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

Kale, Sandip M., Jaganathan, Deepa, Ruperao, Pradeep, Chen, Charles, Punna, Ramu, Kudapa, Himabindu, Thudi, Mahendar, Roorkiwal, Manish, Katta, Mohan A. V. S. K., Doddamani, Dadakhalandar, Garg, Vanika, Kishor, P. B. Kavi, Gaur, Pooran M., Nguyen, Henry T., Batley, Jacqueline, Edwards, David, Sutton, Tim and Varshney, Rajeev K. (2015) Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports, 5 15296.1-15296.14. doi:10.1038/srep15296

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Author Kale, Sandip M.
Jaganathan, Deepa
Ruperao, Pradeep
Chen, Charles
Punna, Ramu
Kudapa, Himabindu
Thudi, Mahendar
Roorkiwal, Manish
Katta, Mohan A. V. S. K.
Doddamani, Dadakhalandar
Garg, Vanika
Kishor, P. B. Kavi
Gaur, Pooran M.
Nguyen, Henry T.
Batley, Jacqueline
Edwards, David
Sutton, Tim
Varshney, Rajeev K.
Title Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.)
Journal name Scientific Reports   Check publisher's open access policy
ISSN 2045-2322
Publication date 2015-10-19
Sub-type Article (original research)
DOI 10.1038/srep15296
Open Access Status DOI
Volume 5
Start page 15296.1
End page 15296.14
Total pages 14
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Collection year 2016
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2016 Collection
 
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Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
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