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 791.77 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.