TY  - JOUR
AV  - public
UR  - http://dx.doi.org/10.1093/dnares/dsv004
IS  - 2
PB  - Oxford University Press
TI  - Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea
A1  - Das, S
A1  - Upadhyaya, H D
A1  - Bajaj, D
A1  - Kujur, A
A1  - Badoni, S
A1  - Laxmi, A
A1  - Kumar, V
A1  - Tripathi, S
A1  - Laxmipathi Gowda, C L
A1  - Sharma, S
A1  - Singh, S
A1  - Tyagi, A K
A1  - Parida, S K
SN  - 1340-2838
VL  - 22
N2  - 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 ?rst time employed a NGS-based whole-genomeQTL-seq strategy to identify one major genomic region harbouring a robust 100- seed weight QT Lusinganintra-speci?c 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 re?ects the reliability and ef?cacy of QTL-seq as a strategy for rapid genome-wide scanning and ?ne 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-speci?c 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 arti?cial 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.
SP  - 1
Y1  - 2015/04//
EP  - 11
ID  - icrisat8694
KW  - Chickpea
KW  - NGS
KW  - QTL
KW  - QTL-seq
KW  - SNP
JF  - DNA Research
ER  -