ORCID Profile
0000-0001-6446-4603
Current Organisations
International Crops Research Institute for the Semi-Arid Tropics
,
Murdoch University
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Publications
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.
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.
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
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 Small RNA Sequencing Data in Plants
Publisher: Springer US
Date: 2022
DOI: 10.1007/978-1-0716-2067-0_26
Abstract: Over the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. We elaborate on various steps involved in analysis, from processing the raw sequencing reads to identifying miRNAs, their targets, and differential expression studies.
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
Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea
Publisher: Wiley
Date: 03-02-2020
DOI: 10.1111/PBI.13333
Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement
Publisher: Springer Science and Business Media LLC
Date: 21-10-2020
InDel markers: An extended marker resource for molecular breeding in chickpea
Publisher: Public Library of Science (PLoS)
Date: 18-03-2019
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.
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
Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement
Publisher: Elsevier BV
Date: 12-2021
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
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
Genome-wide survey and expression analysis of F-box genes in chickpea
Publisher: Springer Science and Business Media LLC
Date: 13-02-2015
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.
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.
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.
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
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.
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
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.
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
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.
A New Set of ESTs from Chickpea (Cicer arietinum L.) Embryo Reveals Two Novel F-Box Genes, CarF-box_PP2 and CarF-box_LysM, with Potential Roles in Seed Development
Publisher: Public Library of Science (PLoS)
Date: 24-03-2015
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
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
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
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
Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement
Publisher: Elsevier BV
Date: 02-2020
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
Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs
Publisher: Springer Science and Business Media LLC
Date: 14-01-2020
DOI: 10.1038/S41598-019-56903-Z
Abstract: The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F 2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits.
Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don
Publisher: Springer Science and Business Media LLC
Date: 02-2014
DOI: 10.1007/S00299-014-1569-8
Abstract: Transcriptomic data of C. roseus offering le sequence resources for providing better insights into gene ersity: large resource of genic SSR markers to accelerate genomic studies and breeding in Catharanthus . Next-generation sequencing is an efficient system for generating high-throughput complete transcripts/genes and developing molecular markers. We present here the transcriptome sequencing of a 26-day-old Catharanthus roseus seedling tissue using Illumina GAIIX platform that resulted in a total of 3.37 Gb of nucleotide sequence data comprising 29,964,104 reads which were de novo assembled into 26,581 unigenes. Based on similarity searches 58 % of the unigenes were annotated of which 13,580 unique transcripts were assigned 5016 gene ontology terms. Further, 7,687 of the unigenes were found to have Cluster of Orthologous Group classifications, and 4,006 were assigned to 289 Kyoto Encyclopedia of Genes and Genome pathways. Also, 5,221 (19.64 %) of transcripts were distributed to 81 known transcription factor (TF) families. In-silico analysis of the transcriptome resulted in identification of 11,004 SSRs in 26.62 % transcripts from which 2,520 SSR markers were designed which exhibited a non-random pattern of distribution. The most abundant was the trinucleotide repeats (AAG/CTT) followed by the dinucleotide repeats (AG/CT). Location specific analysis of SSRs revealed that SSRs were preferentially associated with the 5'-UTRs with a predicted role in regulation of gene expression. A PCR validation of a set of 48 primers revealed 97.9 % successful lification, and 76.6 % of them showed polymorphism across different Catharanthus species as well as accessions of C. roseus. In summary, this study will provide an insight into understanding the seedling development and resources for novel gene discovery and SSR development for utilization in marker-assisted selective breeding in C. roseus.
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
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
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.
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
Related Organisations
International Crops Research Institute For The Semi-Arid Tropics
Location: India
Related Funding Activities
No related grants have been discovered for Vanika Garg.