Additive and partially dominant effects contribute to crop heterosis

The molecular mechanisms of heterosis remain debated due to discrepancies in factors such as species, phenotypes, hybrid populations, developmental stages or growth environments. Here, heterosis-associated genes and metabolites were screened from differential molecules in parents, and the main inheritance patterns of these molecules were additive and partially dominant effects, namely, at the middle parent levels and between the parental and middle parent levels. The additive and partially dominant effects contributed to heterosis of 17 rice agronomic traits, including grain yield and plant height across developmental stages, and to heterosis of F1 hybrids from different populations or environments in both rice and maize. Furthermore, the two inheritance patterns were associated with parental genomic variants, particularly unique single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), which were correlated with heterosis of agronomic traits. Our study systematically integrates parental genetic variation and highlights the predominant genetic effects of additive and partially dominant in crop heterosis.