Fig. 5: Distinct patterns of cumulative epistatic effects highlighted by three heterotic QTL (hQTL).

The three hQTL were detected for grain yield MPH in the integrated data set: Integrated_GY_hQTL128 (a, d, g), Integrated_GY_hQTL149 (b, e, h), and Integrated_GY_hQTL142 (c, f, i). a–c The phenotypic distribution of grain yield MPH for hybrids harboring different alleles for the peak SNP within hQTL. d–f The phenotypic distribution of grain yield MPH for hybrids with distinct genotype combinations of the peak SNP within hQTL and the SNP showing the most significant epistatic interaction effect with the peak SNP. In each group, the mean MPH value was indicated by red dots and the number of hybrids was shown below the boxplot. Boxes indicated the interquartile range (IQR, the difference between the 75th and the 25th percentile) with the median line, whiskers extend to the most extreme values within 1.5 × IQR. Different letters above the boxes indicated significant differences among groups as determined by the Least Significant Difference (LSD) test (P < 0.05), while groups sharing the same letter are not significantly different. g–i Circled Manhattan plot of epistatic effects between the peak SNP of hQTL and all other SNPs in which the 10 SNPs with most significant epistatic effect was highlighted by red circles and linking lines in the center. Different colors were used to indicate the types of epistatic effects: orange (additive-by-additive), blue (additive-by-dominance), green (dominance-by-additive) and purple (dominance-by-dominance). Significance was assessed by the Wald test, and the thresholds (P < 0.05 after Bonferroni-Holm correction for multiple testing) were indicated as red dashed lines.