eprintid: 9136
rev_number: 30
eprint_status: archive
userid: 1305
dir: disk0/00/00/91/36
datestamp: 2015-11-17 08:59:50
lastmod: 2016-08-19 04:12:48
status_changed: 2015-11-17 08:59:50
type: article
metadata_visibility: show
creators_name: Kale, S M
creators_name: Jaganathan, D
creators_name: Ruperao, P
creators_name: Chen, C
creators_name: Punna, R
creators_name: Kudapa, H
creators_name: Thudi, M
creators_name: Roorkiwal, M
creators_name: Katta, M A V S K
creators_name: Doddamani, D
creators_name: Garg, V
creators_name: Kavi Kishor, P B
creators_name: Gaur, P M
creators_name: Nguyen, H T
creators_name: Batley, J
creators_name: Edwards, D
creators_name: Sutton, T
creators_name: Varshney, R K
icrisatcreators_name: Kale, S M
icrisatcreators_name: Jaganathan, D
icrisatcreators_name: Kudapa, H
icrisatcreators_name: Thudi, M
icrisatcreators_name: Roorkiwal, M
icrisatcreators_name: Katta, M A V S K
icrisatcreators_name: Doddamani, D
icrisatcreators_name: Garg, V
icrisatcreators_name: Gaur, P M
icrisatcreators_name: Varshney, R K
affiliation: ICRISAT (Patancheru)
affiliation: Department of Genetics, Osmania University (Hyderabad)
affiliation: The University of Western Australia, School of Plant Biology and the Institute of Agriculture (Crawley)
affiliation: University of Queensland, School of Agriculture and Food Science (Queensland)
affiliation: Oklahoma State University, Department of Biochemistry and Molecular Biology (Stillwater)
affiliation: Cornell University, Biotechnology Building (Ithaca)
affiliation: University of Missouri, National Center for Soybean Biotechnology and Division of Plant Sciences (Columbia)
affiliation: South Australian Research and Development Institute (Adelaide)
affiliation: University of Adelaide, Australia and School of Agriculture (Adelaide)
country: India
country: Australia
country: USA
title: Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
ispublished: pub
subjects: s1.1
subjects: s2.13
divisions: D3
crps: crp1.5
full_text_status: public
keywords: Chickpea, Drought tolerance, QTL Study, Genomics, QTL analysis
note: 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; http://www.generationcp.org/). This work has been carried out as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium.
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.
date: 2015-10-19
date_type: published
publication: Scientific Reports
number: 15296
publisher: Nature Publishing Group
pagerange: 01-14
id_number: 10.1038/srep15296
refereed: TRUE
issn: 2045-2322
official_url: http://dx.doi.org/10.1038/srep15296
related_url_url: https://scholar.google.co.in/scholar?hl=en&q=Prioritization+of+candidate+genes+in+%E2%80%9CQTL-hotspot%E2%80%9D+region+for+drought+tolerance+in+chickpea+%28Cicer+arietinum+L.%29&btnG=
related_url_type: pub
citation:   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     
document_url: http://oar.icrisat.org/9136/1/srep15296.pdf