Development of a 60k iSelect to Facilitate Cowpea Breeding

Researchers at the University of California, Riverside, in partnership with colleagues in Burkina Faso, China, Ghana, Nigeria and Senegal have designed a 60,000-assay iSelect BeadArray for cowpea (Vigna unguiculata [L.] Walp) that successfully assays 49,000 SNPs. Cowpea is an important food and fodder crop plant throughout sub-Saharan Africa, a popular vegetable crop in China and a traditional food of the Southern USA.  Applications of this new resource include a new high-density consensus genetic linkage map and SNP marker haplotypes for favorable alleles of a long list of traits including several that are the primary objectives of breeding activities funded by the USAID Feed the Future Program. These traits include drought tolerance at seedling and terminal stages, heat tolerance during reproductive development, resistance to the opportunistic pathogen Macrophomina phaseolina, and resistance to pervasive insects of West Africa including aphids, flower thrips and pod sucking bugs. SNPs for the cowpea 60k iSelect were selected from a discovery panel composed of 37 accessions mainly covering gene pools from West and East Africa landraces, China and the USA. The sequenced and annotated common bean (Phaseolus vulgaris L.) genome was used as a guide for selection of SNPs from a draft genome assembly of cowpea. Cowpea is a warm season legume, like soybean, common bean and pigeon pea, and has as small (620 Mb) genome. Some technical and logistical aspects of the iSelect platform that are well suited to the initial users of this new tool will be discussed.