A Genetically-Anchored Genome Assembly for Cowpea Facilitated by a High-Density Genotyping Assay

Cowpea (Vigna unguiculata (L.) Walp), native to Africa and a member of the Fabaceae family, is one of the most important legume crops in the semiarid tropics covering Africa, Asia, Southern Europe, Southern United States and Central and South America, where it is a good source of protein, fiber, and certain vitamins and minerals. Cowpea is a warm season legume along with soybean and common bean, although it is more drought and heat tolerant than its legume relatives. Despite its relevance to agriculture in the developing world and its resilience, cowpea has received little attention relative to other crops of major significance. It is presently the most widely grown legume that lacks a published reference genome sequence. Using the recently developed Illumina iSelect genotyping assay for cowpea, we have genotyped five biparental RIL populations and developed a consensus genetic map containing over 37,000 SNPs mapped to ~3,200 bins in ~800 cM. This map is being used to genetically anchor an initial whole-genome shotgun (WGS) assembly of cowpea accession IT97K-499-35, which includes sequences for about 97% of all known cowpea genes (Close et al. 2011, PAG XIX). Sequences from about 4,000 minimal tiling path BACs are being incorporated to increase the number of anchored scaffolds and help resolve the order within recombination bins.