title: mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea.
abstract: The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (Caq(a)PN4.1: 867.8 kb and Caq(a)PN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (Caq(b)PN4.1: 637.5 kb and Caq(b)PN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
authors.forename: Shouvik
authors.initials: S
authors.lastname: Das
authors.affiliation: National Bureau of Plant Genetic Resources Regional Station, Shimla, Himachal Pradesh 171004, India.
authors.forename: Mohar
authors.initials: M
authors.lastname: Singh
authors.affiliation: National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
authors.forename: Rishi
authors.initials: R
authors.lastname: Srivastava
authors.affiliation: National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bajaj
authors.affiliation: National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
authors.forename: Maneesha S
authors.initials: MS
authors.lastname: Saxena
authors.affiliation: National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India.
authors.forename: Jai C
authors.initials: JC
authors.lastname: Rana
authors.affiliation: National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India.
authors.forename: Kailash C
authors.initials: KC
authors.lastname: Bansal
authors.affiliation: National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India swarup@nipgr.ac.in swarupdbt@gmail.com.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
mesh_terms: D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics*; D018745:Genome, Plant; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
keywords: SNP; chickpea; mQTL-seq; pod number; wild accessions