Hybridization reshapes maize phenotypic plasticity through coordinated changes in environmental responses and genetic architecture

Phenotypic plasticity is central to crop adaptation under climate variability, yet how hybridization reshapes it remains unclear. Here, we integrate multi-environment phenotypes, environmental variables, and genomic data from 456 maize inbred lines and 912 corresponding hybrids evaluated across 11 environments to dissect the environmental and genetic bases of plasticity for flowering time, plant height, and ear weight. Reaction-norm analyses reveal two- to three-fold greater plasticity variation in inbreds than hybrids, indicating more uniform plastic responses in hybrids. Environmental association analyses demonstrate that inbreds and hybrids respond to the same environmental factors with different magnitudes or even opposite directions (e.g., correlations between diurnal temperature range and flowering time ranged from -0.73 to -0.14 in inbreds but 0.22 to 0.46 in hybrids). Genome-wide association analyses identify distinct parental loci for plasticity, with more loci and larger effects in hybrids. Functional validation shows that ZmBAF60_13, a chromatin-remodeling gene found only in the inbred panel, negatively regulates flowering-time plasticity. Integrating multiple environmental indices improves phenotype prediction accuracy by up to 16% over single-index models. Together, this study reveals that hybrids exhibit reduced plasticity variation and differ from inbreds in environmental responses and genetic associations, providing a framework for predicting crop performance under climate variability.