Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.
Figure 3: Genome-wide association scans for 3036 soybean accessions for flower color, seed-coat color, and domestication. a Manhattan plot for flower color. The solid horizontal line denotes the Bonferroni-adjusted significance threshold. Chromosomal regions of known genes (T, I, R, W1) or loci (PD05 and qSW) are indicated by dashed vertical lines. bManhattan plot for seed-coat color. c Manhattan plot for domestication. d Local Manhattan plot (top) and LD heatmap (bottom) surrounding the T locus on chromosome 6. Dashed lines indicate the region of the T locus. Physical locations (kb) are indicated under the Manhattan plot. e Local Manhattan plot (top) and LD heatmap (bottom) surrounding the qSW locus on chromosome 17. A bar indicates the region of the qSWlocus.