National Science Foundation BREAD: Advancing the Cowpea Genome for Food Security

Cowpea is diploid with 2n=22 chromosomes and a genome size of 620 Mb. Unlike other legumes, cowpea lacks a published reference genome. A highly fragmented draft genome sequence assembly has been available from previous work since 2011 (harvest-blast.org; harvest-web.org) and is derived from 60x short-reads combined with BAC-end and gene survey Sanger sequences. This project will elevate the sequence of cowpea to state-of-the art by: (1) adding long-read sequences and an optical map; (2) anchoring contigs to a recently developed genetic map containing 37,372 SNPs; and (3) improving browser access for the broader legume community. This will enable deeper utilization of cowpea germplasm for gene discovery and marker development, while providing a stronger foundation for the cowpea genetics and breeding community. Genetic intercrosses will be conducted to produce new pre-breeding lines that will theoretically carry optimal combinations of traits present within elite lines using a recently developed multi-parent advanced generation intercross (MAGIC) population based on eight parental lines. Marker-trait information, in the context of the genome sequence and haplotypes, will be disseminated for broad adoption of marker-informed breeding. This work is tightly linked to leading breeding programs in Burkina Faso, Ghana, Mozambique, Nigeria and Senegal through USAID Feed the Future and CGIAR 'Tropical Legumes' projects.