title: High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS).
abstract: This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.
authors.affiliation: National Institute Of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India.
authors.forename: Subodh
authors.initials: S
authors.lastname: Verma
authors.affiliation: National Institute Of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India.
authors.forename: Shefali
authors.initials: S
authors.lastname: Gupta
authors.affiliation: National Institute Of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India.
authors.forename: Nitesh
authors.initials: N
authors.lastname: Bandhiwal
authors.affiliation: Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
authors.forename: Tapan
authors.initials: T
authors.lastname: Kumar
authors.affiliation: Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
authors.forename: Chellapilla
authors.initials: C
authors.lastname: Bharadwaj
authors.affiliation: National Institute Of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India.
authors.forename: Sabhyata
authors.initials: S
authors.lastname: Bhatia
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D029863:Cicer / Q000235:genetics*; D008040:Genetic Linkage; D018745:Genome, Plant; D060005:Genotyping Techniques / Q000379:methods; D029902:Medicago / Q000235:genetics; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics*