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

Saxena, R.K., Patel, K., Obarley, Y., Kumar, V., Kim, C., Singh, V., Shaun, A., Kuruvinashetti, M.S., Rhee, H., Kim, B., Zhang, W., Sameer Kumar, C.V., Karwa, A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2014) Whole genome re-sequencing based classification of heterotic pools for accelerating hybrid breeding in pigeonpea. In: 6th International Food Legume Research Conference/7th International Conference on Legume Genetics and Genomics, 7 - 11 July 2014, TCU Place Saskatoon, Saskatchewan, Canada


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.

Item Type: Conference Paper
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