eprintid: 8694
rev_number: 14
eprint_status: archive
userid: 1305
dir: disk0/00/00/86/94
datestamp: 2015-05-04 06:37:33
lastmod: 2015-08-06 08:27:55
status_changed: 2015-05-04 06:37:33
type: article
metadata_visibility: show
creators_name: Das, S
creators_name: Upadhyaya, H D
creators_name: Bajaj, D
creators_name: Kujur, A
creators_name: Badoni, S
creators_name: Laxmi, A
creators_name: Kumar, V
creators_name: Tripathi, S
creators_name: Laxmipathi Gowda, C L
creators_name: Sharma, S
creators_name: Singh, S
creators_name: Tyagi, A K
creators_name: Parida, S K
icrisatcreators_name: Upadhyaya, H D
icrisatcreators_name: Laxmipathi Gowda, C L
icrisatcreators_name: Sharma, S
icrisatcreators_name: Singh, S
affiliation: National Institute of Plant Genome Research (NIPGR) (New Delhi)
affiliation: ICRISAT (Patancheru)
affiliation: National Research Centre on Plant Biotechnology (NRCPB) (New Delhi)
affiliation: Indian Agricultural Research Institute (IARI) (New Delhi)
country: India
title: Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea
ispublished: pub
subjects: s1.1
divisions: D3
crps: crp1.5
full_text_status: public
keywords: Chickpea,NGS,QTL,QTL-seq,SNP
abstract: A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genomeQTL-seq strategy to identify one major genomic region harbouring a robust 100- seed weight QT Lusinganintra-specific 221 chickpea mapping population (desicv.ICC7184×desicv.ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177genes) major SWQTL (CaqSW1.1) regionintoa 35 kb genomic intervalondesi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic 9 (COP9) signalo some complex subunit  (CSN8) gene of the see xhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homo zygous individuals duringseed development.The coding SNP mined in this potential seed weight- governing candidate CSN8 genewas found to be present exclusively in all cultivated species/ genotypes, but notin any wild species/genotypes of primary, secondary and tertiary gene pools.This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.
date: 2015-04
publication: DNA Research
volume: 22
number: 2
publisher: Oxford University Press
pagerange: 1-11
id_number: http://dx.doi.org/doi: 10.1093/dnares/dsv004
refereed: TRUE
issn: 1340-2838
official_url: http://dx.doi.org/10.1093/dnares/dsv004
related_url_url: https://scholar.google.co.in/scholar?hl=en&q=Deploying+QTL-seq+for+rapid+delineation+of+a+potential+candidate+gene+underlying+major+trait-associated+QTL+in+chickpea+&btnG=
related_url_type: pub
citation:   Das, S and Upadhyaya, H D and Bajaj, D and Kujur, A and Badoni, S and Laxmi, A and Kumar, V and Tripathi, S and Laxmipathi Gowda, C L and Sharma, S and Singh, S and Tyagi, A K and Parida, S K  (2015) Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea.  DNA Research, 22 (2).  pp. 1-11.  ISSN 1340-2838     
document_url: http://oar.icrisat.org/8694/1/DNA%20Res-2015-Das-dnares-dsv004.pdf