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

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-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% R(2) 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.

SUBMITTER: Das S

PROVIDER: S-EPMC4463844 | biostudies-other | 2015 Jun

REPOSITORIES: biostudies-other

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

Das Shouvik S Upadhyaya Hari D HD Bajaj Deepak D Kujur Alice A Badoni Saurabh S Laxmi Kumar Vinod V Tripathi Shailesh S Gowda C L Laxmipathi CL Sharma Shivali S Singh Sube S Tyagi Akhilesh K AK Parida Swarup K SK

DNA research : an international journal for rapid publication of reports on genes and genomes 20150427 3

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 ...[more]

PMID: 25922536

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Dataset Information

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

Publications

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

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