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

Abstract

• 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. Bambara groundnut ( Vigna subterranea [L.] Verdc) is a highly nutritious grain legume with a significant potential to develop various commercial food and feed products. It is a resilient crop able to grow under harsh climates and poor soil conditions. 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. Genetically diverse and locally adapted Bambara groundnut landrace varieties and exotic collections are present in South Africa for strategic breeding to improve yield and yield-related traits and nutritional quality. The objective of this study was to determine the magnitude of the genetic diversity and population structure of Bambara groundnut collections of South Africa using high throughput single nucleotide polymorphisms (SNP) markers. Ninety-three genotypes were assessed using genotyping with 2286 SNP markers and some unique complementary morpho-agronomic traits of the crop. The mean genetic diversity value was 0.32, revealing moderate genetic differences among the assessed genotypes. Cluster and structure analyses grouped the test genotypes into two distinct categories. Further, the analysis of molecular variance partitioned the total genetic variation into among genotypes (90%), within genotypes (8%) and among populations (2%). The results revealed two heterotic groups for hybridization and selection programs. The following unique genotypes were selected: ARC Bamb 37 (with spreading growth type), ARC Bamb 49 (bunch type), ARC Bamb 61 (semi-bunch) and ARC Bamb 83 (spreading) using the SNP markers and desirable agronomic traits. The study provided new insight on Bambara groundnut genetic profiles of South African collections which will assist in conservation strategy and management of the crop for effective breeding.