Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

Sandip M. Kale(International Crops Research Institute for the Semi-Arid Tropics), Deepa Jaganathan(International Crops Research Institute for the Semi-Arid Tropics), Pradeep Ruperao(The University of Queensland), Charles Chen(Oklahoma State University), Punna Ramu(Cornell University), Himabindu Kudapa(International Crops Research Institute for the Semi-Arid Tropics), Mahendar Thudi(International Crops Research Institute for the Semi-Arid Tropics), Manish Roorkiwal(International Crops Research Institute for the Semi-Arid Tropics), Mohan A. V. S. K. Katta(International Crops Research Institute for the Semi-Arid Tropics), Dadakhalandar Doddamani(International Crops Research Institute for the Semi-Arid Tropics), Vanika Garg(International Crops Research Institute for the Semi-Arid Tropics), P. B. Kavi Kishor(Osmania University), Pooran M. Gaur(International Crops Research Institute for the Semi-Arid Tropics), Henry T. Nguyen(University of Missouri), Jacqueline Batley(The University of Western Australia), David Edwards(The University of Western Australia), Tim Sutton(South Australian Research and Development Institute), Rajeev K. Varshney(The University of Western Australia)
Scientific Reports
October 19, 2015
10.1038/srep15296
Cited by 158Open Access
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Abstract

A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. 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 phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split 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.

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