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
Loading...
Date
2025-02-22
Journal Title
Journal ISSN
Volume Title
Publisher
UoEm
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.
Description
Article
Keywords
DArT markers, Genetic diversity, Population structure, Genome wide association, Vigna subterranea, SNP markers
Citation
https://doi.org/10.1007/s10681-025-03478-8