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

Kale, S M and Jaganathan, D and Ruperao, P and Chen, C and Punna, R and Kudapa, H and Thudi, M and Roorkiwal, M and Katta, M A V S K and Doddamani, D and Garg, V and Kavi Kishor, P B and Gaur, P M and Nguyen, H T and Batley, J and Edwards, D and Sutton, T and Varshney, R K (2015) Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports (15296). 01-14. ISSN 2045-2322

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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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, Drought tolerance, QTL Study, Genomics, QTL analysis
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 17 Nov 2015 08:59
Last Modified: 19 Aug 2016 04:12
Official URL:
Acknowledgement: The authors are thankful to Dr. Xinpeng Qi and Dr. Hon-Ming Lam for providing scripts to generate a bin map image. Technical assistance from Jaipal Gaud is greatly appreciated. The work has been undertaken as a part of Australia–India strategic research fund (AISRF) project funded by Department of Science and Technology (DST) and Tropical Legumes I (TLI) project funded by Bill and Melinda Gates Foundation (BMGF) through CGIAR-Generation Challenge Program (GCP; This work has been carried out as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium.
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