Whole Genome Re-Sequencing for Pigeonpea Improvement

In order to use the draft genome sequence information for pigeonpea (Cajanus cajan) improvement, whole genome re-sequencing (WGRS) has been used in two specialized genetic stocks i.e. reference set and parental lines of hybrids. A total of 2.15 Tb of sequence data with the coverage ranging from 5X to 12X was generated across reference set comprising of 117 breeding lines, 168 landraces and 7 wild species accessions. In the case of 104 parental lines of hybrid (10 cytoplasmic male sterile, 13 maintainers and 81 restorer lines) WGRS yielded 511 GB sequence data with the coverage ranging from 5X to 10X. A total of 13.8 and 3.4 million sequence variations (SNPs and INDELs) have been identified in reference set and parental lines of hybrids respectively. The reference set has been analysed to assess genomic regions that might have undergone domestication and human selection and genome wide association study (GWAS) for yield related traits such as harvest index and days to maturity. In parallel efforts have been initiated to define heterotic pools using WGRS data and phenotyping data on parental lines of hybrids and F₁hybrids. Parental lines of hybrids are being used to develop testcrosses in factorial mating design.  F₁hybrids along with parental lines will be phenotyped for yield and yield related traits. The availability of genome-wide SNP variations combined with the phenotypic data will provide candidate genomic regions associated with yield and yield related traits as well as those associated with heterosis and hetereotic pools for accelerating pigonpea improvement.