Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea
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Shouvik Das, Hari D. Upadhyaya, Deepak Bajaj, Alice Kujur, Saurabh Badoni, laXMI Narnoliya, Vinod Kumar, Shailesh Tripathi, CL Laxmipathi Gowda, Shivali Sharma, Sube Singh, Akhilesh K. Tyagi, Swarup K. Parida. (3/5/2015). 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.
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.
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