Core collection of Taiwanese soybeans

Vegetable soybean (Glycine max L.) stands as a significant crop in East Asia, distinguished by unique phenotypic traits such as seed size, coat color, and sweetness, setting it apart from grain soybeans. These traits are likely attributed to intensive, extensive, and long-term selection processes, yet the genomic alterations underlying these variations remain inadequately elucidated. Here, we established a core collection panel comprising 52 vegetable soybean and 192 grain soybean samples, selected from a pool of 2,394 Taiwanese accessions. Through population structure, genetic diversity, and differentiation analyses, we observed reduced genetic variability in vegetable soybeans compared to grain soybeans, with significant differentiation between the two types. Our investigation identified 159 significant signatures within 67 putative regions linked to selective breeding in vegetable soybeans, many of which overlap with previously identified genomic loci, indicating selective breeding footprints. Phenotypic variation patterns suggest that improved productivity in vegetable soybeans may be achieved by pyramiding specific favorable alleles. Furthermore, we pinpointed two promising genes, GmAP2-2 and GmTFL1b (Dt1), as potential focal points for future vegetable soybean breeding, given their roles in flowering time and seed development. This comprehensive study underscores the utility of core collection panels and provides valuable insights into soybean genetics, laying the groundwork for future breeding endeavors and research in vegetable soybeans.