Diversity analysis and genome-wide association studies of seed weight trait in Bambara groundnut (Vigna subterranea (L.) Verdc.) using DArTseq-derived SNP markers

Abstract Bambara groundnut is an indigenous legume cultivated in Africa and referred to as ‘poor man’s crop. Seed weight is an important trait that end-users consider in Bambara groundnut because it is associated with better yield. The crop is drought tolerant compared to other legumes. In Kenya, the crop is grown by women and the diversity of the accessions grown is unknown. Lack of information on the crop’s diversity and population structure make selection and genetic improvement of the crop difficult. The objective of this study was to: i. determine the genetic diversity and population structure of 86 Bambara groundnut accessions from western and coastal Kenya using 4,399 SNP markers and ii) identify SNPs associated with the seed weight of the Bambara groundnut collection. The DArT complexity reduction approach in combination with Illumina short-read sequencing (HiSeq 2000) was applied. Population structure analysis revealed three distinct genetic clusters implying that the accessions were from three major gene pools. Analysis of molecular variance showed a low level of differentiation among the populations implying the need to broaden the genetic base of the collection tested in this study. The study revealed 8 significant DArTseq derived SNP markers (P < 0.05) distributed across Bambara groundnut contigs 1, 2, 3, and 5 associated with seed weight. The study demonstrated low genetic variation among the populations but a high genetic variability within population. There will be a need to validate the generated markers and conduct whole genome association studies with other economically important traits in Bambara groundnut.