GenXu1/Maize_Expression_Dominance: The incomplete dominance of gene expression controlled by Trans-eQTL hotspots contributes to heterosis in maize

Heterosis is a key phenomenon in genetics research and agricultural production and is primarily attributed to non-additive genetic effects. To address how these effects manifest at the transcriptomic level and contribute to phenotypic heterosis, we integrate transcriptomic and phenotypic data from a large population of maize hybrids and their inbred parents. We find that ~30 of expressed seedling genes in a substantial proportion of hybrids deviate from mid-parent expression, indicative of incomplete dominance patterns. While hybrid gene expression per se is primarily regulated by cis-eQTLs, non-additive expression is disproportionately controlled by trans-eQTL hotspots. We functionally validate ZmR1, a transcription factor associated with seedling trait heterosis, as a regulator of incomplete dominance across hundreds of genes. Overexpression of ZmR1 increases heterosis and modulates genes involved in anthocyanin and lignin metabolism. These results highlight a complex genetic architecture underlying heterosis and provide a pathway for harnessing heterosis for further crop improvement.