Efficiency of SNP and SSR-based Analysis of GeneticDiversity, Population Structure, and Relationships amongCowpea (Vigna unguiculata (L.) Walp.) Germplasm fromEast Africa and IITA Inbred Lines

摘要

The extent of genetic diversity and relatedness of cowpea germplasm from East Africa are poorly understood. A set of 13microsatellites (SSR) and 151 single nucleotide polymorphisms (SNPs) markers were applied to assess the levels of geneticdiversity in a sample of 95 accessions of local cowpea germplasm and inbred lines of Vigna unguiculata. The average geneticdiversity (D), as quantified by the expected heterozygosity, was higher for SSR loci (0.52) than for SNPs (0.34). Thepolymorphic information content was 0.48 for SSR and 0.28 for SNP while the fixation index was 0.095 for SSR and 0.15 forSNPs showing moderate differentiation and high gene flow among cowpea accessions from East African countries. Theresults of data analysis of both SSR and SNP markers showed similar clustering patterns suggesting a substantial degree ofassociation between origin and genotype. Principal coordinate analysis (PCoA) with SSR and SNP markers showed thataccessions were grouped into two and three broad groups across the first two axes, respectively. Our study found that SNPmarkers were more effective than SSR in determining the genetic relationship among East African local cowpea accessionsand IITA inbred lines. Based on this analysis, five local cowpea accessions Tvu-13490, Tvu-6378, Tvu-13448, Tvu-16073,and 2305675 were identified to be tightly clustered sharing several common alleles with the drought tolerant variety Danilawhen analyzed with SSR and SNP markers. The findings will assist and contribute to future genetic diversity studies aimed atthe genetic improvement of local Eastern Africa cowpea accessions for improved overall agronomic performance in generaland breeding for drought tolerant in particular.