BREAD: Advancing the Cowpea Genome for Food Security

University Of California-Riverside, Riverside CA

Investigators

Abstract

Cowpea, also known as black-eyed pea in the U.S.A., is a protein-rich grain-producing plant native to Africa. When cowpea is combined with starchy grains such as corn, sorghum or rice, the result is a complete source of major nutrients for energy and growth. It also provides protein-rich leaves and is used for animal feed. Cowpea is the primary source of protein for people in sub-Saharan Africa (SSA) where it is presently produced on over 20 million acres mainly by farmers with small land holdings. Its popularity is also due to its resilience to low rainfall and heat while also enriching the soil. Despite its relevance to food security in Africa and elsewhere, there has been relatively little basic research on cowpea. Advances in next generation sequencing technology have made it possible to "read" the genetic material of cowpea and decipher the instructions (genes and genetic variation) that ultimately provide for crop improvement. Producing an optimized reference genome sequence for cowpea is one of the main goals of this project, a feat that has been accomplished for human, mouse, cow and economically important crop plants such as corn, soybean, rice, bean and poplar. A broader purpose is to provide genetic resources to improve decision-making abilities within an existing network of African cowpea breeders. Breeders develop new varieties by making crosses between parents that carry favorable traits and selecting progeny containing favorable characteristics of both parents. This project will provide new materials for progeny selection in addition to knowledge that will facilitate the development of new cowpea varieties for increased food production. Cowpea (Vigna unguiculata) is in the family Fabaceae, tribe Phaseoleae which includes other warm season legumes such as soybean, common bean and pigeon pea, as well as Vigna species adzuki bean and mung bean. 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.