Extended Data Fig. 8: Evaluating the contribution of dominance and over-dominance effects QTLs identified in indica-japonica segregating populations.

In rice hybrids, male parents generally have much better yield performance than female parents, so better parent heterosis mostly refers to the advantage over male parents. Therefore, the over-parent heterosis observed in hybrids is predominantly attributable to the influence of positive partial dominance effect loci contributed by female parents, as well as over-dominance effect loci from both parental lines. Thus, female-contributed QTLs that displayed positive dominance effects and the QTLs that demonstrated over-dominance effects were included for analysis. The d/a index is applied to measure the magnitude of dominance effect. d/a ≤ 1 and >1 refer to positive partial dominance (blue) and over dominance effect (orange), respectively.