Antagonistic Transcriptional and Metabolic Networks Are Associated with Anthocyanin Accumulation in Maize Seedlings

Background: Anthocyanin accumulation is a developmentally regulated trait shaped by complex interactions between metabolic and transcriptional networks. However, dissecting the regulatory mechanisms underlying anthocyanin biosynthesis is often complicated by confounding variation in plant growth and environmental conditions. Methods: Here, we used a time-resolved multi-omics approach to investigate anthocyanin accumulation in maize seedlings by comparing an anthocyanin-rich inbred line PH19401 with an anthocyanin-deficient line YPX across five developmental stages. Results: Untargeted metabolomic and transcriptomic profiling revealed progressive divergence between the two lines beginning at early development stages. Using a dual-line, intersection-based filtering strategy, we identified a refined set of metabolites and genes closely associated with anthocyanin accumulation. These candidates were enriched in pathways related to phenylpropanoid metabolism, energy metabolism, and redox regulation. Weighted gene co-expression network analysis (WGCNA) identified two transcriptional modules that showed opposing associations with anthocyanin content. The positively associated module was centered on MYB transcription factors, consistent with canonical regulation of flavonoid biosynthesis, whereas the negatively associated module was enriched in genes involved in primary metabolism and signaling. Integration of transcriptomic and metabolomic datasets further revealed coordinated relationships between MYB hub genes and flavonoid intermediates, linking transcriptional regulation with metabolic output. Together, these results support a model in which anthocyanin accumulation is associated with activation of MYB-centered transcriptional programs and broader metabolic reprogramming that enhances precursor supply and redox balance, while competing transcriptional programs favor primary metabolism. Conclusions: This study provides a systems-level perspective on anthocyanin biosynthesis in maize seedlings and establishes an analytical framework for dissecting developmentally regulated metabolic traits.