Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers

Abstract

Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.

Phenotypic and genotypic diversity of Bambara groundnut (Vigna subterranea L. Verdc) germplasm in Malawi

“…This is in contrary with the phenotypic data, which revealed a total variation of 53 % among the Bambara groundnut germplasm using Principal component analysis. But the results are in agreement with the study by Uba et al, 2021 where the AMOVA reported that 89% of genetic variation occurred among the populations, 8% between regions, and 3% between populations. The greater the genetic diversity of the germplasm, the greater the likelihood of success in breeding desirable traits.…”

“…Through QDS, small holder farmers can produce seed to engage in integrated seed system, including informal and formal seed systems to meet the various demands on the market (Mastenbroek et al, 2021, Almekinders & Louwaars, 2002. Currently there is low production of Bambara groundnut in Malawi (Figure S3) and some of the major reasons for its low production and productivity is the lack of introduction of high yielding genotypes in areas of cultivation, inadequate knowledge of taxonomy, lack of genetic improvement and adaptation to speci c agro-ecological zones ( Pungulani et al, 2012;Uba et al, 2021). Variation within individual gene loci/among alleles of a gene, or gene combinations, between individual plants or plant populations are referred to as genetic diversity (Sood et al, 2016).…”

The Exploitation of Orphan Legumes for Food, Income, and Nutrition Security in Sub-Saharan Africa

“…Likewise, 493 SNPs were used for the genotyping of a population of 281 Kersting’s groundnut accessions from Benin using the DArTseqTM approach with about 10.6% of the SNPs found to be aligned to the reference genomes of adzuki bean and mung bean, an indication of an evolutionary relationship of Kersting’s groundnut with adzuki bean and mung bean ( Akohoue et al, 2020 ; Paliwal et al, 2021 ). Uba et al (2021) utilized DArTseq and SNP for genetic diversity and population structure studies on some genotypes of BG obtained from Nigeria, Cameroun, West Africa, East, and Southern Africa regions. The analyses of the results revealed that the mean gene diversity was highest 0.478) in Nigeria/Cameroon and West Africa region within the populations across the five regions and revealed the highest Shannon diversity index (0.787) in the West African region.…”

“…The analyses of the results revealed that the mean gene diversity was highest 0.478) in Nigeria/Cameroon and West Africa region within the populations across the five regions and revealed the highest Shannon diversity index (0.787) in the West African region. Likewise, it also indicated that among the populations the genotypes in the unknown origin population from the United Kingdom was more closely related to the Western Africa population (0.018), and then the Nigeria/Cameroon populations (0.020) which were all grouped into a single subpopulation which was the largest based on the population structure generated by ADMIXTURE model among the 270 BG genotypes evaluated ( Uba et al, 2021 ). Not much effort has been done in the use of gene technology or modern biotechnology for the genetic improvement of orphan legumes.…”

Genetic diversity and population structure of some Nigerian accessions of Bambara groundnut (Vigna subterranea (L.) Verdc.,) using DArT SNP markers

“…(Atoyebi et al 2017). Molecular research provides new insight on the population structure of African Bambara groundnut germplasm which will help in conservation strategy and management of the crop (Uba et al 2021). Published research works relating to African orphan crops emphasized on the need for more molecular research to harness the hidden potentials (Mayes et al 2013;Ntundu et al 2006).…”