Cowpea (Vigna unguiculata (L.) Walp) is an important legume crop with immense potential for nutritional and food security, income generation, and livestock feed in Sub-Saharan Africa. The crop is highly tolerant to heat and drought stresses which makes it an extremely important crop for improving resilience in crop production in the face of climate change. This study was carried out to assess the genetic diversity and population structure of 90 cowpea accessions using single nucleotide polymorphism (SNP) markers. Out of 11,940 SNPs used, 5864 SNPs were polymorphic and maintained for genome diversity analysis. Polymorphic information content (PIC) values ranged from 0.22 to 0.32 with a mean value of 0.27. The model-based Bayesian STRUCTURE analysis classified 90 cowpea accessions into four subpopulations at K = 4, while the distance-based cluster analysis grouped the accessions into three distinct clusters. The analysis of molecular variance (AMOVA) revealed that 59% and 69% of the total molecular variation was attributed to among individual variation for model-based and distance-based populations, respectively, and 18% was attributed to within individual variations. Furthermore, the low heterozygosity among cowpea accessions and the high inbreeding coefficient observed in this study suggests that the accessions reached an acceptable level of homozygosity. This study would serve as a reference for future selection and breeding programs of cowpea with desirable traits and systematic conservation of these plant genetic resources.

The identification of high-yielding and stable genotypes for cultivation across differential production regions is among the key breeding objectives in cowpea improvement programs. This study was aimed to determine genotype-by-environment interaction (GEI) for grain yield to select high-yielding and stable cowpea genotypes for production in South Africa and identical agro-ecologies, and for cultivar development. Fifty cowpea genotypes were tested for grain yield across seven environments of South Africa using a 10 × 5 alpha lattice design replicated three times, during the 2019/2020 and 2020/2021 planting seasons. Grain yield data were subjected to analysis of variance (ANOVA), additive main effects and multiplicative interaction (AMMI) and the genotype-by-environment interaction (GGE) biplot analyses. ANOVA and AMMI showed significant genotype, environment and GEI effects. High grain yield was recorded for genotypes G35 (0.47 t ha⁻¹), G1 (0.45 t ha⁻¹) and G47 (0.43 t ha⁻¹) across test environments. AMMI stability values (ASV); identified Acc-Cowp44 as the most stable genotype across all sites, recording the lowest ASV of 0.03. The comparison view of GGE biplot revealed Acc-Cowp29, Acc-Cowp38 and Acc-Cowp5 as ideal genotypes, possessing high grain yield of 0.19, 0.47 and 0.36 t ha⁻¹, respectively. The identified genotypes are recommended for production and inclusion in subsequent breeding activities.