Population structure and genetic diversity of cowpea germplasm from Senegal within a global framework

Characterizing the genetic diversity of crop germplasm is essential for its effective use in breeding programs. In this study, we genotyped 95 cowpea ( Vigna unguiculata ) accessions from Senegal, including cultivated, intermediate, and wild types, using the Illumina Cowpea iSelect Consortium Array (51,128 SNPs). We first compared the genetic diversity of the Senegalese collection with that of the UCR minicore collection, which represents global cultivated cowpea diversity, and then conducted a detailed analysis of the Senegalese accessions. Principal component analysis and population structure revealed the six clusters previously identified in the UCR minicore, as well as three additional groups unique to the Senegalese collection, at the optimal K (K = 9). The genetic diversity of Senegalese cultivated accessions ranked among the highest across all minicore subpopulations. These findings indicate that Senegalese cowpea germplasm is a valuable genetic resource for broadening global cowpea diversity. Within the Senegalese collection, population structure did not consistently reflect geographic origin, except for accessions from Saint Louis. Wild accessions formed a distinct and homogeneous cluster. Overall, the observed diversity highlights promising opportunities for identifying beneficial alleles that can be leveraged in cowpea breeding programs.