Transcriptome dynamics and allele-specific regulation underlie wheat heterosis at the anthesis and grain-filling stages

This study establishes two complementary models to decode the molecular regulation of heterosis in wheat. The "dual-engine" model demonstrates stage-specific gene expression patterns: non-additive effects predominantly drive early growth vigor during the anthesis stage, whereas additive expression patterns stabilize grain development and yield-related traits at the grain-filling stage. The "two-phase regulatory shift" model captures the dynamic temporal progression of heterotic regulation, evolving from trans-regulation-driven plastic responses at the anthesis stage to cis-regulation-mediated homeostatic control at the grain-filling stage. Importantly, the preferential coupling between cis-regulation/additive and trans-regulation/non-additive expression provides molecular evidence supporting the complementary nature of the models. We further identified developmentally specific modules (the anthesis-stage Red module and grain-filling-stage Brown module) with their core regulatory networks through weighted gene co-expression network analysis. These findings preliminarily characterize the multi-layered cooperative networks regulating heterosis development, potentially offering valuable theoretical clues for deciphering the molecular mechanisms underlying wheat heterosis.