ORCID Profile
0000-0001-9457-9508
Current Organisations
Lincoln University
,
University of Missouri Columbia
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Publisher: Springer Science and Business Media LLC
Date: 03-04-2008
Abstract: Previous work showed that the maize primary root adapts to low Ψ w (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low Ψ w . To identify mechanisms that determine these responses to low Ψ w , transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation. Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs . sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit. The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.
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.
Publisher: Mary Ann Liebert Inc
Date: 06-2018
Abstract: Expected values for tissue tonometry and bioimpedance spectroscopy (BIS) in the lower extremity of young people have not been established. These measures are commonly used to assess tissue changes in adult, breast cancer-related lymphedema of the arm. In tropical regions, identification of tissue changes in the lower limbs related to lymphatic filariasis is required hence expected values and factors contributing to variation in tissue tonometry and BIS in two tropical populations were investigated. A convenience s le of healthy volunteers aged 8-21 in Myanmar and Australia was recruited. Tissue compressibility at the calf and anterior and posterior thigh was measured using three tonometry devices and free fluid in each leg was assessed using BIS. Data were collected about possible modifiers: leg dominance, age, gender, body mass index (BMI), hydration, and menstrual cycle. Paired t-test and linear regression compared the objective measures with possible modifiers within each population. Statistical significance was set at p < 0.05 with a 95% confidence interval. In Myanmar, increases in free fluid, tissue compressibility, and limb circumference were associated with being older, female, underweight, or in the second half of the menstrual cycle. In young Australians, increases in tissue compressibility and limb circumference were associated with being older or in the second half of the menstrual cycle. When assessing tissue compressibility and free fluid in young people using tonometry and gender, BIS, limb dominance and BMI should be considered in a local context and attempts should be made to minimize the potential influences of hydration and the female menstrual cycle.
Publisher: Wiley
Date: 13-06-2018
DOI: 10.1111/PCE.13203
Publisher: Springer Science and Business Media LLC
Date: 09-02-2022
DOI: 10.1007/S00122-022-04045-8
Abstract: The major soy protein QTL, cqProt-003, was analysed for haplotype ersity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein in iduals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.
Publisher: Frontiers Media SA
Date: 11-08-2015
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.
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.
Publisher: Frontiers Media SA
Date: 19-07-2016
Publisher: Cold Spring Harbor Laboratory
Date: 13-10-2021
DOI: 10.1101/2021.10.12.464159
Abstract: Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait associated region within a 173 kb linkage block was identified and variants in the region were characterised, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the third exon of gene 20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304bp deletion and have identified additional nested variation present in high-protein in iduals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximise protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterisation and modification. The major soy protein QTL, cqProt-003, was analysed for haplotype ersity and global distribution, results indicate 304bp deletion and variable tandem repeats in protein coding regions are likely causal candidates.
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.
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.
Publisher: Wiley
Date: 16-05-2018
DOI: 10.1111/PBI.12929
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.
No related grants have been discovered for Babu Valliyodan.