Abstract
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 introgressed a rare haplotype associated with large seeds at the Css-1 locus from an African buff seed type cultivar, IT82E-18 (18.5 g/100 seeds), into a blackeye seed type cultivar, CB27 (22 g/100 seed). Four recombinant inbred lines derived from these two parents were chosen for marker-assisted breeding based on SNP genotyping with a goal of stacking large seed haplotypes into a CB27 background. Foreground and background selection 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 28.7g/100 seed and 24.8 g/100 seed for cycles 1 and 2, respectively. One cycle 1 introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28–35 g/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. A principal component analysis was used to explore the relationships between the parents relative to a core set of landraces and improved varieties based on high-density SNP data. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to accessions collected from Southeastern Africa. Therefore this quantitative trait locus has a strong potential to develop larger seeded varieties for other growing regions which is demonstrated in this work using a California pedigree.
Highlights
Seed size is one of the most universal features that distinguishes domesticated plants from their wild relatives
In the principal component analysis IT82E-18 clusters with landraces from South–East Africa while California Blackeye 27 (CB27) forms a cluster with other California varieties, landraces from the Middle East, and North Africa that are only separated from the West-African landraces by principal component 2 (Supplementary Sheet ‘PCA’)
Distribution of Css-1 Out of all 214 accessions studied in the principal component analysis only 19 carry the SNP haplotype of IT82E-18 and all of these are from countries in South and East Africa (Supplementary Sheet “Distribution of Css-1”)
Summary
Seed size is one of the most universal features that distinguishes domesticated plants from their wild relatives. Larger seeds produce more competitive seedlings under cultivated conditions (Purugganan and Fuller, 2009) and are preferred for most culinary preparations of naked grain This is true for cowpea (Vigna unguiculata) where the demand for large seeds continues for most market classes, especially blackeyes, and rough seed types grown for flour production. Genetic mapping using experimental populations has tagged a few seed size associated quantitative trait loci (QTLs) with markers that could be useful in breeding (Fatokun et al, 1992; Egbadzor et al, 2013b; Lucas et al, 2013a) Two of these publications report on the orthology of seed size based on comparative mapping to known seed size associated loci in the genomes of cowpea relatives mung bean (Vigna radiata) and soy bean (Glycine max). Knowledge of marker-trait associations from these studies can be essential components of marker-assisted breeding strategies to help develop varieties with larger seeds
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