Publications of NIPGR Scientists
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Item Identification of a stable drought-tolerant high-yielding line for chickpea crop improvement(Springer Nature Publishing AG, 2025) Gupta, Santosh Kumar; Dwivedi, Vikas; Kute, Nandakumar Surendra; Francis, Philip; Parida, Swarup K.; Chattopadhyay, DebasisChickpea (Cicer arietinum L.) is grown in marginal land with low input and is, therefore, drought-prone. In order to develop a drought-tolerant line, a bi-parental recombinant inbred line (RIL) mapping population was generated by inter-crossing between two varieties JGK3 (ICCV 95334) and Himchana1 (ICCX-810800) having contrasting root traits. Ninety-two genetically diverse RILs of F8 generation were selected based on their total root length to root dry weight ratio (RL/DW). The leaf relative water content of these RILs under low soil moisture did not show any strong correlation with the RL/DW. Twenty RILs having high RL/DW were evaluated for seed yield in a field under rainfed condition without any supplementary irrigation. The best performing RIL, which performed better than the check varieties, was reevaluated for a further year under rainfed condition. The genotypic constitution of this superior low soil moisture tolerant individual RIL was determined by constructing its recombination map using genome-wide SNPs obtained through genotyping-by-sequencing. The RIL possesses the superior alleles of the genomic QTL region known to govern drought tolerance in chickpea. The phenotypic and genotypic characterization of RILs in our study identified a chickpea pre-breeding line that can be used as a genetic donor for developing drought-tolerant high-yielding chickpea varieties and our results provide an evidence that total root length to root dry weight ratio can be used as a quantitative trait for assessing drought tolerance.Item Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping(BioMed Central Ltd, 2017) Sahu, Kamlesh Kumar; Chattopadhyay, DebasisBACKGROUND: Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication. RESULTS: Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima's D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima's D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition. CONCLUSION: Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species.Item High-Throughput SNP discovery and genotyping for constructing a saturated linkage map of Chickpea (Cicer arietinum L.)(Oxford University Press, 2012) Gaur, Rashmi; Azam, Sarwar; Jeena, Ganga; Khan, Aamir Waseem; Choudhary, Shalu; Jain, Mukesh; Yadav, Gitanjali; Tyagi, Akhilesh K.; Chattopadhyay, Debasis; Bhatia, SabhyataThe present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP geno- typing assay based on Illumina’s GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.Item Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species(Elsevier B.V., 2009) Nayak, Spurthi N.; Balaji, Jayashree; Upadhyaya, Hari D.; Hash, C. Tom; Kavi Kishor, P.B.; Chattopadhyay, Debasis; Rodriquez, Lina Marıa; Blair, Matthew W.; Baum, Michael; McNally, Kenneth; This, Dominique; Hoisington, David A.; Varshney, Rajeev K.The transcription factor, DREB2A, is one of the promising candidate genes involved in dehydration tolerance in crop plants. In order to isolate DREB2A homologues across cereals (rice, barley and sorghum) and legumes (common bean and chickpea), specific or degenerate primers were used. Gene/phylogenetic trees were constructed using a non-redundant set of 19 DREB1A and 27 DREB2A amino acid sequences and were combined with taxonomic/species tree to prepare reconciled phylogenetic trees. In total, 86 degenerate primers were designed for different clades and 295 degenerate primer combinations were used to amplify DREB homologues in targeted crop species. Successful amplification of DREB2A was obtained in case of sorghum. In parallel, gene-specific primers were used to amplify DREB2A homologues in rice, barley, common bean and chickpea. Seven to eight diverse genotypes from targeted species were used for sequence analysis at DREB2A locus identified/isolated. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, three SNPs with five haplotypes were observed in barley whereas a single SNP was observed in rice, sorghum and chickpea. Parsimony based phylogenetic tree revealed distinct clustering of cereals and legumes. Furthermore, alignment of corresponding amino acid sequences showed conservation of AP2 domain across the targeted species.