Identification of Candidate Genes from a "QTL-Hotspot" Region for Drought Tolerance in Chickpea Using Whole Genome Resequencing Based Bin Mapping

With the objective to identify candidate genes for drought tolerance related traits in chickpea, 232 recombinant inbred lines were sequenced using advanced whole genome re-sequencing based skim sequencing approach. A total of 497.6 Gb of Illumina paired read sequence data were generated for 232 samples which resulted in identification of 62,370 SNPs, distributed on 8 chromosomes. A total of 1,610 bins were identified using bin mapping approach. More than 60% bins were of ≤ 1 Mb size while ~70 % bins had ≤ 10 genes. The recombination bins were subsequently used as molecular markers for linkage mapping and QTL analysis. The QTL analysis has identified 134 QTLs for 17 traits and two drought tolerance indices, out of which 71 were major QTLs (PVE>10%) and 63 were minor QTLs (PVE<10%). The detailed analysis of QTLs from "QTL-hotspot" region reported earlier on CaLG04 were analyzed and 76 candidate genes were identified. Further, a priory candidate gene analysis was carried out using candidate genes along with SNPs from CaLG04  wherein, 23 genes were found enriched for six different traits viz. 100 seed weight, biomass, drought tolerance indices, plant height, number of pods per plant and shoot dry weight. Quantitative gene expression studies showed differential expression of some of these genes in drought tolerant and susceptible lines. Further characterization of these genes will help to understand their role in drought tolerance mechanism in chickpea.