Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea.
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.
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
Shouvik
S
Das
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
Hari D
HD
Upadhyaya
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
Deepak
D
Bajaj
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
Alice
A
Kujur
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
Saurabh
S
Badoni
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
Laxmi
National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India.
Vinod
V
Kumar
Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.
Shailesh
S
Tripathi
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
C L Laxmipathi
CL
Gowda
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
Shivali
S
Sharma
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
Sube
S
Singh
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
Akhilesh K
AK
Tyagi
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India swarup@nipgr.ac.in swarupdbt@gmail.com.
Swarup K
SK
Parida
D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D029863:Cicer / Q000235:genetics*; D008040:Genetic Linkage; D005838:Genotype; D018895:Microsatellite Repeats; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics*
D010940:Plant Proteins
NGS; QTL; QTL-seq; SNP; chickpea