Diversity, population structure, and linkage disequilibrium among cowpea accessions

Abstract

Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor-joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUCTURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005-0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48-0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for great physical distances between markers. The LD decay distance varied among chromosomes with the average distance of 80-100 kb across the genome. Thus, crop improvement is possible, and the LD will facilitate genome-wide association studies on quality attributes and critical agronomic traits in cowpea.