Genetic diversity and structure of Asian cowpea germplasm

Cowpea (Vigna unguiculata L. Walp., 2n = 2x = 22) is a vital dryland legume crop, renowned for its affordable dietary protein and essential nutrients for humans and animals. Cowpea originated in Africa and spread to various parts of the world through human migration, eventually reaching Asia. However, genetic diversity and structure in Asia cowpea remain poorly understood. This study utilized 6334 SilicoDArT and 14,482 single nucleotide polymorphism (SNP) markers to assess the genetic diversity and population structure of 405 cowpea accessions from 17 different countries, sourced from the National Agriculture and Food Research Organization (NARO) genebank in Japan. We used population structure, principal component analysis, discriminant analysis of principal components, and phylogenetic tree analysis to group the accessions into two main genetic populations. The accessions were further classified into six subgroups of African and Asian populations, corresponding to the geographical origins of the accessions. South Asian accessions showed the highest differentiation, with Nepalese accessions forming a distinct group along with Japanese accessions, highlighting that the rich genetic resources preserved within these regions may harbor valuable traits for breeding. In contrast, Southeast Asian and West African accessions exhibited low to moderate differentiation, suggesting recently shared genetic ancestry. AMOVA demonstrated that most genetic variation existed within accessions, while variation between populations was minimal. These findings highlight the rich genetic potential within the Asian cowpea germplasm, particularly in Nepalese and Japanese accessions. This study provides critical insights into breeding strategies aimed at enhancing the adaptability and productivity of cowpea in diverse environments.