Comprehensive Genome Sequencing Analysis of 292 Cajanus Accessions

With an objective to catalogue genome variations in the world germplasm collection of pigeonpea (Cajanus cajan), a reference set comprising of 292 Cajanus accessions including 117 breeding lines, 168 landraces and 7 wild relatives’ accessions was subjected to whole genome re-sequencing (WGRS). A total of 2.15 Tb of sequence data with the coverage ranging from 5X to 12X and >90% coverage was generated. Across 292 Cajanus accessions 13.8 million sequence variations (SNPs and INDELs) with average of 41.1 variations per Kb were identified. Comparison of the genetic variations patterns among wild Cajanus accessions, landraces and breeding lines showed higher allelic diversity in wild Cajanus accessions followed by landraces and breeding lines. Detailed analysis has also provided genomic regions that might have undergone domestication and human selection. In parallel genome wide association study (GWAS) with WGRS data and available trait phenotyping data have provided significant associations with a number of yield related traits such as harvest index and days to maturity. These trait associated SNPs along with data here provide a valuable resource for the analysis of Cajanus accessions and to facilitate future breeding.