Genetic differentiation and diversity upon genotype and phenotype in cowpea (Vigna unguiculata L. Walp.)

The evolution of species is complex and subtle which always associates with the genetic variation and environment adaption during active/passive spread or migration. In crops, this process is usually driven and influenced by human activities such as domestication, cultivation and immigration. One method to discover this process is to analyze the genetic diversity of those crops in different regions. This research first assessed the similarity and differentiation between genetic diversity of genotype and phenotype in 768 world-wild cowpea germplasm which were collected by USDA and US breeding programs. Totally 1048 genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) and 17 agronomic traits were used to analyze the genetic diversity, distance, cluster and phylogeny. The group differentiation was analyzed based on both the genotype distances from 1048 SNP markers and the phenotypic (Mahalanobis) distance D2 from 11 traits. A consistent result of diversity in genotype (polymorphism information content, PIC) and phenotype (Shannon and Simpson index) indicated that the East Africa and South Asia sub-continents were the original and secondary regions of cowpea domestication. Both dendrograms built by genetic distance present relationship among different regions, and the Mantel coefficient showed medium correlation level (r = 0.58) between genotype and phenotype. The information of both genotypic and phenotypic differentiations may help us to understand evolution and migration of cowpea more comprehensively and also will inform breeders how to use cowpea germplasm in breeding programs.