Introgression of a Rare Haplotype from Southeastern Africa to Breed Cowpeas with Larger Seeds

Seed size distinguishes most crops from their wild relatives and is an important quality trait for the grain legume cowpea. In order to breed cowpea varieties with larger seeds we associated allelic variation with the inheritance of seed size and introgressed a rare haplotype at the Css-1 locus from a Mozambican buff seed type cultivar, IT82E-18 (18.5g/100 seeds), into a Californian blackeye seed type cultivar, CB27 (22g/100 seed). Selections were performed during two cycles of backcrossing based on genome-wide SNP markers. The average seed size of introgression lines homozygous for haplotypes associated with large seeds was 26.8g/100 seed. One introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28-35g/100 seeds). Field-based performance trials helped identify breeding lines that not only have large seeds but are also desirable in terms of yield, maturity, and plant architecture when compared to industry standards. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to the Southeast African genepool of domesticated cowpea. Based on knowledge of association studies and selections facilitated by SNP genotyping, we used an African parent with relatively small seeds to increase the seed size of a Californian cultivar by up to 52%. Knowledge of candidate genes, orthology and deployment of the Css-1 locus will be facilitated by a recently developed 60K Infinium assay. Other interests include exploring linkage disequilibrium surrounding Css-1 and its effects on the nutritional composition of cowpea seeds.