Whole Genome Re-Sequencing of 300 Cajanus Accessions Provides Targets for Domestication and Genomic Regions Associated with Agronomic Traits

In the developing world, climate change, unpredicted rainfall and drought have started to further exacerbate challenges to crop production. It is, therefore, imperative that we shift our focus towards developing climate smart crops. In this direction, pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to play an important role in supplying food and nutritional security in developing countries of Asia, Africa and the tropical Americas. The reference set comprised of 300 Cajanus genotypes has been used for whole genome re-sequencing encompassing breeding lines, landraces and wild species accessions. Genomic variations/regions that were targets of domestication and modern breeding were also identified. Genome-wide association analysis (GWAS) has provided several candidate genes associated with agronomically important traits, including for days to 50% flowering, days to 75% maturity, seeds per pod and 100 seed weight. Pigeonpea candidates for these traits share sequence similarity to genes functionally characterized in other plants from biological pathways for flowering time control, seed development and pod dehiscence. This work will allow improved marker assisted selection and genomic selection for key traits to improve the yield and sustainability of this important tropical grain legume.