Whole genome re-sequencing based classification of heterotic pools for accelerating hybrid breeding in pigeonpea

Hybrid technology has potential to elevate the yield levels in pigeonpea. Recently, the world’s first grain legume hybrid of pigeonpea ICPH 2671 has been released for commercial cultivation in India, which showed 47% yield advantage over the check varieties. To develop such hybrids, breeders make thousands of random crosses between cytoplasmic male sterile (CMS) lines and tester lines. Genomic diversity along with the phenotyping data have been used for predicting best possible combinations and defining heterotic pools in many crop species such as maize, rice, sunflower and rapeseeds. In order to define heterotic pools in pigeonpea, a set of 104 parental lines (10 CMS, 12 maintainers and 82 restorers) have been re-sequenced following whole genome re-sequencing (WGRS) approach. WGRS yielded 511 GB sequence data with the coverage ranging from 5X to 10X. A total of 3.4 million SNPs could be identified across 104 lines, while comparing individual genotypes with the reference genome and SNPs ranged from a minimum of 15,388 to a maximum of 84, 851. Structural variations such as copy number and presence/ absence variations are being identified. In parallel, these parental lines are being used to develop testcrosses in factorial mating design. F1 hybrids along with parental lines will be phenotyped for yield and yield related traits. In brief, the availability of genome-wide SNP variations combined with the phenotypic data should provide clues on candidate genomic regions associated with yield and yield related traits as well as those associated with heterosis and hetereotic pools in pigeonpea for accelerating hybrid improvement

Towards defining heterotic pools for accelerating hybrid breeding in pigeonpea

Recently released pigeonpea hybrids for cultivation in farmers’ fields have shown their potential to elevate the yield levels. For instance, the world’s first grain legume hybrid of pigeonpea ICPH 2671 showed 47% yield advantage over the check varieties. Generally, the development of such hybrids is based on selection efficiency of breeding program; breeders make thousands of random crosses between cytoplasmic male sterile (CMS) lines and tester lines. In order to enhance the selection efficiency, genomic diversity along with the phenotyping data have been used for predicting the best possible parental combinations. This approach has been successfully used in defining heterotic pools in many crop species such as maize, rice, sunflower, and rapeseeds.. With an aim to define heterotic pools in pigeonpea, a set of 104 parental lines (09 CMS, 13 maintainers and 82 restorers) have been re-sequenced following whole genome re-sequencing (WGRS) approach. WGRS yielded a total of 511 GB data with the coverage ranging from 5X to 10X. A total of 3.4 million SNPs have been identified across parental lines. Structural variations such as copy number and presence/ absence variations have been also identified. In parallel, these parental lines have been used to develop test crosses in factorial mating design. F1 hybrids along with parental lines were phenotyped for yield and yield related traits at two locations in India, namely ICRISAT, Telangana State and ARS-Gulbarga, Karnataka. The availability of genome-wide SNP variations combined with the phenotypic data will be used for deploying genomic selection to define hetereotic pools in pigeonpea for accelerating hybrid breeding program