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-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.