Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)

The appearance of the seed is an important aspect of consumer preference for cowpea ( Vigna unguiculata [L.] Walp.). Seed coat pattern in cowpea has been a subject of study for over a century. This study makes use of newly available resources, including mapping populations, a reference genome and additional genome assemblies, and a high-density single nucleotide polymorphism genotyping platform, to map various seed coat pattern traits to three loci, concurrent with the Color Factor ( C ), Watson ( W ), and Holstein ( H ) factors identified previously. Several gene models encoding proteins involved in regulating the later stages of the flavonoid biosynthesis pathway have been identified as candidate genes, including a basic helix-loop-helix gene ( Vigun07g110700 ) for the C locus, a WD-repeat gene ( Vigun09g139900 ) for the W locus and an E3 ubiquitin ligase gene ( Vigun10g163900 ) for the H locus. A model of seed coat development, consisting of six distinct stages, is described to explain some of the observed pattern phenotypes.