Fig. 2

Epistatic interactions between soybean chromosome 3 (Gm03) and chromosomes 5 (Gm05) and 16 (Gm16). a Heat map of SNP: SNP interactions between five SNPs on Gm03 and ss715585486 (Gm05). b Heat map of SNP: SNP interactions between three SNPs onGm03 and ss715585444 (Gm16). Colors represent the -log10-transformed P value of each interaction. Statistically significant interactions are highlighted with arrows. c and d Impact of the AA allele of ss715585486 (Gm05) and the TT allele of ss715585444 (Gm16) on IDC score. Allelic combinations are provided on the X-axis with IDC visual scores on the Y-axis. These alleles confer a one-point improvement on the IDC scale. Lines that are heterozygous at the related loci were ruled out. e and (f) Candidate gene prediction for epistatic loci. The top panels show –log10 transformed P-values of the SNP: SNP interactions plotted in chromosomal position. Middle panels show all putative genes within the regions of interest; candidate genes of interest are highlighted in red. Linkage disequilibrium (r2) of chromosomal regions of interest for epistatic interactions are plotted in bottom panels