Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/104881
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Type: Journal article
Title: Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.)
Author: Kale, S.
Jaganathan, D.
Ruperao, P.
Chen, C.
Punna, R.
Kudapa, H.
Thudi, M.
Roorkiwal, M.
Katta, M.
Doddamani, D.
Garg, V.
Kishor, P.
Gaur, P.
Nguyen, H.
Batley, J.
Edwards, D.
Sutton, T.
Varshney, R.
Citation: Scientific Reports, 2015; 5(1):15296-1-15296-14
Publisher: Nature Publishing Group
Issue Date: 2015
ISSN: 2045-2322
2045-2322
Statement of
Responsibility: 
Sandip M Kale, Deepa Jaganathan, Pradeep Ruperao, Charles Chen, Ramu Punna, Himabindu Kudapa, Mahendar Thudi, Manish Roorkiwal, Mohan AVSK Katta, Dadakhalandar Doddamani, Vanika Garg, P B Kavi Kishor, Pooran M Gaur, Henry T Nguyen, Jacqueline Batley, David Edwards, Tim Sutton and Rajeev K Varshney
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.
Keywords: Drought tolerance; chickpeas
Rights: This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
DOI: 10.1038/srep15296
Appears in Collections:Agriculture, Food and Wine publications
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