title: First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations.
abstract: Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Vinay
authors.initials: V
authors.lastname: Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Aamir W
authors.initials: AW
authors.lastname: Khan
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Vanika
authors.initials: V
authors.lastname: Garg
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.|School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D036561:Cajanus / Q000235:genetics*; D056915:DNA Copy Number Variations; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide
keywords: deletions; insertions; next-generation sequencing; pigeonpea; single-nucleotide polymorphism; whole genome re-sequencing
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