Fig. 4

Schematic illustration of the inference of additive, dominant, and epistatic QTLs. a Schematic illustration of the inference of additive and dominant QTLs represented by two genes, Gene A and Gene B, respectively, based on the differential patterns of GWAS signals across maternal and F₁ populations, and the MPH of F₁ hybrids. Strong (uppercase letter) and weak (lowercase letter) genotypes are defined by the corresponding strong and weak phenotype of the maternal lines, respectively. The paternal genome always provides a strong allele, marked in red. b Schematic illustration of the inference of epistatic QTLs represented by two genes, Gene C and Gene D, that are epistatically repressed by unknown Gene X in maternal genomes. When the maternal Gene x allele is combined with the dominant X allele from the paternal genome, Gene C and Gene D are activated and exhibit additive and dominant effects, respectively. D × A and D × D represent the epistatic effects of dominant by additive and dominant by dominant interactions, respectively. c A putative model for the interpretation of the regulatory interactions between Genes C and D, and Gene X. In the maternal genome, Gene X with homozygous, recessive alleles represses the transcription of Genes C and D (left panel). In the F₁ hybrid, the dominant X allele from the paternal genome complements the recessive x allele of Gene X, and the repressive effect on Gene C and D is relieved. Then, transcription of Gene C and D is activated with different expression dosages based on their additive and dominant effects