Genetic diversity and population structure analyses of South African Bambara groundnut (Vigna subterranea [L.] Verdc) collections using SNP markers

•Bambara groundnut productivity in South Africa is low (0.62 t/ha) compared to the attainable yield of the crop reaching up to 3 t/ha.•The low productivity is attributable to a lack of improved and high yielding cultivars that are locally bred and adapted in the country.•This paper presents baseline information on Bambara groundnut genetic profile of South African collections for effective breeding and conservation.•The magnitude of the genetic diversity and population structure of Bambara groundnut collections of South Africa using high throughput single nucleotide polymorphisms (SNP) markers are highlighted to guide current and future Bambara groundnut research and development by selection genetically unique genotypes for breeding.