Fig 1.
Characterization of soybeans cultivars in the panel based on (a) commercial release year by decades (336 samples); (b) maturity group (302 samples); (c) stem termination type (260 samples).
Table 1.
SNPs marker distribution and linkage disequilibrium blocks in Brazilian soybean cultivars over 20 chromosomes (Chr).
Fig 2.
Population structure and phylogenetic tree of a set of 370 Brazilian soybean cultivars evaluated with 19,576 SNPs; (a) Delta K-values for k = 1–12; (b) Principal component analysis (PCA) plot; (c) Bar plot of individual cultivars considering K = 2. Group I (blue) with 287 cultivars and Group II (red) with 83 cultivars; The colors represent the grouping as determined by population structure analysis; (d) Bar plot of individual cultivars considering K = 3. Each individual is represented by a single vertical line with lengths proportional to each of the inferred clusters; (e) UPGMA Phylogenetic tree inferred from whole-genome SNPs of all accessions. The colors represent the grouping as determined by population structure analysis K = 2.
Table 2.
Intrapopulation genetic diversity in groups I and II of Brazilian cultivars.
Fig 3.
Distribution of the Brazilian soybean cultivars in Groups I and II considering (a) Year of release (336 accessions); (b) Maturity group (302 accessions) and (c) Stem termination type (260 accessions).
Fig 4.
Population structure of the Group I, composed of 287 Brazilian soybean cultivars evaluated with 19,576 SNPs; (a) Delta K-values for k = 1–12; (b) Principal component analysis (PCA) plot; (c) Bar plot of individual cultivars considering K = 7. The colors represent the grouping as determined by population structure analysis; Each individual is represented by a single vertical line with lengths proportional to each of the inferred clusters; (d) UPGMA Phylogenetic tree inferred from whole-genome SNPs of all accessions. The colors represent the grouping as determined by population structure analysis K = 7 with 287 accessions of Group I.
Table 3.
Matrix of Nei’s Diversity (Upper triangular) and FST values (Lower triangular) between subgroups of group I.
Table 4.
Distribution of cultivars in each subgroup based on population structure of group I and maturity groups of Brazilian soybean cultivars.
Fig 5.
Linkage disequilibrium decay in all samples (red line), group I (yellow line) and group II (green line) 1,206.19 kb.
Fig 6.
Circus plot representing the haplotype blocks distribution on soybean chromosome regions, SNP number per block, FST values, SNPs under selection and associated QTLs.
Considering the concentric circles from the outside inward, the outermost (and first) black circle indicates the numbered chromosomes. The second track is a histogram of the physical position of the 1753 haplotype blocks and its sizes in kb. The third track is the physical position of the 19,576 SNPs and the chromosomes regions of Euchromatin (red) and heterochromatin (blue). The fourth track shows the number of SNPs present in each of the haplotype blocks. The fifth track shows de FST. The sixth track shows de posterior odds (PO) of the SNPS and the 547 SNPs under selection between the group I and group II genotypes (red triangle). The seventh and the inner most track shows the distribution over the chromosomes of the 440 QTLs associated to SNPs under selection.
Table 5.
QTL categories which SNPs under selection were associated across the 20 soybean chromosomes discovered by comparing Brazilian soybean cultivars from groups I and II.