Cowpea (Vigna unguiculata [L.] Walp) is one of the most important food and nutritional security crops. It is one of the main sources of dietary protein and folic acid for millions of people in sub-Saharan Africa and other parts of the developing world. Cowpea is a diploid (2n = 22) with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea was domesticated in Africa, from where it spread into all continents and now is commonly grown in many parts of Asia, Europe, United States and Central and South America. Domestication of cowpea has, in general, resulted in a determinate growth habit, increased pod and seed size, early flowering, and reduction of pod shattering. However, the genetic control of these traits is largely unknown. This lack of domestication-related knowledge in cowpea has limited the utilization of broad germplasm for crop improvement. This dissertation investigates the genetic basis of domestication traits using recently developed genetic and genomic resources available for cowpea and studies the effect of two seed size loci in a different genetic background. In the first chapter, regions of the cowpea genome that played an important role in cowpea domestication were identified. A total of 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTLs) for these nine traits. Four regions were identified showing QTL clustering for these traits, including one region on Vu08 where four QTLs related to increased organ size (seed weight, pod length, leaf length and leaf width) were mapped. Using sequence homology comparison with common bean, a candidate gene (Vigun08g217000) for increased organ size was identified. This gene codes for a histidine kinase 2 and the Arabidopsis ortholog AHK2 (AT5G35750.1) has been shown to regulate, among other things, plant organ size. The second chapter investigates the genetic basis of seed size, which is a main domestication target and one of the key yield determinants. A “mini-core” panel of 368 genetically diverse cowpea accessions, mainly landraces, was used to evaluate four seed size-related traits (seed weight, length, width, and density). A genome-wide association study (GWAS) and meta-analysis identified 17 loci associated with seed size. One locus was common to weight, width and length, suggesting pleiotropy. By integrating synteny based-analysis with common bean, six candidate genes (Vigun05g036000, Vigun05g039600, Vigun05g204200, Vigun08g217000, Vigun11g187000, and Vigun11g191300) which are implicated in multiple functional categories related to seed size were identified. In the third chapter, two seed size QTLs were targeted for introgression in the background of a popular cultivar from Senegal “Pakau”. Four combinations of the positive (large seed size) alleles of the two QTL were observed in the backcross progenies and were analyzed to test the effect on seed phenotype of these QTL in the Pakau genetic background: no positive QTL alleles, positive allele of Css-1 only, positive allele of Css-4 only, and positive alleles of both QTL.
The results of this dissertation provide a basis for further fine mapping of genes controlling domestication traits and a foundation for the utilization and exploitation of diverse landraces and wild relatives in cowpea breeding programs.
