Molecular characterization of some wild accessions of cowpea (Vigna spp.) using single nucleotide polymorphisn (SNP) marker

Abstract

Molecular characterization of five wild cowpea (Vigna spp.) accessions was conducted at the African Bioscience Molecular Laboratory, Ibadan, Nigeria, using Single Nucleotide Polymorphism (SNP) markers. SNP analysis revealed allele counts ranging from 48 to 86, indicating nucleotide variation across accessions. All accessions exhibited singleton alleles, suggesting rare genetic variants. Four accessions (TVnu-561, TVnu-563, TVnu-1148, and TVnu-1395) showed transcriptional activity, while TVnu-59 did not. The SNP data generated moderate polymorphism, with a high Minor Allele Frequency (MAF) of 0.80 and heterozygosity of 0.32, reflecting similar genetic diversity among transcribed accessions. The Polymorphic Information Content (PIC) value of 0.26 indicated multiple alleles with comparable frequencies. Sequence alignments revealed the co-existence of multiple alleles at specific loci. Haplotype analysis showed that TVnu-561 and TVnu-1395 (haplotypes 1 and 3) were 40% monomorphic, while TVnu-563, TVnu-1148, and TVnu-1395 (haplotype 2) exhibited 60% polymorphism. Notably, TVnu-1395 displayed both monomorphic and polymorphic traits, suggesting partial genetic divergence. Variations in haplotype sequences were influenced by the number of annealing sites in the genome. These findings provide insight into intra-specific genetic variation among wild cowpea accessions and may inform future breeding strategies aimed at improving cowpea genetic resources.