Core collection of Taiwanese soybeans

NOTICE At the authors' request, the data files for this submission
have been removed from public view due to concerns regarding compliance
with data usage agreements. (June 2024) 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.