SNP VARIATION AND PHYLOGENETIC PATTERNS OF THE CPDNA RPOA GENE IN BAMBARA GROUNDNUT (VIGNA SUBTERRANEA (L.) VERDC) GENOTYPES

Abstract

Bambara groundnut (Vigna subterranea (L.) Verdc), a legume native to Africa, has the potential to address food security challenges on the continent. However, it is an underutilised crop because there hasn't been enough research done on its genetic diversity, selection, and breeding, particularly with the use of genomic tools. Chloroplast DNA (cpDNA) is a short, compact, circular, and double-stranded DNA structure present in plants. Its size ranges from 83 to 292 kilobases. It exhibits uniparental inheritance, with maternal inheritance being more prevalent in angiosperms and paternal inheritance in gymnosperms. This study was aimed at assessing the single nucleotide polymorphism (SNPs) and phylogenetic analysis of rpoA gene sequences in Bambara groundnut genotypes from Nigeria, West-African Subregion, using polymerase chain reaction (PCR) and agarose gel electrophoresis. PCR amplification of the rpoA gene shows the resulting fragments observed on the gel had an approximate length of 1000 base pairs (bp). This consistent fragment length of around 1000 bp was observed across all seven different genotypes of Vigna subterranea that were examined in the study. A total of 442 SNP variations were detected in the 5’ untranslated region (5’-UTR) region and 437 in the 3’ untranslated region (3’-UTR) regions from the sequence of seven genotypes of Vigna subterranea rpoA gene, which represent 4.2 and 4.4%, respectively, which suggest a certain diversity within the studied genotypes. The frequency of the predominant allele varied, with GDK having the lowest frequency at 0.58, while GNR had the highest frequency at 0.89. GNR exhibited a total gene diversity of 0.480, and the Shannon diversity index reached its peak at 0.786 in the DWS genotype. Genetic distances between pairs of regions showed variability, ranging from 0.001 to 0.050. Notably, higher similarity was observed between the KSSB-KSSC and DWS-DAG genotypes. Cluster analysis based on genotypic data grouped the 7 samples into 4 clusters. Based on genotypic data, it can be concluded that there is a significant degree of genetic diversity in the germplasm genotyped that can be used by plant breeders in crop improvement programmes. This diversity can be valuable for breeding programmes aimed at developing more resilient or improved varieties of this plant species