Rutwik Barmukh

Enhancing drought tolerance in chickpea, an important grain legume for people in the semi-arid regions of the world, is crucial for improving its productivity in the context of changing climatic scenarios. Terminal drought is one of the major constraints limiting chickpea production and causes up to 50% yield losses. Extensive genotypic and phenotypic data analyses revealed the presence of a QTL cluster on CaLG04 harbouring robust main-effect QTLs for 12 traits and explaining up to 58.20% phenotypic variation, referred as “QTL-hotspot”. To identify candidate genes related to drought tolerance, we narrowed down the “QTL-hotspot” region from ca. 3 Mb to ~300 kb by using a combination of bin mapping based QTL analysis and gene enrichment analysis. As a result, the “QTL-hotspot” region was split into two sub-regions, namely “QTL-hotspot_a” (139.22 kb; 15 genes) and “QTL-hotspot_b” (153.36 kb; 11 genes). Subsequently, we characterized the fine mapping population derived from ICC4958 (drought tolerant) and ICC1882 (drought sensitive) using different phenotyping platforms like LeasyScan, lysimeter and under field conditions. We identified major QTLs for canopy development, biomass, yield and water-use related traits co-localized in “QTL-hotspot” region, explaining up to 74% phenotypic variation. Our results provided crucial evidence of genetic linkages between traits phenotyped at multiple levels of plant organization, thereby increasing our cognizance of complex traits like drought. Analyses of genetic variation in the refined “QTL-hotspot” region among 3,000 diverse chickpea genomes identified mutations in five promising candidate genes that can be deployed in chickpea breeding programs and future sustainable agriculture.