Integrated Transcriptomic and Metabolomic Analyses Reveal Diurnal Regulation of Carbon–Nitrogen Metabolism in Maize

Background: Diurnal rhythms are orchestrated by an endogenous clock that synchronizes multiple metabolic processes in plants. While maize growth exhibits diurnal rhythmic characteristics, the regulatory framework governing the rhythmic patterns of its carbon–nitrogen (C/N) metabolism remains to be systematically characterized. Methods: In this study, multi-omics analysis was performed to dissect the diurnal regulatory mechanism responsible for C/N allocation in maize. Results: Maize seedlings display a distinct diurnal pattern in biomass accumulation, characterized by net gains during the light period and partial losses during darkness. A total of 923 metabolites and 3702 rhythmic genes were detected through multi-omics analysis. Among these, 46 rhythmic genes and 16 metabolites were identified within the C/N metabolic pathways, encompassing carbon fixation, the Calvin cycle, starch and sucrose synthesis, glycolysis, the tricarboxylic acid cycle (TCA), the pentose phosphate pathway (PPP), and nitrogen assimilation. Furthermore, ZmDBB10, ZmMYB23, and ZmAPRR9 were identified as three candidate transcription factors potentially orchestrating the diurnal characteristics of C/N metabolism. Conclusions: These transcription factors may drive time-dependent metabolite accumulation by modulating key synthase genes within the C/N metabolic network, potentially contributing to diurnal homeostasis of C/N metabolism and promoting growth adaptability in maize.