Record Details

Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

NIPGR Digital Knowledge Repository (NDKR)

View Archive Info
 
 
Field Value
 
Title Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea
 
Creator Das, Shouvik
Upadhyaya, Hari D.
Bajaj, Deepak
Kujur, Alice
Badoni, Saurabh
Laxmi
Kumar, Vinod
Tripathi, Shailesh
Gowda, C. L. Laxmipathi
Sharma, Shivali
Singh, Sube
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Chickpea
NGS
QTL
QTL-seq
SNP
 
Description Accepted date: 20 March 2015
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-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. 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 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in 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.
The authors acknowledge the financial support for this research study provided
by a research grant from the Department of Biotechnology (DBT), Government
of India (102/IFD/SAN/2161/2013-14). S.D. and A.K. acknowledge the CSIR
(Council of Scientific and Industrial Research) and DBT for Junior/Senior
Research Fellowship awards. Funding to pay the Open Access publication
charges for this article was provided by the National Institute of Plant Genome
Research (NIPGR).
 
Date 2016-01-04T05:07:05Z
2016-01-04T05:07:05Z
2015
 
Type Article
 
Identifier DNA Res., 22(3): 193- 203
1756-1663
http://172.16.0.77:8080/jspui/handle/123456789/496
http://dnaresearch.oxfordjournals.org/content/22/3/193
10.1093/dnares/dsv004
 
Language en_US
 
Publisher Oxford University Press