Single nucleotide polymorphism (SNP)-based genetic diversity in a set of Burkina Faso cowpea germplasm

Abstract

The potential of cowpea to address food security in Burkina Faso in particular is well established as it is a nutritious, cash and cover crop. However, there is limited information on existing germplasm diversity in Burkina Faso. This study was designed to gather some information on the genetic diversity in a set of cowpea lines introduced from different breeding programs. The diversity was therefore assessed using 181 single nucleotide polymorphism (SNP) markers on 50 cowpea lines. Leaf samples of young plants were collected using LGC genomics genotyping platform protocols for DNA extraction and genotyping. Data were then analyzed using 3 software for pair-wise distance, phylogenetic pattern by UPGMA and for the descriptive statistics determination. The phylogenetic pattern of this germplasm revealed seven clusters. The lines were almost grouped based on their geographical origin, and the breeding background. Thus, materials which originated from Burkina Faso were clustered in the same group while those from IITA/Nigeria were also almost all clustered in the same group. The genetic distance was low (≤0.29) suggesting a narrow genetic base in the cowpea germplasm used in this study. SNPs were efficient in the study of the diversity and a core collection of 20 lines was generated for further use in the breeding program.