A New SNP-Genotyping Resource for Cowpea and Its Deployment for Breeding

Cowpea (Vigna unguiculata L. Walp.), native to Africa and a member of the Fabaceae family, is a primary source of protein for millions of people in Sub-Saharan Africa and other parts of the developing world, where it is grown for fresh and dry grains, edible pods and leaves, or used for hay or forage. Until recently cowpea has lacked genomic resources to support modern breeding approaches. As part of the five-year project "USAID Feed the Future Innovation Lab for Climate Resilient Cowpea", an Illumina “60k” iSelect BeadChip has been developed. SNPs for the iSelect assay were discovered using whole-genome shotgun sequencing of 37 cowpea breeding parents and landrace accessions relevant to Africa, China and the USA. The majority of these SNPs target cowpea sequences corresponding to 20,788 gene models of Phaseolus vulgaris (common bean), a close relative of the genus Vigna. This platform is being used to genotype 10 bi-parental recombinant inbred line populations, breeding lines from West African programs and diverse germplasm. Primary target traits for Burkina Faso, Ghana, Nigeria, Senegal and California include drought and heat tolerance, seed qualities, yield, and resistance to Macrophomina phaseolina, aphids, flower thrips and pod-sucking bugs. This new genotyping resource supports high-density genetic mapping, pedigree validation, germplasm characterization and marker-assisted breeding of cowpea. Funding sources for this work on food security include USAID, USDA and the CGIAR Generation Challenge Program.