Heterosis has been widely used in a

Heterosis has been widely used in agriculture, but the molecular mechanism for thisremains largely elusive. In Arabidopsis hybrids and allopolyploids, increased photosyntheticand metabolic activities are linked to altered expression of circadian clock regulators,including CIRCADIAN CLOCK ASSOCIATED1 (CCA1). It is unknown whether a similarmechanism mediates heterosis in maize hybrids. Here we report that higher levels of carbonfixation and starch accumulation in the maize hybrids are associated with altered temporalgene expression. Two maize CCA1 homologs, ZmCCA1a and ZmCCA1b, are diurnally up-regulated in the hybrids. Expressing ZmCCA1 complements the cca1 mutant phenotype inArabidopsis, and overexpressing ZmCCA1b disrupts circadian rhythms and biomass heter-osis. Furthermore, overexpressing ZmCCA1b in maize reduced chlorophyll content andplant height. Reduced height stems from reduced node elongation but not total node num-ber in both greenhouse and field conditions. Phenotypes are less severe in the field than inthe greenhouse, suggesting that enhanced light and/or metabolic activities in the field cancompensate for altered circadian regulation in growth vigor. Chromatin immunoprecipita-tion-sequencing (ChIP-seq) analysis reveals a temporal shift of ZmCCA1-binding targets tothe early morning in the hybrids, suggesting that activation of morning-phased genes in thehybrids promotes photosynthesis and growth vigor. This temporal shift of ZmCCA1-bindingtargets correlated with nonadditive and additive gene expression in early and late stages ofseedling development. These results could guide breeding better hybrid crops to meet thegrowing demand in food and bioenergy.