First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations

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 791.77million paired-end reads were generated with an effective mapping depth of similar to 12X per accession. Analysis of WGRS data provided 5465676 genome-wide variations including 4686422 SNPs and 779254 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, 2630904 accession-specific variations comprising of 2278571 SNPs (86.6%), 166243 deletions (6.3%) and 186090 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.