Moving Closer to Genes for Drought Tolerance in Chickpea (Cicer arietinum)

Chickpea is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50% production losses in chickpea. Analysis of phenotypic data for 20 drought tolerance traits in 1-7 seasons at 1-5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04, referred as "QTL-hotspot" explaining 58.20% phenotypic variation for 13 drought tolerance traits. Introgression of the "QTL-hotspot", through marker-assisted backcrossing, in different genetic backgrounds has enhanced yield under drought conditations. A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region. 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 above mentioned phenotyping data splitted 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.