Whole Genome Resequencing Reveals Genome Wide Variations Among Parental Lines of Mapping Populations in Pigeonpea

With an objective to implement molecular breeding in pigeonpea for fusarium wilt, sterility mosaic diseases and agronomical important traits, a range of mapping populations namely recombinant inbred lines, introgression lines, multi-parental advanced generation intercross, nested association mapping population have been developed. Whole genome resequencing has been undertaken on a panel of 20 parental lines on MiSeq platform. Resequencing yielded 791.77 million paired-ends reads of read length from 150 to 250 bp, which covered 157 Gb of high quality raw data. Around 89% of raw reads from 18 cultivated lines and 82% from 2 wild relatives could be aligned to the pigeonpea reference genome. The effective mapping depth ranged from 8X (MN 1) to 17X (ICP 14486) with an average of ~12X per parental line. Comprehensive data analysis has provided a total of 4,686,422 SNPs and 779,254 InDels across 20 parental lines. Furthermore, pair-wise SNPs in crossing parentals were found in the range of 195,546 (ICP 8863 × ICPL 87119) to 3,543,406 (ICPW 12 × ICPW 29). Line specific SNPs and Indels were identified in each parental line. Line specific SNPs were ranged from 601 SNPs in ICPL 85010 to 2,202,592 SNPs in ICPW 12. Structural variations such as copy number variations (CNV) have been identified across the pigeonpea parental lines, which were minimum in ICPB 2049 (48) to maximum in ICPW 12 (446). These data will be useful for high-throughput genotyping of different mapping populations and in turn would be helpful in locating genes/genomic segments responsible for economically important traits.