Genome-wide characterization of vegetable soybean core collection reveals genetic diversity for breeding efforts in Sub-Saharan Africa

<title>Abstract</title> <p> Vegetable soybean [ <italic>Glycine max</italic> (L.) Merr] is an underutilized legume with considerable potential to improve nutrition and diversify cropping systems in Sub-Saharan Africa (SSA). To support its genetic improvement, a soybean panel including the World Vegetable Center large-seeded soybean core collection and SSA elite grain soybeans was characterized using genome-wide single-nucleotide polymorphism (SNP) markers. Genetic groups were investigated using principal component analysis (PCA), population structure, discriminant analysis of principal components (DAPC), and phylogenetic analysis. Genome-wide analyses consistently resolved the collection into three major genetic groups. Population differentiation reflected both market class and breeding history, with two clusters grouping predominantly vegetable soybean accessions and one cluster containing mainly SSA elite grain soybeans. Analysis of molecular variance indicated that 83.78% of the total genetic variation resided within populations, whereas 16.22% occurred among populations. Cluster 1 exhibited the highest genetic diversity (PIC = 0.253; He = 0.262), whereas cluster 3, comprising predominantly SSA elite grain soybeans, showed comparatively lower diversity (PIC = 0.188; He = 0.178), indicating a relatively narrow genetic base. Pairwise F _ST and Nei's genetic distance further demonstrated moderate genetic differentiation among the three populations. The results demonstrate that the World Vegetable Center large-seeded soybean core collection represents a valuable reservoir of genetic diversity for vegetable soybean improvement. The identified population structure and diversity patterns provide a useful foundation for germplasm conservation, parental selection, and the development of vegetable soybean cultivars adapted to Sub-Saharan Africa. </p>