018
DOI: 10.1111/PCE.13466
Abstract: The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume-based farming is particularly important in Africa, where small-scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to African households as well as natural fertilization for the soil. Although the consumption of traditionally grown legumes has started to decline, the production of soybeans (Glycine max Merr.) is spreading fast, especially across southern Africa. Predictions of future land-use allocation and production show that the soybean is poised to dominate future production across Africa. Land use models project an expansion of harvest area, whereas crop models project possible yield increases. Moreover, a seed change in farming strategy is underway. This is being driven largely by the combined cash crop value of products such as oils and the high nutritional benefits of soybean as an animal feed. Intensification of soybean production has the potential to reduce the dependence of Africa on soybean imports. However, a successful "soybean bonanza" across Africa necessitates an intensive research, development, extension, and policy agenda to ensure that soybean genetic improvements and production technology meet future demands for sustainable production.
Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies
Publisher: Springer Science and Business Media LLC
Date: 09-08-2012
DOI: 10.1007/S12038-012-9228-0
Abstract: Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practices for crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-arid tropics (SAT), namely, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), as compared to other crop species like cereals, has been very slow. With the advances in next-generation sequencing (NGS) and high-throughput (HTP) genotyping methods, there is a shift in development of genomic resources including molecular markers in these crops. For instance, 2,000 to 3,000 novel simple sequence repeats (SSR) markers have been developed each for chickpea, pigeonpea and groundnut. Based on Sanger, 454/FLX and Illumina transcript reads, transcriptome assemblies have been developed for chickpea (44,845 transcript assembly contigs, or TACs) and pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypes of mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 million reads for pigeonpea. Alignment of these Illumina reads with respective transcriptome assemblies have provided more than 10,000 SNPs each in chickpea and pigeonpea. A variety of SNP genotyping platforms including GoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed in chickpea and pigeonpea. By using above resources, the first-generation or comprehensive genetic maps have been developed in the three legume speciesmentioned above. Analysis of phenotyping data together with genotyping data has provided candidate markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases in groundnut and sterility mosaic disease (SMD) and fertility restoration in pigeonpea. Together with these traitassociated markers along with those already available, molecular breeding programmes have been initiated for enhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance to foliar diseases in groundnut. These trait-associated robust markers along with other genomic resources including genetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legumes.
Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 2008
Identification of low Ca2+stress-induced embryo apoptosis response genes inArachis hypogaeaby SSH-associated library lift (SSHaLL)
Publisher: Wiley
Date: 16-06-2015
DOI: 10.1111/PBI.12415
Abstract: Calcium is a universal signal in the regulation of wide aspects in biology, but few are known about the function of calcium in the control of early embryo development. Ca(2+) deficiency in soil induces early embryo abortion in peanut, producing empty pods, which is a general problem however, the underlying mechanism remains unclear. In this study, embryo abortion was characterized to be caused by apoptosis marked with cell wall degradation. Using a method of SSH cDNA libraries associated with library lift (SSHaLL), 62 differentially expressed genes were isolated from young peanut embryos. These genes were classified to be stress responses, catabolic process, carbohydrate and lipid metabolism, embryo morphogenesis, regulation, etc. The cell retardation with cell wall degradation was caused by up-regulated cell wall hydrolases and down-regulated cellular synthases genes. HsfA4a, which was characterized to be important to embryo development, was significantly down-regulated under Ca(2+) -deficient conditions from 15 days after pegging (DAP) to 30 DAP. Two AhCYP707A4 genes, encoding abscisic acid (ABA) 8'-hydroxylases, key enzymes for ABA catabolism, were up-regulated by 21-fold under Ca(2+) -deficient conditions upstream of HsfA4a, reducing the ABA level in early embryos. Over-expression of AhCYP707A4 in Nicotiana benthamiana showed a phenotype of low ABA content with high numbers of aborted embryos, small pods and less seeds, which confirms that AhCYP707A4 is a key player in regulation of Ca(2+) deficiency-induced embryo abortion via ABA-mediated apoptosis. The results elucidated the mechanism of low Ca(2+) -induced embryo abortion and described the method for other fields of study.
Feeding the future
Publisher: Springer Science and Business Media LLC
Date: 07-2013
DOI: 10.1038/499023A
Cereal Genomics: An Overview
Publisher: Kluwer Academic Publishers
Satellite imagery and household survey for tracking chickpea adoption in Andhra Pradesh, India
Publisher: Informa UK Limited
Date: 11-04-2016
Orphan legume crops enter the genomics era!
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.PBI.2008.12.004
Abstract: Many of the world's most important food legumes are grown in arid and semi-arid regions of Africa and Asia, where crop productivity is h ered by biotic and abiotic stresses. Until recently, these crops have also suffered from a dearth of genomic and molecular-genetic resources and thus were 'orphans' of the genome revolution. However, the community of legume researchers has begun a concerted effort to change this situation. The driving force is a series of international collaborations that benefit from recent advances in genome sequencing and genotyping technologies. The focus of these activities is the development of genome-scale data sets that can be used in high-throughput approaches to facilitate genomics-assisted breeding in these legumes.
Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 2014
Widening the genetic base of cultivated gene pool following introgression from wild Lens taxa
Publisher: Wiley
Date: 27-06-2018
DOI: 10.1111/PBR.12615
High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus
Publisher: Springer Science and Business Media LLC
Date: 10-03-2015
DOI: 10.1007/S00122-015-2488-Y
Abstract: We characterise the distribution of crossover and non-crossover recombination in Brassica napus and Cicer arietinum using a low-coverage genotyping by sequencing pipeline SkimGBS. The growth of next-generation DNA sequencing technologies has led to a rapid increase in sequence-based genotyping for applications including ersity assessment, genome structure validation and gene-trait association. We have established a skim-based genotyping by sequencing method for crop plants and applied this approach to genotype-segregating populations of Brassica napus and Cicer arietinum. Comparison of progeny genotypes with those of the parental in iduals allowed the identification of crossover and non-crossover (gene conversion) events. Our results identify the positions of recombination events with high resolution, permitting the mapping and frequency assessment of recombination in segregating populations.
Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 15-12-2017
Validation of markers linked to late leaf spot and rust resistance, and selection of superior genotypes among diverse recombinant inbred lines and backcross lines in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 07-01-2015
Mitochondrial SSRs and their utility in distinguishing wild species, CMS lines and maintainer lines in pigeonpea (Cajanus cajan L.)
Publisher: Springer Science and Business Media LLC
Date: 07-07-2015
DOI: 10.1007/S10681-015-1504-2
Abstract: Analysis of the pigeonpea mitochondrial genome sequence identified 25 SSRs. Mononucleotide SSR motifs were the most abundant repeats followed by dinucleotide and trinucleotide repeats. Primer pairs could be designed for 24 SSRs, 23 of which were polymorphic amongst the 22 genotypes consisting of cytoplasmic male sterile (CMS or A) line, maintainer or B line and wild Cajanus species representing six different CMS systems viz., A 1 , A 2 , A 4 , A 5 , A 6 and A 8 . These markers lified a total of 107 alleles ranging from 2 to 10 with an average of 4.65 alleles per locus. The polymorphic information content for these markers ranged from 0.09 to 0.84 with an average of 0.52 per marker. Hence, the present study adds a novel set of 24 mitochondrial SSR markers to the markers repository in pigeonpea, which would be useful to distinguish the genotypes based on mitochondrial genome types in evolutionary and phylogenetic studies.
Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 12-05-2017
DOI: 10.1038/S41598-017-01535-4
Abstract: Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F 2 , were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F 2 ) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs 921.21 cM), PRIL_C (484 SNPs 798.25 cM) and F 2 (996 SNPs 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.
The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development
Publisher: Wiley
Date: 16-05-2018
DOI: 10.1111/PCE.13210
Abstract: Chickpea is one of the world's largest cultivated food legumes and is an excellent source of high-quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage, and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here, we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across different plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivars, ICC 4958 has been used to generate RNA-Seq data from 27 s les at 5 major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after quality control (QC) were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, and seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from "QTL-hotspot" region associated with drought stress response in chickpea were validated.
Legume Crops Phylogeny and Genetic Diversity for Science and Breeding
Publisher: Informa UK Limited
Date: 24-10-2014
First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations
Publisher: Wiley
Date: 29-01-2016
DOI: 10.1111/PBI.12528
Root Genomics
Publisher: Springer Berlin Heidelberg
Date: 2011
Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.)
Publisher: Public Library of Science (PLoS)
Date: 14-05-2021
DOI: 10.1371/JOURNAL.PONE.0251669
Abstract: Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom ® CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.
Plant Genetics and Molecular Biology: An Introduction
Publisher: Springer International Publishing
Date: 2018
DOI: 10.1007/10_2017_45
Abstract: The rapidly evolving technologies can serve as a potential growth engine in agriculture as many of these technologies have revolutionized several industries in the recent past. The tremendous advancements in biotechnology methods, cost-effective sequencing technology, refinement of genomic tools, and standardization of modern genomics-assisted breeding methods hold great promise in taking the global agriculture to the next level through development of improved climate-smart seeds. These technologies can dramatically increase our capacity to understand the molecular basis of traits and utilize the available resources for accelerated development of stable high-yielding, nutritious, input-use efficient, and climate-smart crop varieties. This book aimed to document the monumental advances witnessed during the last decade in multiple fields of plant biotechnology such as genetics, structural and functional genomics, trait and gene discovery, transcriptomics, proteomics, metabolomics, epigenomics, nanotechnology, and analytical tools. This book will serve to update the scientific community, academicians, and other stakeholders in global agriculture on the rapid progress in various areas of agricultural biotechnology. This chapter provides a summary of the book, "Plant Genetics and Molecular Biology." Graphical Abstract.
Current Status and Prospects of Genomic Selection in Legumes
Publisher: Springer International Publishing
Date: 2017
Cytoplasmic Male Sterility-Associated Chimeric Open Reading Frames Identified by Mitochondrial Genome Sequencing of Four Cajanus Genotypes
Publisher: Oxford University Press (OUP)
Date: 20-06-2013
Genomic Selection for Crop Improvement: An Introduction
Publisher: Springer International Publishing
Date: 2017
Pigeonpea composite collection and identification of germplasm for use in crop improvement programmes
Publisher: Cambridge University Press (CUP)
Date: 06-01-2011
DOI: 10.1017/S1479262110000419
Abstract: Pigeonpea ( Cajanus cajan (L.) Millsp. is one of the most important legume crops as major source for proteins, minerals and vitamins, in addition to its multiple uses as food, feed, fuel, soil enricher, or soil binder, and in fencing, roofing and basket making. ICRISAT's genebank conserves 13,632 accessions of pigeonpea. The extensive use of few parents in crop improvement is contrary to the purpose of collecting a large number of germplasm accessions and has resulted in a narrow base of cultivars. ICRISAT, in collaboration with the Generation Challenge Program, has developed a composite collection of pigeonpea consisting of 1000 accessions representing the ersity of the entire germplasm collection. This included 146 accessions of mini core collection and other materials. Genotyping of the composite collection using 20 microsatellite or simple sequence repeat (SSR) markers separated wild and cultivated types in two broad groups. A reference set comprising 300 most erse accessions has been selected based on SSR genotyping data. Phenotyping of the composite collection for 16 quantitative and 16 qualitative traits resulted in the identification of promising erse accessions for the four important agronomic traits: early flowering (96 accessions), high number of pods (28), high 100-seed weight (88) and high seed yield lant (49). These accessions hold potential for their utilization in pigeonpea breeding programmes to develop improved cultivars with a broad genetic base. Pigeonpea germplasm has provided sources of resistance to abiotic and biotic stresses and cytoplasmic-male sterility for utilization in breeding programmes.
Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.)
Publisher: Springer Science and Business Media LLC
Date: 06-03-2010
Selection and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) under Heat and Salt Stress Conditions
Publisher: Frontiers Media SA
Date: 21-12-2015
Genome-based analysis of the transcriptome from mature chickpea root nodules
Publisher: Frontiers Media SA
Date: 11-07-2014
Consistent variation across soil types in salinity resistance of a diverse range of chickpea (Cicer arietinum L.) genotypes
Publisher: Wiley
Date: 05-01-2011
Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea
Publisher: Wiley
Date: 03-02-2020
DOI: 10.1111/PBI.13333
Identification and Validation of Selected Universal Stress Protein Domain Containing Drought-Responsive Genes in Pigeonpea (Cajanus cajan L.)
Publisher: Frontiers Media SA
Date: 06-01-2016
Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation
Publisher: Springer Science and Business Media LLC
Date: 23-02-2022
Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal
Publisher: Springer Science and Business Media LLC
Date: 30-05-2015
DOI: 10.1007/S10681-015-1472-6
Abstract: Yield under drought stress is a highly complex trait with large influence to even a minor fluctuation in the environmental conditions. Genomics-assisted breeding holds great promise for improving such complex traits more efficiently in less time, but requires markers associated with the trait of interest. In this context, a recombinant inbred line mapping population (TAG 24 × ICGV 86031) was used to identify markers associated with quantitative trait loci (QTLs) for yield and yield related traits at two important locations of West Africa under well watered and water stress conditions. Among the traits analyzed under WS condition, the harvest index (HI) and the haulm yield (HYLD) were positively correlated with the pod yield (PYLD) and showed intermediate broad sense heritability. QTL analysis using phenotyping and genotyping data resulted in identification of 52 QTLs. These QTLs had low phenotypic variance ( %) for all the nine traits namely plant height, primary branching, SPAD chlorophyll meter reading, percentage of sound mature kernels, 100 kernel weight, shelling percentage, HI, HYLD and PYLD. Interestingly, few QTLs identified in this study were also overlapped with previously reported QTLs detected for drought tolerance related traits identified earlier in Indian environmental conditions using the same mapping population. Accumulating these many small-effect QTLs into a single genetic background is nearly impossible through marker-assisted backcrossing and even marker-assisted recurrent selection. Under such circumstances, the deployment of genomic selection is the most appropriate approach for improving such complex traits with more precision and in less time.
Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut
Publisher: Elsevier BV
Date: 02-2017
Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis
Publisher: Frontiers Media SA
Date: 02-12-2015
Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement
Publisher: Springer Science and Business Media LLC
Date: 21-10-2020
Fine mapping and gene cloning in the post-NGS era: advances and prospects
Publisher: Springer Science and Business Media LLC
Date: 10-02-2020
DOI: 10.1007/S00122-020-03560-W
Abstract: Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
Translational Root Genomics for Crop Improvement
Publisher: Wiley
Date: 10-10-2012
A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 20-10-2020
DOI: 10.1007/S00122-020-03702-0
Abstract: Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the ersity of these loci has shown the role of different alleles in different resistant genotypes. Two genes ( C . cajan_03691 and C.cajan_18888 ) for FW resistance and four genes ( C . cajan_07858, C . cajan_20995, C . cajan_21801 and C . cajan_17341 ) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.
Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems
Publisher: Springer Science and Business Media LLC
Date: 27-06-2019
DOI: 10.1038/S41598-019-45770-3
Abstract: In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.
Exciting journey of 10 years from genomes to fields and markets: Some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.PLANTSCI.2015.09.009
Abstract: Legume crops such as chickpea, pigeonpea and groundnut, mostly grown in marginal environments, are the major source of nutrition and protein to the human population in Asia and Sub-Saharan Africa. These crops, however, have a low productivity, mainly due to their exposure to several biotic and abiotic stresses in the marginal environments. Until 2005, these crops had limited genomics resources and molecular breeding was very challenging. During the last decade (2005-2015), ICRISAT led demand-driven innovations in genome science and translated the massive genome information in breeding. For instance, large-scale genomic resources including draft genome assemblies, comprehensive genetic and physical maps, thousands of SSR markers, millions of SNPs, several high-throughput as well as low cost marker genotyping platforms have been developed in these crops. After mapping several breeding related traits, several success stories of translational genomics have become available in these legumes. These include development of superior lines with enhanced drought tolerance in chickpea, enhanced and pyramided resistance to Fusarium wilt and Ascochyta blight in chickpea, enhanced resistance to leaf rust in groundnut, improved oil quality in groundnut and utilization of markers for assessing purity of hybrids arental lines in pigeonpea. Some of these stories together with future prospects have been discussed.
Allelic relationships of flowering time genes in chickpea
Publisher: Springer Science and Business Media LLC
Date: 25-09-2014
Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut (Arachis hypogaea L.)
Publisher: Elsevier BV
Date: 04-2014
Next-generation sequencing for identification of candidate genes forFusariumwilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
Publisher: Wiley
Date: 23-09-2016
DOI: 10.1111/PBI.12470
Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/FP13088
Abstract: Terminal drought is a major constraint to chickpea productivity. Carbon isotope discrimination (Δ13C), an integrator of plant behaviour influencing transpiration efficiency (TE), is an important component of yield under drought. The variation in Δ13C and its association with yield was assessed in the reference collection of chickpea germplasm. Drought stress reduced shoot biomass by 36–39% and grain yield by 23%. Mean Δ13C was low and the range of genetic variation was high under drought stress. Largely, high Δ13C accessions were early in flowering (40–50 days), moderate in shoot biomass, high in seed yields and high in harvest index (HI). Δ13C was positively correlated with seed yield in both the years under drought stress, only in 2008–09 under optimal irrigation. This positive association was very close with HI. Among the yield components, Δ13C was closely associated with pod numbers per unit area and seed size under drought stress. Path coefficients showed no direct association of Δ13C with grain yield but an indirect negative association through shoot biomass at maturity and a close positive association through HI. The closest association of HI or shoot biomass was seen in the maturity group of accessions that experienced the optimum terminal drought stress.
Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties
Publisher: Proceedings of the National Academy of Sciences
Date: 05-12-2006
Abstract: Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world's major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudooutbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs.
Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes
Publisher: Oxford University Press (OUP)
Date: 12-01-2013
Evolving Molecular Marker Technologies in Plants: From RFLPs to GBS
Publisher: Springer Netherlands
Date: 2013
Genome-Wide Investigation of Apyrase (APY) Genes in Peanut (Arachis hypogaea L.) and Functional Characterization of a Pod-Abundant Expression Promoter AhAPY2-1p
Publisher: MDPI AG
Date: 27-02-2023
DOI: 10.3390/IJMS24054622
Abstract: Peanut (Arachis hypogaea L.) is an important food and feed crop worldwide and is affected by various biotic and abiotic stresses. The cellular ATP levels decrease significantly during stress as ATP molecules move to extracellular spaces, resulting in increased ROS production and cell apoptosis. Apyrases (APYs) are the nucleoside phosphatase (NPTs) superfamily members and play an important role in regulating cellular ATP levels under stress. We identified 17 APY homologs in A. hypogaea (AhAPYs), and their phylogenetic relationships, conserved motifs, putative miRNAs targeting different AhAPYs, cis-regulatory elements, etc., were studied in detail. The transcriptome expression data were used to observe the expression patterns in different tissues and under stress conditions. We found that the AhAPY2-1 gene showed abundant expression in the pericarp. As the pericarp is a key defense organ against environmental stress and promoters are the key elements regulating gene expression, we functionally characterized the AhAPY2-1 promoter for its possible use in future breeding programs. The functional characterization of AhAPY2-1P in transgenic Arabidopsis plants showed that it effectively regulated GUS gene expression in the pericarp. GUS expression was also detected in flowers of transgenic Arabidopsis plants. Overall, these results strongly suggest that APYs are an important future research subject for peanut and other crops, and AhPAY2-1P can be used to drive the resistance-related genes in a pericarp-specific manner to enhance the defensive abilities of the pericarp.
Emerging role of plant long non coding RNAs (lncRNAs) in salinity stress response
Publisher: Elsevier BV
Date: 12-2023
Exploiting genomic resources for efficient conservation and use of chickpea, groundnut, and pigeonpea collections for crop improvement
Publisher: Wiley
Date: 11-2013
Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs
Publisher: Springer Science and Business Media LLC
Date: 02-07-2015
Genetic Mapping and Quantitative Trait Loci Analysis for Disease Resistance Using F2 and F5 Generation‐based Genetic Maps Derived from ‘Tifrunner’ × ‘GT‐C20’ in Peanut
Publisher: Wiley
Date: 11-2013
A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 06-06-2010
Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform
Publisher: Wiley
Date: 07-2013
Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea
Publisher: Oxford University Press (OUP)
Date: 25-08-2022
DOI: 10.1093/JXB/ERAC348
Abstract: ‘QTL-hotspot’ is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of ‘QTL-hotspot’ on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the ‘QTL-hotspot’ region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the ‘QTL-hotspot’ region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.
Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
Publisher: Springer Science and Business Media LLC
Date: 16-11-2021
DOI: 10.1186/S13059-021-02520-X
Abstract: Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP -binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.
Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.)
Publisher: Springer Science and Business Media LLC
Date: 21-10-2014
Rapid delivery systems for future food security
Publisher: Springer Science and Business Media LLC
Date: 28-09-2021
Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage
Publisher: Oxford University Press (OUP)
Date: 26-06-2009
DOI: 10.1093/JXB/ERP194
New possibilities for trait improvement via mobile CRISPR-RNA
Publisher: Elsevier BV
Date: 11-2023
High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers
Publisher: Wiley
Date: 10-2009
Genetic Variation and Association Mapping of Seed-Related Traits in Cultivated Peanut (Arachis hypogaea L.) Using Single-Locus Simple Sequence Repeat Markers
Publisher: Frontiers Media SA
Date: 11-12-2017
Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/CP10165
Abstract: The genomic DNA profiles of 48 chickpea cultivars released in nine countries and of historical significance to the chickpea breeding programs at ICRISAT and in Ethiopia were evaluated using 48 simple sequence repeat (SSR) markers. Across the cultivars, a total of 504 alleles representing the 48 SSR loci were detected with frequencies ranging from three to 22 (mean 10.5) alleles per locus. The polymorphism information content (PIC) for the SSR markers varied from 0.37 to 0.91 (mean 0.77). A subset of only three highly informative SSR markers (TA176, TA2, TA180) enabled complete discrimination among all 48 chickpea cultivars tested. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching dissimilarity matrix resolved the 48 cultivars into two major clusters representing desi and kabuli types. These cluster groupings of the cultivars were consistent with the pedigree information available for the cultivars as to the phenotypic classes of chickpea types. Analysis of the temporal patterns of the SSR ersity by classifying 48 chickpea cultivars into four periods of release revealed increasing tendencies in the overall genetic ersity from 0.42 for the earliest varieties developed in the 1970s to 0.62 for those released in the 1980s, and reached a maximum and equivalent level of 0.72 for the varieties developed in the 1990s and 2000s. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic ersity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprint identification of cultivars.
Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement
Publisher: Elsevier BV
Date: 02-2020
A western Sahara centre of domestication inferred from pearl millet genomes
Publisher: Springer Science and Business Media LLC
Date: 06-08-2018
DOI: 10.1038/S41559-018-0643-Y
Abstract: There have been intense debates over the geographic origin of African crops and agriculture. Here, we used whole-genome sequencing data to infer the domestication origin of pearl millet (Cenchrus americanus). Our results supported an origin in western Sahara, and we dated the onset of cultivated pearl millet expansion in Africa to 4,900 years ago. We provided evidence that wild-to-crop gene flow increased cultivated genetic ersity leading to ersity hotspots in western and eastern Sahel and adaptive introgression of 15 genomic regions. Our study reconciled genetic and archaeological data for one of the oldest African crops.
Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review
Publisher: MDPI AG
Date: 12-2021
Abstract: Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
Breeding pigeonpea cultivars for intercropping: Synthesis and strategies
Publisher: Japanese Society of Breeding
Date: 2018
DOI: 10.1270/JSBBS.17105
Vernalization response in chickpea is controlled by a major QTL
Publisher: Springer Science and Business Media LLC
Date: 07-10-2015
Technologies for Intensification of Production and Uses of Grain Legumes for Nutrition Security
Publisher: Indian National Science Academy
Date: 10-2016
Functional genomics to study stress responses in crop legumes: Progress and prospects
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/FP13191
Abstract: Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stress-responsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.
Salt sensitivity in chickpea
Publisher: Wiley
Date: 02-03-2010
DOI: 10.1111/J.1365-3040.2009.02051.X
Abstract: The growth of chickpea (Cicer arietinum L.) is very sensitive to salinity, with the most susceptible genotypes dying in just 25 mm NaCl and resistant genotypes unlikely to survive 100 mm NaCl in hydroponics germination is more tolerant with some genotypes tolerating 320 mm NaCl. When growing in a saline medium, Cl(-), which is secreted from glandular hairs on leaves, stems and pods, is present in higher concentrations in shoots than Na(+). Salinity reduces the amount of water extractable from soil by a chickpea crop and induces osmotic adjustment, which is greater in nodules than in leaves or roots. Chickpea rhizobia show a higher 'free-living' salt resistance than chickpea plants, and salinity can cause large reductions in nodulation, nodule size and N(2)-fixation capacity. Recent screenings of erse germplasm suggest significant variation of seed yield under saline conditions. Both dominance and additive gene effects have been identified in the effects of salinity on chickpea and there appears to be sufficient genetic variation to enable improvement in yield under saline conditions via breeding. Selections are required across the entire life cycle with a range of rhizobial strains under salt-affected, preferably field, conditions.
Understanding sheath blight resistance in rice: the road behind and the road ahead
Publisher: Wiley
Date: 29-01-2020
DOI: 10.1111/PBI.13312
Cytogenetics to functional genomics: six decades journey of Professor P.K. Gupta
Publisher: Wiley
Date: 22-03-2022
DOI: 10.1111/PBI.13795
Abstract: We had the fortune of starting our scientific/research careers in the Molecular Biology and Crop Biotechnology Laboratory of Professor P.K. Gupta at Ch. Charan Singh University, Meerut, UP, India. Here, we describe the most important scientific contributions of our beloved mentor in the area of cytotaxonomy, cytogenetics, mutation breeding, quantitative genetics, molecular biology, crop biotechnology and plant genomics, on his 85th birthday. Important contributions made in the development and use of genomics resources including the development and use of different kinds of molecular markers, genetic and physical mapping, quantitative trait locus (QTL) interval mapping, genome‐wide association mapping and molecular breeding including marker‐assisted selection have been briefly summarized. Efforts have been also made to give readers a glimpse of important contributions in the study of cytology/apomixis of grasses, cytotaxonomic studies in asteraceae/fabaceae, nuclear/repetitive DNA content in Lolium , interspecific/intergeneric relationships involving the genus Hordeum and re‐examining taxonomy of the tribe Triticeae.
Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)
Publisher: Wiley
Date: 25-12-2019
DOI: 10.1111/PBI.13311
From genome studies to agricultural biotechnology: closing the gap between basic plant science and applied agriculture
Publisher: Elsevier BV
Date: 04-2010
Omics Techniques in Crop Research: An Overview
Publisher: Wiley
Date: 14-03-2012
Molecular Mapping of Flowering Time Major Genes and QTLs in Chickpea (Cicer arietinum L.)
Publisher: Frontiers Media SA
Date: 06-07-2017
Back to wild relatives for future breeding through super-pangenome
Publisher: Elsevier BV
Date: 09-2023
Aspergillus flavus infection triggered immune responses and host-pathogen cross-talks in groundnut during in-vitro seed colonization
Publisher: Springer Science and Business Media LLC
Date: 29-08-2017
DOI: 10.1038/S41598-017-09260-8
Abstract: Aflatoxin contamination, caused by fungal pathogen Aspergillus flavus , is a major quality and health problem delimiting the trade and consumption of groundnut ( Arachis hypogaea L.) worldwide. RNA-seq approach was deployed to understand the host-pathogen interaction by identifying differentially expressed genes (DEGs) for resistance to in-vitro seed colonization (IVSC) at four critical stages after inoculation in J 11 (resistant) and JL 24 (susceptible) genotypes of groundnut. About 1,344.04 million sequencing reads have been generated from sixteen libraries representing four stages in control and infected conditions. About 64% and 67% of quality filtered reads (1,148.09 million) were mapped onto A ( A. duranensis ) and B ( A. ipaёnsis ) subgenomes of groundnut respectively. About 101 million unaligned reads each from J 11 and JL 24 were used to map onto A. flavus genome. As a result, 4,445 DEGs including defense-related genes like senescence-associated proteins, resveratrol synthase, 9s-lipoxygenase, pathogenesis-related proteins were identified. In A. flavus , about 578 DEGs coding for growth and development of fungus, aflatoxin biosynthesis, binding, transport, and signaling were identified in compatible interaction. Besides identifying candidate genes for IVSC resistance in groundnut, the study identified the genes involved in host-pathogen cross-talks and markers that can be used in breeding resistant varieties.
Phylogenetic diversity of Mesorhizobium in chickpea
Publisher: Springer Science and Business Media LLC
Date: 29-04-2014
DOI: 10.1007/S12038-014-9429-9
Abstract: Crop domestication, in general, has reduced genetic ersity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence ersity for further phylogenetic analysis. Phylogenetic analysis and sequence ersity for 3 genes demonstrated that sequences from C. reticulatum were more erse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60 percent) could have more various symbionts than cultivated chickpea (80 percent). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more erse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic ersity.
Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.)
Publisher: Springer Science and Business Media LLC
Date: 11-11-2011
Identification of quantitative trait loci associated with iron deficiency chlorosis resistance in groundnut (Arachis hypogaea)
Publisher: Wiley
Date: 13-03-2020
DOI: 10.1111/PBR.12815
Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features
Publisher: Springer Science and Business Media LLC
Date: 2009
Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes
Publisher: Oxford University Press (OUP)
Date: 26-10-2012
Large genetic variation for heat tolerance in the reference collection of chickpea ( Cicer arietinum L.) germplasm
Publisher: Cambridge University Press (CUP)
Date: 05-01-2011
DOI: 10.1017/S1479262110000407
Abstract: Chickpea is the third most important pulse crop worldwide. Changes in cropping system that necessitate late planting, scope for expansion in rice fallows and the global warming are pushing chickpeas to relatively warmer growing environment. Such changes demand identification of varieties resilient to warmer temperature. Therefore, the reference collection of chickpea germplasm, defined based on molecular characterization of global composite collection, was screened for high temperature tolerance at two locations in India (Patancheru and Kanpur) by delayed sowing and synchronizing the reproductive phase of the crop with the occurrence of higher temperatures ( ≥ 35°C). A heat tolerance index (HTI) was calculated using a multiple regression approach where grain yield under heat stress is considered as a function of yield potential and time to 50% flowering. There were large and significant variations for HTI, phenology, yield and yield components at both the locations. There were highly significant genotypic effects and equally significant G × E interactions for all the traits studied. A cluster analysis of the HTI of the two locations yielded five cluster groups as stable tolerant ( n = 18), tolerant only at Patancheru ( n = 34), tolerant only at Kanpur ( n = 23), moderately tolerant ( n = 120) and stable sensitive ( n = 82). The pod number per plant and the harvest index explained ≥ 60% of the variation in seed yield and ≥ 49% of HTI at Kanpur and ≥ 80% of the seed yield and ≥ 35% of HTI at Patancheru, indicating that partitioning as a consequence of poor pod set is the most affected trait under heat stress. A large number of heat-tolerant genotypes also happened to be drought tolerant.
Proteome analysis of Aspergillus flavus isolate-specific responses to oxidative stress in relationship to aflatoxin production capability
Publisher: Springer Science and Business Media LLC
Date: 21-02-2018
DOI: 10.1038/S41598-018-21653-X
Abstract: Aspergillus flavus is an opportunistic pathogen of plants such as maize and peanut under conducive conditions such as drought stress resulting in significant aflatoxin production. Drought-associated oxidative stress also exacerbates aflatoxin production by A. flavus . The objectives of this study were to use proteomics to provide insights into the pathogen responses to H 2 O 2 -derived oxidative stress, and to identify potential biomarkers and targets for host resistance breeding. Three isolates, AF13, NRRL3357, and K54A with high, moderate, and no aflatoxin production, were cultured in medium supplemented with varying levels of H 2 O 2 , and examined using an iTRAQ (Isobaric Tags for Relative and Absolute Quantification) approach. Overall, 1,173 proteins were identified and 220 were differentially expressed (DEPs). Observed DEPs encompassed metabolic pathways including antioxidants, carbohydrates, pathogenicity, and secondary metabolism. Increased lytic enzyme, secondary metabolite, and developmental pathway expression in AF13 was correlated with oxidative stress tolerance, likely assisting in plant infection and microbial competition. Elevated expression of energy and cellular component production in NRRL3357 and K54A implies a focus on oxidative damage remediation. These trends explain isolate-to-isolate variation in oxidative stress tolerance and provide insights into mechanisms relevant to host plant interactions under drought stress allowing for more targeted efforts in host resistance research.
Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development
Publisher: MDPI AG
Date: 12-06-2023
Abstract: The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we ided the 111 potential soybean J-proteins into 12 main clades (I–XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality.
Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)
Publisher: Frontiers Media SA
Date: 03-05-2018
Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.)
Publisher: Wiley
Date: 22-06-2020
DOI: 10.1111/PBI.13422
Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes
Publisher: Frontiers Media SA
Date: 2013
Genetic mapping and quantitative trait locus analysis of resistance to sterility mosaic disease in pigeonpea [Cajanus cajan (L.) Millsp.]
Publisher: Elsevier BV
Date: 08-2011
Characterizing Agronomic and Shoot Morphological Diversity across 263 Wild Emmer Wheat Accessions
Publisher: MDPI AG
Date: 25-03-2023
DOI: 10.3390/AGRICULTURE13040759
Abstract: Wild emmer, the direct progenitor of modern durum and bread wheat, has mostly been studied for grain quality, biotic, and abiotic stress-related traits. Accordingly, it should also have a certain amount of ersity for morphological and agronomic traits. Despite having a high chance of huge ersity, it has not been deeply explored. In the current study, 263 wild emmer accessions collected from different regions of Israel, Turkey, Lebanon, and Syria were characterized for a total of 19 agronomic and shoot morphological traits. Three trials were carried out in Western Australia, which demonstrated a large variation in these traits. The average phenotypic ersity (H’) was 0.91 as quantified by Shannon’s ersity index. A high heritability was recorded for most of the traits, where biomass lant and yield lant were identified as the most potential traits. Correlation analysis revealed several significant associations between traits, including significant positive correlation between yield and tiller number, first leaf area, spike length, and biomass lant. The principal component analysis (PCA) demonstrated that most of the traits contributed to the overall observed variability. The cluster analysis categorized 263 accessions into five clusters on average. On the other hand, accessions were categorized into eight populations based on the collection region and a comparative analysis demonstrated considerable variations between populations for plant height, spike length, and flag leaf area. Despite the low yield, several wild emmer accessions demonstrated superior performance compared to modern bread wheat cultivars, when selection was based on combining yield with multiple traits. These observations indicate that wild emmer contains a broad gene pool for several agronomic and shoot morphological traits, which can be utilized for bread and durum wheat improvement.
Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice
Publisher: Elsevier BV
Date: 2005
An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data
Publisher: Public Library of Science (PLoS)
Date: 08-07-2014
Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)
Publisher: Public Library of Science (PLoS)
Date: 19-10-2016
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication
Publisher: Springer Science and Business Media LLC
Date: 05-2019
Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications
Publisher: Wiley
Date: 23-04-2020
DOI: 10.1111/PBI.13374
MAGIC populations in crops: current status and future prospects
Publisher: Springer Science and Business Media LLC
Date: 09-04-2015
DOI: 10.1007/S00122-015-2506-0
Abstract: MAGIC populations present novel challenges and opportunities in crops due to their complex pedigree structure. They offer great potential both for dissecting genomic structure and for improving breeding populations. The past decade has seen the rise of multiparental populations as a study design offering great advantages for genetic studies in plants. The genetic ersity of multiple parents, recombined over several generations, generates a genetic resource population with large phenotypic ersity suitable for high-resolution trait mapping. While there are many variations on the general design, this review focuses on populations where the parents have all been inter-mated, typically termed Multi-parent Advanced Generation Intercrosses (MAGIC). Such populations have already been created in model animals and plants, and are emerging in many crop species. However, there has been little consideration of the full range of factors which create novel challenges for design and analysis in these populations. We will present brief descriptions of large MAGIC crop studies currently in progress to motivate discussion of population construction, efficient experimental design, and genetic analysis in these populations. In addition, we will highlight some recent achievements and discuss the opportunities and advantages to exploit the unique structure of these resources post-QTL analysis for gene discovery.
Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs
Publisher: Wiley
Date: 13-12-2021
DOI: 10.1002/TPG2.20177
Abstract: Since the first reported crop pangenome in 2014, advances in high‐throughput and cost‐effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape ( Brassica napus L.), soybean [ Glycine max (L.) Merr.], rice ( Oryza sativa L.), wheat ( Triticum aestivum L.), and barley ( Hordeum vulgare L.). Compared with single‐reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic ersity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
Publisher: Springer Science and Business Media LLC
Date: 05-2019
DOI: 10.1038/S41588-019-0405-Z
Abstract: Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created ersity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that ersity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
Integrating genomics for chickpea improvement
Publisher: Springer Science and Business Media LLC
Date: 06-04-2020
DOI: 10.1007/S00122-020-03584-2
Abstract: Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is le scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.
Resistance to Aspergillus flavus in maize and peanut: Molecular biology, breeding, environmental stress, and future perspectives
Publisher: Elsevier BV
Date: 06-2015
Future Prospects for Chickpea Research
Publisher: Springer International Publishing
Date: 2017
Impact of Genomics on Chickpea Breeding
Publisher: Springer International Publishing
Date: 2017
Breeding More Crops in Less Time: A Perspective on Speed Breeding
Publisher: MDPI AG
Date: 10-02-2022
Abstract: Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, speed breeding (SB), relying mainly on photoperiod extension, temperature control, and early seed harvest, has the potential to accelerate the rate of plant improvement. Well demonstrated in the case of long-day plants, the SB protocols are being extended to short-day plants to reduce the generation interval time. Flexibility in SB protocols allows them to align and integrate with erse research purposes including population development, genomic selection, phenotyping, and genomic editing. In this review, we discuss the different SB methodologies and their application to hasten future plant improvement. Though SB has been extensively used in plant phenotyping and the pyramiding of multiple traits for the development of new crop varieties, certain challenges and limitations h er its widespread application across erse crops. However, the existing constraints can be resolved by further optimization of the SB protocols for critical food crops and their efficient integration in plant breeding pipelines.
Sequencing the Chickpea Genome
Publisher: Springer International Publishing
Date: 2017
Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms
Publisher: Springer Science and Business Media LLC
Date: 05-03-2020
DOI: 10.1038/S41598-020-60187-Z
Abstract: Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNA-seq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein ( Araip . 3WN1Q ) and another SNP from gene coding for the lipid transfer protein ( Aradu . 03ENG ) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes.
Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers
Publisher: Wiley
Date: 16-10-2015
DOI: 10.1111/JIPB.12380
Abstract: Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic ersity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene ersity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene ersity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE ided these peanut lines into two populations (P1, P2), which was consistent with the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic ersity of breeding materials to broaden the genetic base and for molecular genetics studies.
Genomics of plant genetic resources: An introduction
Publisher: Cambridge University Press (CUP)
Date: 15-06-2011
The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales
Publisher: Wiley
Date: 18-11-2020
DOI: 10.1111/PBI.13499
Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea
Publisher: Springer Science and Business Media LLC
Date: 13-01-2016
DOI: 10.1038/SREP19228
Abstract: Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed ergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.
Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
Publisher: Springer Science and Business Media LLC
Date: 05-03-2016
Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species
Publisher: Springer Science and Business Media LLC
Date: 18-11-2006
DOI: 10.1007/S00122-006-0440-X
Abstract: Genic microsatellites or EST-SSRs derived from expressed sequence tags (ESTs) are desired because these are inexpensive to develop, represent transcribed genes, and often a putative function can be assigned to them. In this study we investigated 2,553 coffee ESTs (461 from the public domain and 2,092 in-house generated ESTs) for identification and development of genic microsatellite markers. Of these, 2,458 ESTs (all >100 bp in size) were searched for SSRs using MISA--search module followed by stackPACK clustering that revealed a total of 425 microsatellites in 331 (13.5%) non-redundant ESTs/consensus sequences suggesting an approximate frequency of 1 SSR/2.16 kb of the analysed coffee transcriptome. Identified microsatellites mainly comprised of di-/tri-nucleotide repeats, of which repeat motifs AG and AAG were the most abundant. A total of 224 primer pairs could be designed from the non-redundant SSR-positive ESTs (excluding those with only mononucleotide repeats) for possible use as potential genic markers. Of this set, a total of 24 (10%) primer pairs were tested and 18 could be validated as usable markers. Sixteen of these markers revealed moderate to high polymorphism information content (PIC) across 23 genotypes of C. arabica and C. canephora, while 2 markers were found to be monomorphic. All the markers also showed robust cross-species lifications across 14 Coffea and 4 Psilanthus species. The apparent broad cross-species/genera transferability was further confirmed by cloning and sequencing of the lified alleles. Thus, the study provides an insight about the frequency and distribution of SSRs in coffee transcriptome, and also demonstrates the successful development of genic-SSRs. It is expected that the potential markers described here would add to the repertoire of DNA markers needed for genetic studies in cultivated coffee and also related taxa that constitute the important secondary genepool for coffee improvement.
From Mendel’s discovery on pea to today’s plant genetics and breeding
Publisher: Springer Science and Business Media LLC
Date: 07-10-2016
DOI: 10.1007/S00122-016-2803-2
Abstract: This work discusses several selected topics of plant genetics and breeding in relation to the 150th anniversary of the seminal work of Gregor Johann Mendel. In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin's theory of evolution was based on differential survival and differential reproductive success, Mendel's theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin's concepts were continuous variation and "soft" heredity Mendel espoused discontinuous variation and "hard" heredity. Thus, the combination of Mendelian genetics with Darwin's theory of natural selection was the process that resulted in the modern synthesis of evolutionary biology. Although biology, genetics, and genomics have been revolutionized in recent years, modern genetics will forever rely on simple principles founded on pea breeding using seven single gene characters. Purposeful use of mutants to study gene function is one of the essential tools of modern genetics. Today, over 100 plant species genomes have been sequenced. Mapping populations and their use in segregation of molecular markers and marker-trait association to map and isolate genes, were developed on the basis of Mendel's work. Genome-wide or genomic selection is a recent approach for the development of improved breeding lines. The analysis of complex traits has been enhanced by high-throughput phenotyping and developments in statistical and modeling methods for the analysis of phenotypic data. Introgression of novel alleles from landraces and wild relatives widens genetic ersity and improves traits transgenic methodologies allow for the introduction of novel genes from erse sources, and gene editing approaches offer possibilities to manipulate gene in a precise manner.
Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea)
Publisher: Frontiers Media SA
Date: 18-07-2017
An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)
Publisher: Public Library of Science (PLoS)
Date: 18-07-2012
Traits of relevance to improve yield under terminal drought stress in chickpea (C. arietinum L.)
Publisher: Elsevier BV
Date: 04-2013
Neglecting legumes has compromised human health and sustainable food production
Publisher: Springer Science and Business Media LLC
Date: 02-08-2016
Abstract: The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner 'nutritious seeds for a sustainable future'. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.
AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.PLANTSCI.2009.01.006
Abstract: Amplified fragment length polymorphism (AFLP) was employed to assess the ersity in the elite germplasm collection of Jatropha curcas, which has gained tremendous significance as a biofuel plant in India and many other countries recently. Forty-eight accessions, collected from six different states of India, were used with seven AFLP primer combinations that generated a total of 770 fragments with an average of 110 fragments per primer combination. A total of 680 (88%) fragments showed polymorphism in the germplasm analyzed, of which 59 (8.7%) fragments were unique (accession specific) and 108 (15.9%) fragments were rare (present in less than 10% accessions). In order to assess the discriminatory power of seven primer combinations used, a variety of marker attributes like polymorphism information content (PIC), marker index (MI) and resolving power (RP) values were calculated. Although the PIC values ranged from 0.20 (E-ACA/M-CAA) to 0.34 (E-ACT/M-CTT) with an average of 0.26 per primer combination and the MI values were observed in the range of 17.60 (E-ACA/M-CAA) to 32.30 (E-ACT/M-CTT) with an average of 25.13 per primer combination, the RP was recognized the real attribute for AFLP to determine the discriminatory power of the primer combination. The RP values for different primer combinations varied from 23.11 (E-ACA/M-CAA) to 46.82 (E-ACT/M-CTT) with an average of 35.21. Genotyping data obtained for all 680 polymorphic fragments were used to group the accessions analyzed using the UPGMA-phenogram and principal component analysis (PCA). Majority of groups obtained in phenogram and PCA contained accessions as per geographical locations. In general, accessions coming from Andhra Pradesh were found erse as these were scattered in different groups, whereas accessions coming from Chhattisgarh showed occurrence of higher number of unique/rare fragments. Molecular ersity estimated in the present study combined with the datasets on other morphological/agronomic traits will be very useful for selecting the appropriate accessions for plant improvement through conventional as well as molecular breeding approaches.
Exploring Germplasm Diversity to Understand the Domestication Process in Cicer spp. Using SNP and DArT Markers
Publisher: Public Library of Science (PLoS)
Date: 10-07-2014
Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)
Publisher: Springer Science and Business Media LLC
Date: 15-05-2008
Abstract: Cultivated peanut or groundnut ( Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable licon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, ersity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species.
Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome
Publisher: Springer Science and Business Media LLC
Date: 06-02-2018
Identification of eight chromosomes and a microsatellite marker on 1AS associated with QTL for grain weight in bread wheat
Publisher: Springer Science and Business Media LLC
Date: 06-2000
Genetic diversity ofJatropha curcascollections from different islands in Indonesia
Publisher: Cambridge University Press (CUP)
Date: 05-03-2018
DOI: 10.1017/S1479262117000387
Abstract: Jatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic ersity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic ersity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic ersity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of erse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.
Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers
Publisher: Wiley
Date: 17-04-2018
DOI: 10.1111/PBR.12554
Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype × environment interaction on prediction accuracy in chickpea
Publisher: Springer Science and Business Media LLC
Date: 03-08-2018
DOI: 10.1038/S41598-018-30027-2
Abstract: Genomic selection (GS) by selecting lines prior to field phenotyping using genotyping data has the potential to enhance the rate of genetic gains. Genotype × environment (G × E) interaction inclusion in GS models can improve prediction accuracy hence aid in selection of lines across target environments. Phenotypic data on 320 chickpea breeding lines for eight traits for three seasons at two locations were recorded. These lines were genotyped using DArTseq (1.6 K SNPs) and Genotyping-by-Sequencing (GBS 89 K SNPs). Thirteen models were fitted including main effects of environment and lines, markers, and/or naïve and informed interactions to estimate prediction accuracies. Three cross-validation schemes mimicking real scenarios that breeders might encounter in the fields were considered to assess prediction accuracy of the models (CV2: incomplete field trials or sparse testing CV1: newly developed lines and CV0: untested environments). Maximum prediction accuracies for different traits and different models were observed with CV2. DArTseq performed better than GBS and the combined genotyping set (DArTseq and GBS) regardless of the cross validation scheme with most of the main effect marker and interaction models. Improvement of GS models and application of various genotyping platforms are key factors for obtaining accurate and precise prediction accuracies, leading to more precise selection of candidates.
Marker-assisted introgression of resistance to fusarium wilt race 2 in Pusa 256, an elite cultivar of desi chickpea
Publisher: Springer Science and Business Media LLC
Date: 07-2017
DOI: 10.1007/S00438-017-1343-Z
Abstract: Fusarium wilt caused by F. oxysporum f. sp. ciceris causes extensive damage to chickpea (Cicer arietinum L.) in many parts of the world. In the central part of India, pathogen race 2 (Foc 2) causes severe yield losses. We initiated molecular marker-assisted backcrossing (MABC) using desi cultivar, Vijay, as a donor to introgress resistance to this race (Foc2) in Pusa 256, another elite desi cultivar of chickpea. To confirm introgression of resistance for this race, foreground selection was undertaken using two SSR markers (TA 37 and TA110), with background selection to observe the recovery of recurrent parent genome using 45 SSRs accommodated in 8 multiplexes. F
Molecular markers and their applications in wheat breeding
Publisher: Wiley
Date: 10-1999
Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut
Publisher: Wiley
Date: 17-09-2019
DOI: 10.1111/PBI.13246
Genome-wide identification, characterization, and expression analysis of small RNA biogenesis purveyors reveal their role in regulation of biotic stress responses in three legume crops
Publisher: Frontiers Media SA
Date: 25-04-2017
Identification of Expressed Resistance Gene Analogs from Peanut (Arachis hypogaea L.) Expressed Sequence Tags
Publisher: Wiley
Date: 18-03-2013
DOI: 10.1111/JIPB.12037
Abstract: Low genetic ersity makes peanut (Arachis hypogaea L.) very vulnerable to plant pathogens, causing severe yield loss and reduced seed quality. Several hundred partial genomic DNA sequences as nucleotide-binding-site leucine-rich repeat (NBS-LRR) resistance genes (R) have been identified, but a small portion with expressed transcripts has been found. We aimed to identify resistance gene analogs (RGAs) from peanut expressed sequence tags (ESTs) and to develop polymorphic markers. The protein sequences of 54 known R genes were used to identify homologs from peanut ESTs from public databases. A total of 1,053 ESTs corresponding to six different classes of known R genes were recovered, and assembled 156 contigs and 229 singletons as peanut-expressed RGAs. There were 69 that encoded for NBS-LRR proteins, 191 that encoded for protein kinases, 82 that encoded for LRR-PK/transmembrane proteins, 28 that encoded for Toxin reductases, 11 that encoded for LRR-domain containing proteins and four that encoded for TM-domain containing proteins. Twenty-eight simple sequence repeats (SSRs) were identified from 25 peanut expressed RGAs. One SSR polymorphic marker (RGA121) was identified. Two polymerase chain reaction-based markers (Ahsw-1 and Ahsw-2) developed from RGA013 were homologous to the Tomato Spotted Wilt Virus (TSWV) resistance gene. All three markers were mapped on the same linkage group AhIV. These expressed RGAs are the source for RGA-tagged marker development and identification of peanut resistance genes.
Next-generation sequencing technologies and their implications for crop genetics and breeding
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.TIBTECH.2009.05.006
Abstract: Using next-generation sequencing technologies it is possible to resequence entire plant genomes or s le entire transcriptomes more efficiently and economically and in greater depth than ever before. Rather than sequencing in idual genomes, we envision the sequencing of hundreds or even thousands of related genomes to s le genetic ersity within and between germplasm pools. Identification and tracking of genetic variation are now so efficient and precise that thousands of variants can be tracked within large populations. In this review, we outline some important areas such as the large-scale development of molecular markers for linkage mapping, association mapping, wide crosses and alien introgression, epigenetic modifications, transcript profiling, population genetics and de novo genome/organellar genome assembly for which these technologies are expected to advance crop genetics and breeding, leading to crop improvement.
Standard care with plastic bag or portable thermal nest to prevent hypothermia at birth: a three-armed randomized controlled trial
Publisher: Springer Science and Business Media LLC
Date: 27-07-2018
DOI: 10.1038/S41372-018-0169-9
Abstract: To assess the efficacy of adding plastic bag or portable thermal nest (PTN) to standard care in preventing hypothermia soon after birth in 1500-2499 g infants. Infants were randomized into standard thermal care alone, plastic bag with standard care or PTN with standard care. Axillary temperature was measured at admission and every 30 min till euthermia. All babies were followed-up till day 7. We recruited 300 infants: plastic bag (101), PTN (99) and standard care group (100). Admission temperature was 36.4 °C (0.52) in plastic bag group, 36.3 °C (0.50) in PTN and 36.1 °C (0.59) in standard care group (p < 0.001). Incidence of hypothermia was lowest in plastic bag group (44.6%), followed by PTN (60%) and standard care (67%). Secondary outcomes were comparable. Addition of plastic bag or PTN to standard care significantly reduces incidence and duration of hypothermia soon after birth. Plastic bag is more effective than PTN.
The Role of Vegetables and Legumes in Assuring Food, Nutrition, and Income Security for Vulnerable Groups in Sub‐Saharan Africa
Publisher: Wiley
Date: 09-2015
DOI: 10.1002/WMH3.148
Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture
Publisher: Oxford University Press (OUP)
Date: 05-03-2018
DOI: 10.1093/JXB/ERY088
Abstract: Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.
Genomics-assisted breeding for drought tolerance in chickpea
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/FP13318
Abstract: Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density ersity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10–24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.
A randomized double-blind controlled trial comparing two regimens of vitamin D supplementation in preterm neonates
Publisher: Springer Science and Business Media LLC
Date: 05-05-2016
DOI: 10.1038/JP.2016.70
Abstract: To compare the efficacy of 400 vs 1000 IU oral vitamin D supplementation in preterm neonates of 27 to 34 weeks gestation. This double-blind randomized controlled trial allocated preterm babies to receive either 400 or 1000 IU of vitamin D3 (n=60 in each group). Primary outcome was prevalence of vitamin D insufficiency (serum vitamin D levels<20 ng ml(-1)) at 40 weeks of corrected gestational age (CGA). At term CGA vitamin D insufficiency was significantly lower in the 1000 IU group than in the 400 IU group (2% vs 64.6%, P⩽0.001). Although elevated vitamin D levels were seen in 9.8% of babies on 1000 IU per day, this was not associated with clinical or biochemical evidence of toxicity. Supplementing preterm babies with 1000 IU of vitamin D3 daily decreases the prevalence of vitamin D insufficiency at term CGA. Excess levels of vitamin D may occur at this dose in some babies.
Genetic diversity of root system architecture in response to drought stress in grain legumes
Publisher: Oxford University Press (OUP)
Date: 07-03-2018
DOI: 10.1093/JXB/ERY082
Abstract: Climate change has increased the occurrence of extreme weather patterns globally, causing significant reductions in crop production, and hence threatening food security. In order to meet the food demand of the growing world population, a faster rate of genetic gains leading to productivity enhancement for major crops is required. Grain legumes are an essential commodity in optimal human diets and animal feed because of their unique nutritional composition. Currently, limited water is a major constraint in grain legume production. Root system architecture (RSA) is an important developmental and agronomic trait, which plays vital roles in plant adaptation and productivity under water-limited environments. A deep and proliferative root system helps extract sufficient water and nutrients under these stress conditions. The integrated genetics and genomics approach to dissect molecular processes from genome to phenome is key to achieve increased water capture and use efficiency through developing better root systems. Success in crop improvement under drought depends on discovery and utilization of genetic variations existing in the germplasm. In this review, we summarize current progress in the genetic ersity in major legume crops, quantitative trait loci (QTLs) associated with RSA, and the importance and applications of recent discoveries associated with the beneficial root traits towards better RSA for enhanced drought tolerance and yield.
Drought and heat stress-related proteins
Publisher: Springer Science and Business Media LLC
Date: 02-04-2019
DOI: 10.1007/S00122-019-03331-2
Abstract: We describe here the recent developments about the involvement of erse stress-related proteins in sensing, signaling, and defending the cells in plants in response to drought or/and heat stress. In the current era of global climate drift, plant growth and productivity are often limited by various environmental stresses, especially drought and heat. Adaptation to abiotic stress is a multigenic process involving maintenance of homeostasis for proper survival under adverse environment. It has been widely observed that a series of proteins respond to heat and drought conditions at both transcriptional and translational levels. The proteins are involved in various signaling events, act as key transcriptional activators and saviors of plants under extreme environments. A detailed insight about the functional aspects of erse stress-responsive proteins may assist in unraveling various stress resilience mechanisms in plants. Furthermore, by identifying the metabolic proteins associated with drought and heat tolerance, tolerant varieties can be produced through transgenic/recombinant technologies. A large number of regulatory and functional stress-associated proteins are reported to participate in response to heat and drought stresses, such as protein kinases, phosphatases, transcription factors, and late embryogenesis abundant proteins, dehydrins, osmotins, and heat shock proteins, which may be similar or unique to stress treatments. Few studies have revealed that cellular response to combined drought and heat stresses is distinctive, compared to their in idual treatments. In this review, we would mainly focus on the new developments about various stress sensors and receptors, transcription factors, chaperones, and stress-associated proteins involved in drought or/and heat stresses, and their possible role in augmenting stress tolerance in crops.
Identification of candidate genome regions controlling disease resistance in Arachis
Publisher: Springer Science and Business Media LLC
Date: 2009
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice
Publisher: Springer Science and Business Media LLC
Date: 24-07-2019
Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops
Publisher: Springer Science and Business Media LLC
Date: 21-04-2021
DOI: 10.1186/S12864-021-07602-5
Abstract: Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana , Oryza sativa (rice), Medicago truncatula , and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC ( Cicer arietinum - 14) , Cc_NAC ( Cajanus cajan - 15) , and Ah_NAC ( Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186 Cc_26125 , Cc_43030 , Cc_43785 , Cc_43786 , Cc_22429 , and Cc_22430 Ah_ann1.G1V3KR.2 , Ah_ann1.MI72XM.2 , Ah_ann1.V0X4SV.1 , Ah_ann1.FU1JML.2 , and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.
Large‐scale analysis of the barley transcriptome based on expressed sequence tags
Publisher: Wiley
Date: 06-09-2004
Genomic interventions for sustainable agriculture
Publisher: Wiley
Date: 22-09-2020
DOI: 10.1111/PBI.13472
Genome wide transcriptome profiling of Fusarium oxysporum f sp. ciceris conidial germination reveals new insights into infection-related genes
Publisher: Springer Science and Business Media LLC
Date: 17-11-2016
DOI: 10.1038/SREP37353
Abstract: Vascular wilt caused by Fusarium oxysporum f. sp. ciceris (Foc ) is a serious disease of chickpea ( Cicer arietinum L.) accounting for approximately 10–15% annual crop loss. The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients. Infection is initiated by conidia that invade the host tissue often by penetration of intact epidermal cells. Here, we report the characterization of the transcriptome of Foc sequenced using Illumina Hiseq technology during its conidial germination at different time points. Genome-wide expression profiling revealed that genes linked to fungal development are transcribed in successive ways. Analysis showed that Foc have large sets of germination-related genes and families of genes encoding secreted effectors, cell wall ectin-degrading enzymes, metabolism related enzymes, transporters and peptidases. We found that metabolism related enzymes are up-regulated at early time point whereas most transporters and secondary metabolites important for tissue colonization and pathogenicity are up-regulated later as evident from the qRT-PCR. The study demonstrated that early conidial germination in Foc is accompanied by rapid shifts in gene expression that prepare the fungus for germ tube outgrowth, host cell invasion and pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.
Introgression of “QTL‐hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars
Publisher: Wiley
Date: 22-01-2021
DOI: 10.1002/TPG2.20076
Abstract: With an aim of enhancing drought tolerance using a marker‐assisted backcrossing (MABC) approach, we introgressed the “ QTL‐hotspot ” region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought‐tolerance related traits into three elite Indian chickpea ( Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92‐3. Of eight simple sequence repeat (SSR) markers in the QTL‐hotspot region, two to three polymorphic markers were used for foreground selection with respective cross‐combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92‐3, respectively. In total, 61 ILs (20 BC 3 F 3 in Pusa 372 20 BC 2 F 3 in Pusa 362, and 21 BC 3 F 3 in DCP 92‐3), with % recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372 BG 3097 and BG 4005 in Pusa 362 IPC(L4‐14), IPC(L4‐16), and IPC(L19‐1) in DCP 92‐3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub‐Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL‐hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.
Using an incomplete block design to allocate lines to environments improves sparse genome‐based prediction in plant breeding
Publisher: Wiley
Date: 16-02-2022
DOI: 10.1002/TPG2.20194
Abstract: Genomic selection (GS) is a predictive methodology that trains statistical machine‐learning models with a reference population that is used to perform genome‐enabled predictions of new lines. In plant breeding, it has the potential to increase the speed and reduce the cost of selection. However, to optimize resources, sparse testing methods have been proposed. A common approach is to guarantee a proportion of nonoverlapping and overlapping lines allocated randomly in locations, that is, lines appearing in some locations but not in all. In this study we propose using incomplete block designs (IBD), principally, for the allocation of lines to locations in such a way that not all lines are observed in all locations. We compare this allocation with a random allocation of lines to locations guaranteeing that the lines are allocated to the same number of locations as under the IBD design. We implemented this benchmarking on several crop data sets under the Bayesian genomic best linear unbiased predictor (GBLUP) model, finding that allocation under the principle of IBD outperformed random allocation by between 1.4% and 26.5% across locations, traits, and data sets in terms of mean square error. Although a wide range of performance improvements were observed, our results provide evidence that using IBD for the allocation of lines to locations can help improve predictive performance compared with random allocation. This has the potential to be applied to large‐scale plant breeding programs.
Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.)
Publisher: Wiley
Date: 12-2020
DOI: 10.1002/TPG2.20071
Abstract: Genetic enhancement for resistance against the pod borer, Helicoverpa armigera is crucial for enhancing production and productivity of chickpea. Here we provide some novel insights into the genetic architecture of natural variation in H. armigera resistance in chickpea, an important legume, which plays a major role in food and nutritional security. An interspecific recombinant inbred line (RIL) population developed from a cross between H. armigera susceptible accession ICC 4958 ( Cicer arietinum ) and resistant accession PI 489777 ( Cicer reticulatum ) was evaluated for H. armigera resistance component traits using detached leaf assay and under field conditions. A high‐throughput Axiom CicerSNP array was utilized to construct a dense linkage map comprising of 3,873 loci and spanning a distance of 949.27 cM. Comprehensive analyses of extensive genotyping and phenotyping data identified nine main‐effect QTLs and 955 epistatic QTLs explaining up to 42.49% and 38.05% phenotypic variance, respectively, for H. armigera resistance component traits. The main‐effect QTLs identified in this RIL population were linked with previously described genes, known to modulate resistance against lepidopteran insects in crop plants. One QTL cluster harbouring main‐effect QTLs for three H. armigera resistance component traits and explaining up to 42.49% of the phenotypic variance, was identified on CaLG03. This genomic region, after validation, may be useful to improve H. armigera resistance component traits in elite chickpea cultivars.
Trait associations in the pangenome of pigeon pea (Cajanus cajan)
Publisher: Wiley
Date: 12-03-2020
DOI: 10.1111/PBI.13354
Public sector soybean (Glycine max) breeding: Advances in cultivar development in the African tropics
Publisher: Wiley
Date: 10-02-2019
DOI: 10.1111/PBR.12682
A novel aphid resistance locus in cowpea identified by combining SSR and SNP markers
Publisher: Wiley
Date: 19-02-2018
DOI: 10.1111/PBR.12563
Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs
Publisher: Public Library of Science (PLoS)
Date: 12-02-2014
Genomic Tools in Groundnut Breeding Program: Status and Perspectives
Publisher: Frontiers Media SA
Date: 17-03-2016
Transcriptome analysis of chickpea during heat stress unveils the signatures of long intergenic non-coding RNAs (lincRNAs) and mRNAs in the heat-QTL region
Publisher: Elsevier BV
Date: 06-2023
New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
Publisher: Frontiers Media SA
Date: 31-03-2017
Genic microsatellite markers in plants: Features and applications
Publisher: Elsevier BV
Date: 2005
DOI: 10.1016/J.TIBTECH.2004.11.005
Abstract: Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional ersity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.
Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys
Publisher: Elsevier BV
Date: 12-2007
NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Publisher: Public Library of Science (PLoS)
Date: 13-10-2015
Single Nucleotide Polymorphisms in HSP17.8 and Their Association with Agronomic Traits in Barley
Publisher: Public Library of Science (PLoS)
Date: 13-02-2013
Genomic resources in plant breeding for sustainable agriculture
Publisher: Elsevier BV
Date: 02-2021
An integrated pipeline of open source software adapted for multi-CPU architectures: Use in the large-scale identification of single nucleotide polymorphisms
Publisher: Hindawi Limited
Date: 2007
DOI: 10.1155/2007/35604
Abstract: The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.
Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation
Publisher: Frontiers Media SA
Date: 14-10-2016
Origin of early maturing pigeonpea germplasm and its impact on adaptation and cropping systems
Publisher: Wiley
Date: 20-03-2019
DOI: 10.1111/PBR.12696
Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion
Publisher: Wiley
Date: 06-11-2013
DOI: 10.1111/PBI.12018
Abstract: The failure of peg penetration into the soil leads to seed abortion in peanut. Knowledge of genes involved in these processes is comparatively deficient. Here, we used RNA-seq to gain insights into transcriptomes of aerial and subterranean pods. More than 2 million transcript reads with an average length of 396 bp were generated from one aerial (AP) and two subterranean (SP1 and SP2) pod libraries using pyrosequencing technology. After assembly, sets of 49 632, 49 952 and 50 494 from a total of 74 974 transcript assembly contigs (TACs) were identified in AP, SP1 and SP2, respectively. A clear linear relationship in the gene expression level was observed between these data sets. In brief, 2194 differentially expressed TACs with a 99.0% true-positive rate were identified, among which 859 and 1068 TACs were up-regulated in aerial and subterranean pods, respectively. Functional analysis showed that putative function based on similarity with proteins catalogued in UniProt and gene ontology term classification could be determined for 59 342 (79.2%) and 42 955 (57.3%) TACs, respectively. A total of 2968 TACs were mapped to 174 KEGG pathways, of which 168 were shared by aerial and subterranean transcriptomes. TACs involved in photosynthesis were significantly up-regulated and enriched in the aerial pod. In addition, two senescence-associated genes were identified as significantly up-regulated in the aerial pod, which potentially contribute to embryo abortion in aerial pods, and in turn, to cessation of swelling. The data set generated in this study provides evidence for some functional genes as robust candidates underlying aerial and subterranean pod development and contributes to an elucidation of the evolutionary implications resulting from fruit development under light and dark conditions.
Phenotyping chickpeas and pigeonpeas for adaptation to drought
Publisher: Frontiers Media SA
Date: 2012
Novel SSR Markers for Polymorphism Detection in Pigeonpea (Cajanus spp.)
Publisher: Wiley
Date: 04-2010
Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project
Publisher: Wiley
Date: 17-04-2018
DOI: 10.1111/PBR.12573
A systematic dissection of the mechanisms underlying the natural variation of silique number in rapeseed (Brassica napus L.) germplasm
Publisher: Wiley
Date: 17-09-2019
DOI: 10.1111/PBI.13224
Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)
Publisher: Frontiers Media SA
Date: 17-02-2015
Genetic variations of HvP5CS1 and their association with drought tolerance related traits in barley (Hordeum vulgare L.)
Publisher: Springer Science and Business Media LLC
Date: 11-08-2017
DOI: 10.1038/S41598-017-08393-0
Abstract: Delta-1-pyrroline-5-carboxylate synthase gene1 ( P5CS1 ) is the key gene involved in the biosynthesis of proline and is significantly induced by drought stress. The exploration of genetic variation in HvP5CS1 may facilitate a better understanding of the mechanism of drought adaptation in barley. In the current study, 41 polymorphisms including 16 single nucleotide polymorphisms (SNPs) and 25 insertions/deletions (indels) were detected in HvP5CS1 among 287 barley ( Hordeum vulgare L.) accessions collected worldwide, with 13 distinct haplotypes identified in the barley collection. Five polymorphisms in HvP5CS1 were significantly ( P 0.001) associated with drought tolerance related traits in barley. The phenotypic variation of a given trait explained by each associated polymorphism ranged from 4.43% to 9.81%. Two sequence variations that were significantly ( P 0.0001) associated with grain yield had marginally significant positive Tajima’s D values in the sliding window, so they might have been selected for environmental adaptation. Meanwhile, two haplotypes HvP5CS1_ H1 and HvP5CS1_ H4, which contained desired alleles of the two variations mentioned above, were significantly ( P 0.001) associated with drought tolerance related traits, and explained 5.00~11.89% of the phenotypic variations. These variations associated with drought tolerance related traits can be used as potential markers for improving drought tolerance in barley.
EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome
Publisher: Springer Science and Business Media LLC
Date: 30-10-2008
DOI: 10.1007/S10142-007-0060-9
Abstract: In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide ersities (pi) ranged from 0 to 40.0 x 10(-3) (average 3.1 x 10(-3)) and 0.52 x 10(-3) to 39.51 x 10(-3) (average 4.37 x 10(-3)) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an licon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved lified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps.
Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding
Publisher: Springer Science and Business Media LLC
Date: 03-07-2020
DOI: 10.1038/S41437-020-0336-6
Abstract: Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For ex le, they have high power and resolution for mapping quantitative trait loci, high genetic ersity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
Shoot traits and their relevance in terminal drought tolerance of chickpea ( Cicer arietinum L.)
Publisher: Elsevier BV
Date: 10-2016
Responses of Aspergillus flavus to Oxidative Stress Are Related to Fungal Development Regulator, Antioxidant Enzyme, and Secondary Metabolite Biosynthetic Gene Expression
Publisher: Frontiers Media SA
Date: 21-12-2016
Genetic Dissection of Novel QTLs for Resistance to Leaf Spots and Tomato Spotted Wilt Virus in Peanut (Arachis hypogaea L.)
Publisher: Frontiers Media SA
Date: 31-01-2017
Genotyping-by-sequencing based genetic mapping reveals large number of epistatic interactions for stem rot resistance in groundnut
Publisher: Springer Science and Business Media LLC
Date: 11-12-2018
DOI: 10.1007/S00122-018-3255-7
Abstract: Genetic mapping identified large number of epistatic interactions indicating the complex genetic architecture for stem rot disease resistance. Groundnut (Arachis hypogaea) is an important global crop commodity and serves as a major source of cooking oil, erse confectionery preparations and livestock feed. Stem rot disease caused by Sclerotium rolfsii is the most devastating disease of groundnut and can cause up to 100% yield loss. Genomic-assisted breeding (GAB) has potential for accelerated development of stem rot resistance varieties in short period with more precision. In this context, linkage analysis and quantitative trait locus (QTL) mapping for resistance to stem rot disease was performed in a bi-parental recombinant inbred line population developed from TG37A (susceptible) × NRCG-CS85 (resistant) comprising of 270 in iduals. Genotyping-by-sequencing approach was deployed to generate single nucleotide polymorphism (SNP) genotyping data leading to development of a genetic map with 585 SNP loci spanning map distance of 2430 cM. QTL analysis using multi-season phenotyping and genotyping data could not detect any major main-effect QTL but identified 44 major epistatic QTLs with phenotypic variation explained ranging from 14.32 to 67.95%. Large number interactions indicate the complexity of genetic architecture of resistance to stem rot disease. A QTL of physical map length 5.2 Mb identified on B04 comprising 170 different genes especially leucine reach repeats, zinc finger motifs and ethyleneresponsive factors, etc., was identified. The identified genomic regions and candidate genes will further validate and facilitate marker development to deploy GAB for developing stem rot disease resistance groundnut varieties.
QTLs for chlorophyll and chlorophyll fluorescence parameters in barley under post-flowering drought
Publisher: Springer Science and Business Media LLC
Date: 11-12-2008
Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications
Publisher: Public Library of Science (PLoS)
Date: 23-01-2014
Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)
Publisher: Public Library of Science (PLoS)
Date: 15-11-2011
Professor Andreas Graner: driven by the quest to unlock crop plant genomes for conservation and utilization of germplasm for breeding
Publisher: Wiley
Date: 07-08-2023
DOI: 10.1111/PBI.14143
Abstract: Professor Andreas Graner stands as a towering figure in international crop plant genomics research, leaving an indelible imprint on the field over the past four decades. As we commemorate the 80th anniversary of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany and Professor Graner's retirement in September 2023, here we celebrate and acknowledge his profound impact on crop genome analyses and genebank genomics. His trailblazing work extends from developing the first integrated RFLP map of barley, establishing the foundation of barley genome sequencing, and advancing functional genomics of malting quality, to pioneering the use of high‐throughput phenomics. As the dedicated custodian of Germany's largest ex situ genebank at IPK Gatersleben, Professor Graner has fortified the institution's collection management and crop research, thereby contributing significantly to global efforts on conservation and utilization of plant genetic resources through genomics approaches. Alongside his impressive array of scientific achievements, Professor Graner's inspiring mentorship has nurtured a new generation of scientists, including us, leaving a lasting legacy in the field. This tribute underscores his enduring influence and celebrates his unwavering dedication to the scientific community.
A decade of Tropical Legumes projects: Development and adoption of improved varieties, creation of market‐demand to benefit smallholder farmers and empowerment of national programmes in sub‐Saharan Af
Publisher: Wiley
Date: 08-2019
DOI: 10.1111/PBR.12744
Nano-enabled stress-smart agriculture
Publisher: Wiley
Date: 18-07-2023
DOI: 10.1002/SAE2.12061
Abstract: Salinity and drought stress substantially decrease crop yield and superiority, directly threatening the food supply needed to meet the rising food needs of the growing total population. Nanotechnology is a step towards improving agricultural output and stress tolerance by improving the efficacy of inputs in agriculture via targeted delivery, controlled release, and enhanced solubility and adhesion while also reducing significant damage. The direct application of nanoparticles (NPs)/nanomaterials can boost the performance and effectiveness of physio‐biochemical and molecular mechanisms in plants under stress conditions, leading to advanced stress tolerance. Therefore, we presented the effects and plant responses to stress conditions, and also explored the potential of nanomaterials for improving agricultural systems, and discussed the advantages of applying NPs at various developmental stages to alleviate the negative effects of salinity and drought stress. Moreover, we feature the recent innovations in state‐of‐the‐art nanobiotechnology, specifically NP‐mediated genome editing via CRISPR/Cas system, to develop stress‐smart crops. However, further investigations are needed to unravel the role of nanobiotechnology in addressing climate change challenges in modern agricultural systems. We propose that combining nanobiotechnology, genome editing and speed breeding techniques could enable the designing of climate‐smart cultivars (particularly bred or genetically modified plant varieties) to meet the food security needs of the rising world population.
Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics
Publisher: Elsevier BV
Date: 12-2013
Systems biology for crop improvement
Publisher: Wiley
Date: 05-05-2021
DOI: 10.1002/TPG2.20098
Abstract: In recent years, generation of large‐scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies—integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
Discovery of genomic regions and candidate genes controlling shelling percentage using QTL ‐seq approach in cultivated peanut (Arachis hypogaea L.)
Publisher: Wiley
Date: 30-01-2019
DOI: 10.1111/PBI.13050
Analytical and Decision Support Tools for Genomics-Assisted Breeding
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.TPLANTS.2015.10.018
Abstract: To successfully implement genomics-assisted breeding (GAB) in crop improvement programs, efficient and effective analytical and decision support tools (ADSTs) are 'must haves' to evaluate and select plants for developing next-generation crops. Here we review the applications and deployment of appropriate ADSTs for GAB, in the context of next-generation sequencing (NGS), an emerging source of massive genomic information. We discuss suitable software tools and pipelines for marker-based approaches (markers/haplotypes), including large-scale genotypic and phenotypic, data management, and molecular breeding approaches. Although phenotyping remains expensive and time consuming, prediction of allelic effects on phenotypes opens new doors to enhance genetic gain across crop cycles, building on reliable phenotyping approaches and good crop information systems, including pedigree information and target haplotypes.
Analyzing Pathways of Nurturing Informal Seed Production into Formal Private Ventures for Sustainable Seed Delivery and Crop Productivity: Experiences from Ethiopia
Publisher: MDPI AG
Date: 22-08-2020
DOI: 10.3390/SU12176828
Abstract: Sustaining crop production and productivity in sub-Saharan Africa requires the availability and use of quality seed of improved varieties by smallholder farmers. The private sector has been considered as the best way to sustain seed supply and crop productivity. Unfortunately, the private sector’s share in the seed production and delivery in sub-Saharan Africa countries has not been very substantial for decades. As a consequence, farmer access to quality seed of recently released varieties remains very low. This manuscript analyzes the experiences of informal seed producers who graduated to formal private seed enterprises to understand the effectiveness of the support they receive to become viable seed ventures. We used comparative research methods to analyze the qualitative and quantitative data collected to understand the underlying mechanisms. The findings showed that the analyzed seed enterprises started with as little as about USD 300 and have already multiplied over tenfold their initial capital. They benefited from a wide variety of supports, e.g., quality seed production, marketing, partnerships, and value chain development trainings and infrastructures, from extension workers, research centers, national and international NGOs, and the other private seed enterprise operators like large public seed enterprises and agro-dealers. The seed enterprises are producing pre-basic, basic, and certified seed of cereals and self-pollinated legume crops delivered directly to farmers, institutional markets, and agro-dealers. The seed production data have been increasing for the past three years with an area expanding from about 30 ha to over 150 ha per year for chickpea. The seed production and delivery practices being employed are smallholder farmer-based practices that are environmentally friendly. For sustainable and reliable seed production and delivery systems in sub-Saharan Africa, a bold step is needed whereby the informal seed production entities are nurtured and upgraded into formal certified seed production ventures that deliver social and economic benefits to the promotors and the communities.
Genomic regions associated with resistance to peanut bud necrosis disease (PBND) in a recombinant inbred line (RIL) population
Publisher: Wiley
Date: 18-09-2019
DOI: 10.1111/PBR.12743
Generation and exploitation of EST-derived SSR markers for assaying molecular diversity in durum wheat populations
Publisher: Springer Science and Business Media LLC
Date: 04-12-2008
Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops
Publisher: Springer Science and Business Media LLC
Date: 10-03-2022
DOI: 10.1007/S00122-022-04060-9
Abstract: Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of erse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops.
Discovery of Major Quantitative Trait Loci and Candidate Genes for Fresh Seed Dormancy in Groundnut
Publisher: MDPI AG
Date: 06-02-2022
Abstract: Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) h ering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter time with greater precision. In this regard, a recombinant inbred line (RIL) population from the cross ICGV 02266 (non-dormant) × ICGV 97045 (dormant) was developed and genotyped with a 5 K mid-density genotyping assay. A linkage map was constructed with 325 SNP loci spanning a total map length of 2335.3 cM and five major QTLs were identified on chromosomes Ah01, Ah11, Ah06, Ah16 and Ah17. Based on differential gene expression using transcriptomic information from dormant (Tifrunner) and non-dormant (ICGV 91114) genotypes, histone deacetylases, histone-lysine N-methyltransferase, cytochrome P450, protein kinases, and ethylene-responsive transcription factor were identified as key regulators involved in the hormonal regulation of dormancy. Six Kompetitive Allele Specific PCR (KASP) markers were successfully validated in the erse panel including selected RILs of the same population and germplasm lines. These validated KASP markers could facilitate faster breeding of new varieties with desired dormancy using marker-assisted early generation selection.
Multiple post‐domestication origins of kabuli chickpea through allelic variation in a diversification‐associated transcription factor
Publisher: Wiley
Date: 19-05-2016
DOI: 10.1111/NPH.14010
Abstract: Chickpea ( Cicer arietinum ) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so‐called kabuli type, has white flowers and light‐colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms ( SNP s) and examined patterns of molecular ersity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic ersity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix–loop–helix ( bHLH ) transcription factor at chickpea's B locus that conditions flower and seed colors, orthologous to Mendel's A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic ersification after initial domestication of cultivated chickpea.
Marker‐Assisted Backcrossing to Introgress Resistance to Fusarium Wilt Race 1 and Ascochyta Blight in C 214, an Elite Cultivar of Chickpea
Publisher: Wiley
Date: 03-2014
Genetics of Fertility Restoration in A4‐Based, Diverse Maturing Hybrids of Pigeonpea [Cajanus cajan (L.) Millsp.]
Publisher: Wiley
Date: 03-2011
Molecular Genetic Diversity and Population Structure in Ethiopian Chickpea Germplasm Accessions
Publisher: MDPI AG
Date: 04-06-2021
DOI: 10.3390/D13060247
Abstract: Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic ersity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from erse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among in iduals, within populations, and among populations. The insights into the genetic ersity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the erse germplasm lines identified in this study can be used for trait dissection and trait improvement.
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
Publisher: Springer Science and Business Media LLC
Date: 17-08-2006
Legume Genomics and Breeding
Publisher: Wiley
Date: 22-03-2010
Genomics-assisted breeding for crop improvement
Publisher: Elsevier BV
Date: 12-2005
DOI: 10.1016/J.TPLANTS.2005.10.004
Abstract: Genomics research is generating new tools, such as functional molecular markers and informatics, as well as new knowledge about statistics and inheritance phenomena that could increase the efficiency and precision of crop improvement. In particular, the elucidation of the fundamental mechanisms of heterosis and epigenetics, and their manipulation, has great potential. Eventually, knowledge of the relative values of alleles at all loci segregating in a population could allow the breeder to design a genotype in silico and to practice whole genome selection. High costs currently limit the implementation of genomics-assisted crop improvement, particularly for inbreeding and/or minor crops. Nevertheless, marker-assisted breeding and selection will gradually evolve into 'genomics-assisted breeding' for crop improvement.
A SWEET solution to rice blight
Publisher: Springer Science and Business Media LLC
Date: 28-04-2026
Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)
Publisher: Oxford University Press (OUP)
Date: 12-05-2011
Molecular Mapping of Oil Content and Fatty Acids Using Dense Genetic Maps in Groundnut (Arachis hypogaea L.)
Publisher: Frontiers Media SA
Date: 22-05-2017
Technological perspectives for plant breeding
Publisher: Springer Science and Business Media LLC
Date: 03-2019
Cereal Genomics II
Publisher: Springer Netherlands
Date: 2013
The Chickpea Genome: An Introduction
Publisher: Springer International Publishing
Date: 2017
Toward the sequence-based breeding in legumes in the post-genome sequencing era
Publisher: Springer Science and Business Media LLC
Date: 17-12-2018
An Open-label Randomized Controlled Trial to Compare Weight Gain of Very Low Birth Weight Babies with or without Addition of Coconut Oil to Breast Milk
Publisher: Oxford University Press (OUP)
Date: 23-03-2018
Abstract: Nutritional guidelines involving the feeding of very low birth weight babies (VLBW) recommend addition of Human Milk Fortifiers to breast milk. Owing to financial constraints, it is a practice in low- and middle-income countries (LMIC) to add coconut oil to aid better weight gain. There are inadequate data on improvement of growth parameters with oral coconut oil supplementation of breast milk. In this randomized controlled trial, we measured growth parameters and body composition of 60 babies who received either breast milk with coconut oil or breast milk alone. Randomization was stratified according to intrauterine growth appropriate for gestational age (n = 30) and small for gestational age (n = 30). There was no difference in weight gain between the two groups. The weight gain velocity was 15 ± 3.6 and 14.4 ± 3.4 g/kg/day (p value = 0.49) in the breast milk alone and in the breast milk with coconut oil group, respectively. There was no difference in increase in head circumference and length. Triceps skinfold thickness (n = 56) was similar in both groups, but subscapular skinfold thickness was significantly more in the coconut oil group. Total body fat percentage did not differ between the groups (25.2 ± 4.3 vs. 25.5 ± 4.3%, p = 0.79). Oral supplementation of coconut oil along with breast milk did not increase growth parameters or result in change in body composition in very low birth weight (VLBW) babies.
Single cell RNA-seq in phytohormone signaling: a promising future
Publisher: Elsevier BV
Date: 11-2023
Root traits confer grain yield advantages under terminal drought in chickpea ( Cicer arietinum L.)
Publisher: Elsevier BV
Date: 02-2017
Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea
Publisher: Springer Science and Business Media LLC
Date: 25-10-2014
Novel genes and genetic loci associated with root morphological traits, phosphorus-acquisition efficiency and phosphorus-use efficiency in chickpea
Publisher: Frontiers Media SA
Date: 28-05-2021
Abstract: Chickpea—the second most important grain legume worldwide—is cultivated mainly on marginal soils. Phosphorus (P) deficiency often restricts chickpea yields. Understanding the genetics of traits encoding P-acquisition efficiency and P-use efficiency will help develop strategies to reduce P-fertilizer application. A genome-wide association mapping approach was used to determine loci and genes associated with root architecture, root traits associated with P-acquisition efficiency and P-use efficiency, and any associated proxy traits. Using three statistical models—a generalized linear model (GLM), a mixed linear model (MLM), and a fixed and random model circulating probability unification (FarmCPU) —10, 51, and 40 marker-trait associations (MTAs), respectively were identified. A single nucleotide polymorphism (SNP) locus (Ca1_12310101) on Ca1 associated with three traits, i.e., physiological P-use efficiency, shoot dry weight, and shoot P content was identified. Genes related to shoot P concentration (NAD kinase 2, dynamin-related protein 1C), physiological P-use efficiency (fasciclin-like arabinogalactan protein), specific root length (4-coumarate–CoA ligase 1) and manganese concentration in mature leaves (ABC1 family protein) were identified. The MTAs and novel genes identified in this study can be used to improve P-use efficiency in chickpea.
Can skin temperature replace rectal temperature monitoring in babies undergoing therapeutic hypothermia in low‐resource settings?
Publisher: Wiley
Date: 08-10-2012
DOI: 10.1111/APA.12010
Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense
Publisher: Springer Science and Business Media LLC
Date: 28-09-2008
Abstract: Hordeum chilense , a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited direct agricultural use in a search for suitable and cost-effective markers. The availability of Expressed Sequence Tags (EST) derived microsatellites or simple sequence repeat (SSR) markers, commonly called as EST-SSRs, for barley ( Hordeum vulgare ) represents a promising source to increase the number of genetic markers available for the H. chilense genome. All of the 82 barley EST-derived SSR primer pairs tested for transferability to H. chilense lified products of correct size from this species. Of these 82 barley EST-SSRs, 21 (26%) showed polymorphism among H. chilense lines. Identified polymorphic markers were used to test the transferability and polymorphism in other Poaceae family species with the aim of establishing H. chilense phylogenetic relationships. Triticum aestivum - H. chilense addition lines allowed us to determine the chromosomal localizations of EST-SSR markers and confirm conservation of the linkage group. From the present study a set of 21 polymorphic EST-SSR markers have been identified to be useful for ersity analysis of H. chilense , related wild barleys like H. murinum , and for wheat marker-assisted introgression breeding. Across-genera transferability of the barley EST-SSR markers has allowed phylogenetic inference within the Triticeae complex.
Prioritization of candidate genes in QTL-hotspot region for drought tolerance in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 19-10-2015
DOI: 10.1038/SREP15296
Abstract: A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “ QTL-hotspot ” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “ QTL-hotspot ” region into two subregions namely “ QTL-hotspot_a ” (15 genes) and “ QTL-hotspot_b ” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data and the candidate genes from the refined “ QTL-hotspot ” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “ QTL-hotspot ” for drought tolerance in chickpea.
Identification and characterization of expressed sequence tags‐derived simple sequence repeats markers from robusta coffee variety ‘CxR’ (an interspecific hybrid of Coffea canephora × Coffea
Publisher: Wiley
Date: 13-12-2004
Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity
Publisher: MDPI AG
Date: 05-02-2022
Abstract: Salinity is increasingly becoming a significant problem for the most important yet intrinsically salt-sensitive grain legume chickpea. Chickpea is extremely sensitive to salinity during the reproductive phase. Therefore, it is essential to understand the molecular mechanisms by comparing the transcriptomic dynamics between the two contrasting genotypes in response to salt stress. Chickpea exhibits considerable genetic variation amongst improved cultivars, which show better yields in saline conditions but still need to be enhanced for sustainable crop production. Based on previous extensive multi-location physiological screening, two identified genotypes, JG11 (salt-tolerant) and ICCV2 (salt-sensitive), were subjected to salt stress to evaluate their phenological and transcriptional responses. RNA-Sequencing is a revolutionary tool that allows for comprehensive transcriptome profiling to identify genes and alleles associated with stress tolerance and sensitivity. After the first flowering, the whole flower from stress-tolerant and sensitive genotypes was collected. A total of ~300 million RNA-Seq reads were sequenced, resulting in 2022 differentially expressed genes (DEGs) in response to salt stress. Genes involved in flowering time such as FLOWERING LOCUS T (FT) and pollen development such as ABORTED MICROSPORES (AMS), rho-GTPase, and pollen-receptor kinase were significantly differentially regulated, suggesting their role in salt tolerance. In addition to this, we identify a suite of essential genes such as MYB proteins, MADS-box, and chloride ion channel genes, which are crucial regulators of transcriptional responses to salinity tolerance. The gene set enrichment analysis and functional annotation of these genes in flower development suggest that they can be potential candidates for chickpea crop improvement for salt tolerance.
Molecular genetics and genomics of abiotic stress responses
Publisher: Frontiers Media SA
Date: 21-08-2014
Application of Genomics to Molecular Breeding of Wheat and Barley
Publisher: Elsevier
Date: 2007
Advances in cereal genomics and applications in crop breeding
Publisher: Elsevier BV
Date: 11-2006
DOI: 10.1016/J.TIBTECH.2006.08.006
Abstract: Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.
Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 15-02-2015
DOI: 10.1007/S10681-015-1394-3
Abstract: The paucity of sequence information flanking the simple sequence repeat (SSR) motifs identified especially in the transcript sequences has been limiting factor in the development of SSR markers for plant genome analysis as well as breeding applications. To overcome this and enhance the genic SSR marker repertoire in chickpea, the draft genome sequence of kabuli chickpea (CDC Frontier) and publicly available transcript sequences consisting of in silico identified SSR motifs were deployed in the present study. In this direction, the 300 bp sequence flanking the SSR motifs were retrieved by aligning 566 SSR containing transcripts of ICCV 2 available in public domain on the reference chickpea genome. A set of 202 novel genic SSRs were developed from a set of 507 primer pairs designed, based on in silico lification of single locus and having no similarity to the publicly available SSR markers. Further, 40 genic SSRs equally distributed on chickpea genome were validated on a select set of 44 chickpea genotypes (including 41 Cicer arietinum and 3 Cicer reticulatum ), out of which 25 were reported to be polymorphic. The polymorphism information content (PIC) value of 25 polymorphic genic SSRs ranged from 0.11 to 0.77 and number of alleles varied from 2 to 9. Clear demarcation among founder lines of multi-parent advanced generation inter-cross (MAGIC) population developed at ICRISAT and near-isogenic nature of JG 11 and JG11 + demonstrates the usefulness of these markers in chickpea ersity analysis and breeding studies. Further, genic polymorphic SSRs reported between parental lines of 16 different mapping populations along with the novel SSRs can be deployed for trait mapping and breeding applications in chickpea.
Improving oil quality by altering levels of fatty acids through marker-assisted selection of ahfad2 alleles in peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 20-08-2018
Milletdb: a multi‐omics database to accelerate the research of functional genomics and molecular breeding of millets
Publisher: Wiley
Date: 02-08-2023
DOI: 10.1111/PBI.14136
Abstract: Millets are a class of nutrient‐rich coarse cereals with high resistance to abiotic stress thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress‐related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi‐omics analysis for millets, which seriously hinders the mining of stress‐related genes and the molecular breeding of millets. Here, a free, web‐accessible, user‐friendly millets multi‐omics database platform (Milletdb, milletdb.novogene.com ) has been developed. The Milletdb contains six millets and their one related species genomes, graph‐based pan‐genomics of pearl millet, and stress‐related multi‐omics data, which enable Milletdb to be the most complete millets multi‐omics database available. We stored GWAS (genome‐wide association study) results of 20 yield‐related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress‐related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., ‘Gene mapping’, ‘Co‐expression’, ‘KEGG/GO Enrichment’ analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through ‘GWAS’, which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress‐related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance
Publisher: Frontiers Media SA
Date: 04-10-2017
Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects
Publisher: Frontiers Media SA
Date: 02-05-2016
Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement
Publisher: Frontiers Media SA
Date: 24-12-2015
Gene Expression and Yeast Two-Hybrid Studies of 1R-MYB Transcription Factor Mediating Drought Stress Response in Chickpea (Cicer arietinum L.)
Publisher: Frontiers Media SA
Date: 24-12-2015
Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)
Publisher: Springer Science and Business Media LLC
Date: 14-06-2014
Comparison of Two Low-cost Methods of Cooling Neonates with Hypoxic Ischemic Encephalopathy
Publisher: Oxford University Press (OUP)
Date: 06-10-2016
Abstract: Several low-cost methods are used in resource-limited settings to provide therapeutic hypothermia in asphyxiated neonates. There is inadequate data about their efficacy and safety. This is a retrospective study comparing two low-cost cooling methods-frozen gel packs (FGP) and phase changing material (PCM). There were 23 babies in FGP and 45 babies in the PCM group. Induction time was significantly shorter with FGP than PCM (45 vs. 90 minutes p -value < 0.001). Proportion of temperature readings outside the target range was significantly higher (9.8% vs. 3.8% p -value < 0.001) and fluctuation of core body temperature was wider (standard deviation of target temperature 0.4 °C vs. 0.28 °C) in the FGP group, compared with PCM group. Both FGP and PCM are effective and safe, comparable with standard servo-controlled cooling equipment. PCM has the advantage of better maintenance of target temperature with less nursing input, when compared with FGP.
Invigorating Hydrological Research Through Journal Publications
Publisher: American Geophysical Union (AGU)
Date: 06-2020
DOI: 10.1029/2018WR024053
Comparative Root Transcriptomics Provide Insights into Drought Adaptation Strategies in Chickpea (Cicer arietinum L.)
Publisher: MDPI AG
Date: 05-03-2020
DOI: 10.3390/IJMS21051781
Abstract: Drought adversely affects crop production across the globe. The root system immensely contributes to water management and the adaptability of plants to drought stress. In this study, drought-induced phenotypic and transcriptomic responses of two contrasting chickpea (Cicer arietinum L.) genotypes were compared at the vegetative, reproductive transition, and reproductive stages. At the vegetative stage, drought-tolerant genotype maintained higher root biomass, length, and surface area under drought stress as compared to sensitive genotype. However, at the reproductive stage, root length and surface area of tolerant genotype was lower but displayed higher root diameter than sensitive genotype. The shoot biomass of tolerant genotype was overall higher than the sensitive genotype under drought stress. RNA-seq analysis identified genotype- and developmental-stage specific differentially expressed genes (DEGs) in response to drought stress. At the vegetative stage, a total of 2161 and 1873 DEGs, and at reproductive stage 4109 and 3772 DEGs, were identified in the tolerant and sensitive genotypes, respectively. Gene ontology (GO) analysis revealed enrichment of biological categories related to cellular process, metabolic process, response to stimulus, response to abiotic stress, and response to hormones. Interestingly, the expression of stress-responsive transcription factors, kinases, ROS signaling and scavenging, transporters, root nodulation, and oxylipin biosynthesis genes were robustly upregulated in the tolerant genotype, possibly contributing to drought adaptation. Furthermore, activation/repression of hormone signaling and biosynthesis genes was observed. Overall, this study sheds new insights on drought tolerance mechanisms operating in roots with broader implications for chickpea improvement.
Identification of a microsatellite on chromosomes 6B and a STS on 7D of bread wheat showing an association with preharvest sprouting tolerance
Publisher: Springer Science and Business Media LLC
Date: 07-1999
A microsatellite marker associated with a QTL for grain protein content on chromosome arm 2DL of bread wheat
Publisher: Springer Science and Business Media LLC
Date: 07-1999
Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance
Publisher: MDPI AG
Date: 03-2020
Abstract: Aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) are the most common aflatoxins produced by Aspergillus flavus in peanuts, with high carcinogenicity and teratogenicity. Identification of DNA markers associated with resistance to aflatoxin production is likely to offer breeders efficient tools to develop resistant cultivars through molecular breeding. In this study, seeds of 99 accessions of a Chinese peanut mini-mini core collection were investigated for their reaction to aflatoxin production by a laboratory kernel inoculation assay. Two resistant accessions (Zh.h0551 and Zh.h2150) were identified, with their aflatoxin content being 8.11%–18.90% of the susceptible control. The 99 peanut accessions were also genotyped by restriction site-associated DNA sequencing (RAD-Seq) for a genome-wide association study (GWAS). A total of 60 SNP (single nucleotide polymorphism) markers associated with aflatoxin production were detected, and they explained 16.87%–31.70% of phenotypic variation (PVE), with SNP02686 and SNP19994 possessing 31.70% and 28.91% PVE, respectively. Aflatoxin contents of accessions with “AG” (existed in Zh.h0551 and Zh.h2150) and “GG” genotypes of either SNP19994 or SNP02686 were significantly lower than that of “AA” genotypes in the mean value of a three-year assay. The resistant accessions and molecular markers identified in this study are likely to be helpful for deployment in aflatoxin resistance breeding in peanuts.
Genome-Enabled Prediction Models for Yield Related Traits in Chickpea
Publisher: Frontiers Media SA
Date: 22-11-2016
Enhancing oleic acid content in two commercially released peanut varieties through marker‐assisted backcross breeding
Publisher: Wiley
Date: 14-06-2021
DOI: 10.1002/CSC2.20512
Abstract: Two elite cultivars of peanut ( Arachis hypogaea L.), GPBD 4 and G 2–52, with high productivity, oil content, resistance to late leaf spot [ Phaeoisariopsis personata (Berk. & Curt) V. Arx.] (LLS) and rust ( Puccinia arachidis Speg.) diseases were improved for oleic acid content using marker‐assisted backcrossing. Since both the recurrent parents already possessed the mutant allele at AhFAD2A , only mutant allele at AhFAD2B was transferred from the donor ‘SunOleic 95R’ (oleate of 80.6%). Three rounds of backcrossing with foreground selection using allele‐specific polymerase chain reaction (PCR) and Kompetitive allele‐specific PCR (KASP) assay identified a large number of plants homozygous for the mutant allele at AhFAD2B in BC n F 2 generations. Evaluation of the advanced generations could identify six and 10 lines with significantly higher oleate than GPBD 4 and G 2–52, respectively. Considering the yield, shelling percentage, oil, and oleate content, the most promising lines HOBC 2 GPS_7 and HOBC 2 G2S_5 were selected with 112 and 142% oleate recovery over GPBD 4 and G 2–52, respectively. Double digest restriction‐site‐associated DNA sequencing of these superior lines showed background genome recovery of 77.5 and 69.0%, respectively. These advanced breeding lines with high oleate (∼80%), resistance to LLS and rust and high productivity are under further trials for possible release as varieties for commercial cultivation.
Development and implementation of high-throughput SNP genotyping in barley
Publisher: Springer Science and Business Media LLC
Date: 2009
A comparative assessment of the utility of PCR-based marker systems in pearl millet
Publisher: Springer Science and Business Media LLC
Date: 23-02-2010
QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 12-01-2022
DOI: 10.1038/S41437-021-00486-X
Abstract: To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F 2 ) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five s les, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.
Next‐generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.)
Publisher: Wiley
Date: 31-05-2019
DOI: 10.1111/PBI.13153
Unraveling candidate genomic regions responsible for delayed leaf senescence in rice
Publisher: Public Library of Science (PLoS)
Date: 15-10-2020
Genetics, genomics and breeding of groundnut (Arachis hypogaea L.)
Publisher: Wiley
Date: 29-08-2018
DOI: 10.1111/PBR.12645
Assessing variability for disease resistance and nutritional quality traits in an interspecific collection of groundnut (Arachis hypogaea)
Publisher: Wiley
Date: 24-09-2018
DOI: 10.1111/PBR.12647
Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time
Publisher: Cold Spring Harbor Laboratory
Date: 03-01-2019
DOI: 10.1101/511170
Abstract: The primary and secondary metabolites of fungi are critical for adaptation to environmental stresses, host pathogenicity, competition with other microbes, and reproductive fitness. Drought-derived reactive oxygen species (ROS) have been shown to stimulate aflatoxin production and regulate development in Aspergillus flavus , and may function in signaling with host plants. Here, we have performed global, untargeted metabolomics to better understand the role of aflatoxin production in oxidative stress responses, and also explore isolate-specific oxidative stress responses over time. Two field isolates of A. flavus , AF13 and NRRL3357, possessing high and moderate aflatoxin production, respectively, were cultured in medium with and without supplementation with 15mM H 2 O 2 , and mycelia were collected following 4 and 7 days in culture for global metabolomics. Overall, 389 compounds were described in the analysis which were examined for differential accumulation. Significant differences were observed in both isolates in response to oxidative stress and when comparing s ling time points. The moderate aflatoxin-producing isolate, NRRL3357, showed extensive stimulation of antioxidant mechanisms and pathways including polyamines metabolism, glutathione metabolism, TCA cycle, and lipid metabolism while the highly aflatoxigenic isolate, AF13, showed a less vigorous response to stress. Carbohydrate pathway levels also imply that carbohydrate repression and starvation may influence metabolite accumulation at the later timepoint. Higher conidial oxidative stress tolerance and antioxidant capacity in AF13 compared to NRRL3357, inferred from their metabolomic profiles and growth curves over time, may be connected to aflatoxin production capability and aflatoxin-related antioxidant accumulation. The coincidence of several of the detected metabolites in H 2 O 2 -stressed A. flavus and drought-stressed hosts suggests their potential role in the interaction between these organisms and their use as markers/targets to enhance host resistance through biomarker selection or genetic engineering. Aspergillus flavus is a fungal pathogen of several important crops including maize and peanut. This pathogen produces carcinogenic mycotoxins known as aflatoxins during infection of plant materials, and is particularly severe under drought stress conditions. This results in significant losses in crop value and poses a threat to food safety and security globally. To combat this, understanding how this fungus responds to environmental stresses related to drought can allow us to identify novel methods of mitigating aflatoxin contamination. Here, we analyzed the accumulation of a broad series of metabolites over time in two isolates of A. flavus with differing stress tolerance and aflatoxin production capabilities in response to drought-related oxidative stress. We identified several metabolites and mechanisms in A. flavus which allow it to cope with environmental oxidative stress and may influence aflatoxin production and fungal growth. These may serve as potential targets for selection in breeding programs for the development of new cultivars, or for alteration using genetic engineering approaches to mitigate excessive aflatoxin contamination under drought stress.
Integrated breeding approaches for improving drought and heat adaptation in chickpea (Cicer arietinum L.)
Publisher: Wiley
Date: 19-09-2018
DOI: 10.1111/PBR.12641
Quantitative genetics and plant genomics: An overview
Publisher: Springer Science and Business Media LLC
Date: 30-05-2010
Plant breeding for increased sustainability: challenges, opportunities and progress
Publisher: Springer Science and Business Media LLC
Date: 11-2022
Legume Genomics: From Genomic Resources to Molecular Breeding
Publisher: Wiley
Date: 11-2013
Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics
Publisher: Oxford University Press (OUP)
Date: 28-03-2017
Reply to: Evaluating two different models of peanut’s origin
Publisher: Springer Science and Business Media LLC
Date: 11-05-2020
The INCREASE project: Intelligent Collections of food‐legume genetic resources for European agrofood systems
Publisher: Wiley
Date: 23-09-2021
DOI: 10.1111/TPJ.15472
Abstract: Food legumes are crucial for all agriculture‐related societal challenges, including climate change mitigation, agrobio ersity conservation, sustainable agriculture, food security and human health. The transition to plant‐based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co‐benefits for human health. The characterization, maintenance and exploitation of food‐legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea ( Cicer arietinum ), common bean ( Phaseolus vulgaris ), lentil ( Lens culinaris ) and lupin ( Lupinus albus and L. mutabilis ), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections , consisting of nested core collections composed of single‐seed descent‐purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on‐farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri‐food and non‐food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
Evaluation and Identification of Stable Chickpea Lines for Yield-Contributing Traits from an Association Mapping Panel
Publisher: MDPI AG
Date: 08-12-2022
Abstract: An association mapping panel consisting of 380 genotypes of chickpea was evaluated for three different years, including 2014–2015, 2015–2016 and 2016–2017, for yield-contributing parameters, including the seed number and seed weight. The AMMI analysis presented mainly concentrated on the seed weight and seed number, which are the two most important yield-contributing traits. The genotypes contributed 93.08% of the total variance, while the interaction effect was comparatively low, with 4.1% for the two traits. AMMI biplot analysis identified IG5986, IG5982, ILC6025 and ICCV14307 as desirable genotypes for the seed weight and IG5893, ILC6891 and IG5856 for the seed number. Identifying stable genotypes would help in strategic planning for yield improvement through component trait breeding.
Assessment and comparison of AFLP and SSR based molecular genetic diversity in Indian isolates of Ascochyta rabiei, a causal agent of Ascochyta blight in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 16-01-2009
Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut
Publisher: MDPI AG
Date: 26-04-2021
DOI: 10.3390/IJMS22094491
Abstract: Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut.
Large‐scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi‐arid tropics of Asia and Africa
Publisher: Wiley
Date: 25-05-2011
Advances in Chickpea Genomic Resources for Accelerating the Crop Improvement
Publisher: Springer International Publishing
Date: 2017
Global Action on Biodiversity May Hinge on Genetic Data Sharing Agreement
Publisher: Wiley
Date: 12-2022
Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley
Publisher: Springer Science and Business Media LLC
Date: 28-12-2008
Groundnut improvement: use of genetic and genomic tools
Publisher: Frontiers Media SA
Date: 2013
Pigeonpea improvement: An amalgam of breeding and genomic research
Publisher: Wiley
Date: 18-11-2018
DOI: 10.1111/PBR.12656
Requirement of Whole-Genome Sequencing and Background History of the National and International Genome Initiatives
Publisher: Springer International Publishing
Date: 2017
Use of immature seed germination and single seed descent for rapid genetic gains in pigeonpea
Publisher: Wiley
Date: 09-10-2017
DOI: 10.1111/PBR.12538
Fast‐Track Introgression of “QTL‐hotspot” for Root Traits and Other Drought Tolerance Traits in JG 11, an Elite and Leading Variety of Chickpea
Publisher: Wiley
Date: 11-2013
Genome-wide analysis and identification of genes related to potassium transporter families in rice (Oryza sativa L.)
Publisher: Elsevier BV
Date: 04-2007
Whole‐genome resequencing‐based QTL ‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut
Publisher: Wiley
Date: 20-10-2019
DOI: 10.1111/PBI.13266
Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea
Publisher: Springer Science and Business Media LLC
Date: 15-05-2017
DOI: 10.1038/S41598-017-01537-2
Abstract: Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F 2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F 2 , respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining % phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs ( qFW11 . 1 , qFW11 . 2 and qFW11 . 3 ) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.
Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea.
Publisher: Wiley
Date: 12-2018
DOI: 10.1111/PBI.13026
Super Annigeri 1 and improved JG 74: two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 28-12-2018
Genomics, trait mapping and molecular breeding in pigeonpea and chickpea
Publisher: The Indian Society of Genetics and Plant Breeding
Date: 2016
Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)
Publisher: Springer Science and Business Media LLC
Date: 26-09-2018
DOI: 10.1038/S41598-018-32674-X
Abstract: Napiergrass ( Cenchrus purpureus Schumach) is a tropical forage grass and a promising lignocellulosic biofuel feedstock due to its high biomass yield, persistence, and nutritive value. However, its utilization for breeding has lagged behind other crops due to limited genetic and genomic resources. In this study, next-generation sequencing was first used to survey the genome of napiergrass. Napiergrass sequences displayed high synteny to the pearl millet genome and showed expansions in the pearl millet genome along with genomic rearrangements between the two genomes. An average repeat content of 27.5% was observed in napiergrass including 5,339 simple sequence repeats (SSRs). Furthermore, to construct a high-density genetic map of napiergrass, genotyping-by-sequencing (GBS) was employed in a bi-parental population of 185 F 1 hybrids. A total of 512 million high quality reads were generated and 287,093 SNPs were called by using multiple de-novo and reference-based SNP callers. Single dose SNPs were used to construct the first high-density linkage map that resulted in 1,913 SNPs mapped to 14 linkage groups, spanning a length of 1,410 cM and a density of 1 marker per 0.73 cM. This map can be used for many further genetic and genomic studies in napiergrass and related species.
Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome
Publisher: Springer Science and Business Media LLC
Date: 06-2006
DOI: 10.1007/S00122-006-0289-Z
Abstract: A set of 111,090 barley expressed sequence tags (ESTs) was searched for the presence of microsatellite motifs [simple sequence repeat (SSRs)] and yielded 2,823 non-redundant SSR-containing ESTs (SSR-ESTs). From this, a set of 754 primer pairs was designed of which 525 primer pairs yielded an licon and as a result, 185 EST-derived microsatellite loci (EST-SSRs) were placed onto a genetic map of barley. The markers show a uniform distribution along all seven linkage groups ranging from 21 (7H) to 35 (3H) markers. Polymorphism information content values ranged from of 0.24 to 0.78 (average 0.48). To further investigate the physical distribution of the EST-SSRs in the barley genome, a bacterial artificial chromosomes (BAC) library was screened. Out of 129 markers tested, BAC addresses were obtained for 127 EST-SSR markers. Twenty-seven BACs, forming eight contigs, were hit by two or three EST-SSRs each. This unexpectedly high incidence of EST-SSRs physically linked at the sub-megabase level provides additional evidence of an uneven distribution of genes and the segmentation of the barley genome in gene-rich and gene-poor regions.
Molecular and morphological diversity in Rhizoctonia bataticola isolates causing dry root rot of chickpea (Cicer arietinum L.) in India
Publisher: Academic Journals
Date: 08-05-2012
DOI: 10.5897/AJB11.3657
Digitally-enabled, patient-centred care in rhinitis and asthma multimorbidity: The ARIA-MASK-air® approach
Publisher: Wiley
Date: 2023
DOI: 10.1002/CLT2.12215
Abstract: MASK‐air ® , a validated mHealth app (Medical Device regulation Class IIa) has enabled large observational implementation studies in over 58,000 people with allergic rhinitis and/or asthma. It can help to address unmet patient needs in rhinitis and asthma care. MASK‐air ® is a Good Practice of DG Santé on digitally‐enabled, patient‐centred care. It is also a candidate Good Practice of OECD (Organisation for Economic Co‐operation and Development). MASK‐air ® data has enabled novel phenotype discovery and characterisation, as well as novel insights into the management of allergic rhinitis. MASK‐air ® data show that most rhinitis patients (i) are not adherent and do not follow guidelines, (ii) use as‐needed treatment, (iii) do not take medication when they are well, (iv) increase their treatment based on symptoms and (v) do not use the recommended treatment. The data also show that control (symptoms, work productivity, educational performance) is not always improved by medications. A combined symptom‐medication score (ARIA‐EAACI‐CSMS) has been validated for clinical practice and trials. The implications of the novel MASK‐air ® results should lead to change management in rhinitis and asthma.
Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 08-03-2011
Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut
Publisher: Springer Science and Business Media LLC
Date: 16-01-2017
DOI: 10.1038/SREP40577
Abstract: Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array ‘Axiom _Arachis ’ with 58 K SNPs and its utility in groundnut genetic ersity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts ( Arachis hypogaea ), fair representation was kept for other diploids ( A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi ). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic ersity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array ‘Axiom _Arachis ’ with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.
Progress in understanding drought tolerance: from alleles to cropping systems
Publisher: Oxford University Press (OUP)
Date: 06-06-2018
DOI: 10.1093/JXB/ERY187
Adrenaline is effective in reversing the inadequate heart rate response in atropine treated organophosphorus and carbamate poisoning
Publisher: Informa UK Limited
Date: 02-11-2020
Marker-trait association study for protein content in chickpea (Cicer arietinum L.)
Publisher: Springer Science and Business Media LLC
Date: 06-2015
DOI: 10.1007/S12041-015-0529-6
Abstract: Chickpea (Cicer arietinum L.) is the second most important cool season food legume cultivated in arid and semiarid regions of the world. The objective of the present study was to study variation for protein content in chickpea germplasm, and to find markers associated with it. A set of 187 genotypes comprising both international and exotic collections, and representing both desi and kabuli types with protein content ranging from 13.25% to 26.77% was used. Twenty-three SSR markers representing all eight linkage groups (LG) lifying 153 loci were used for the analysis. Population structure analysis identified three subpopulations, and corresponding Q values of principal components were used to take care of population structure in the analysis which was performed using general linear and mixed linear models. Marker-trait association (MTA) analysis identified nine significant associations representing four QTLs in the entire population. Subpopulation analyses identified ten significant MTAs representing five QTLs, four of which were common with that of the entire population. Two most significant QTLs linked with markers TR26.205 and CaM1068.195 were present on LG3 and LG5. Gene ontology search identified 29 candidate genes in the region of significant MTAs on LG3. The present study will be helpful in concentrating on LG3 and LG5 for identification of closely linked markers for protein content in chickpea and for their use in molecular breeding programme for nutritional quality improvement.
Related Organisations
Institute Of Plant Genetics And Crop Plant Research
Location: Germany
International Crops Research Institute For The Semi-Arid Tropics
Location: India
Related Funding Activities
Linkage Projects - Grant ID: LP0776586
Start Date: 06-2008
End Date: 12-2012
Amount: $441,724.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP200100341
Start Date: 02-2021
End Date: 01-2025
Amount: $650,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP220100406
Start Date: 2023
End Date: 12-2026
Amount: $928,845.00
Funder: Australian Research Council
View Funded Activity