Diversity analysis and genome‑wide association studies of seed weight trait in Bambara groundnut (Vigna subterranea (L.) Verdc.) using diversity array technology sequence derived single nucleotide polymorphism markers

Abstract

Bambara groundnut is an indigenous drought tolerant legume cultivated in Africa. In

Kenya, the crop is grown by women and the diver- sity of the accessions grown is unknown. Lack of

information on the crop’s diversity and population

structure make genetic improvement of the crop dif- fcult. The objectives of this study were to: (i) deter- mine the genetic diversity and population structure of

86 Bambara groundnut accessions from Kenya using 4,399 SNP markers and, (ii) identify SNPs associated

with the seed weight of the Bambara groundnut col- lection. The DArT complexity reduction approach

in combination with Illumina short-read sequencing

(HiSeq 2000) was applied. Population structure anal- ysis suggested three genetic clusters. Accessions from

the same county grouped into diferent clusters with exception of accessions from Kilif that distinctly

fell into the same cluster. Analysis of molecular vari- ance indicated that 0.16% of the variance was due to genetic diferentiation among the populations, 19% of the variance was as a result of diferentiation among individuals within populations, and 81% variation was within individuals in a population. The study

suggested signifcant DArTseq derived SNP mark- ers (p<0.05) distributed across Bambara groundnut

contigs 1, 2, 3, and 5 associated with hundred seed

weight, though the identifed SNPs were not vali- dated. This study provided an important foundation

by ofering valuable insights into the genetic diversity of Bambara groundnut in traditional cultivation areas in Kenya. These fndings can serve as a starting point for further validation and application in Bambara groundnut breeding programs.