Epigenetic orchestration of sugar signaling in plant development and stress adaptation

Abstract Sugars are not only metabolites but also signals that gate plant growth, fruit ripening, and stress responses. Carbon-sensing pathways (HEXOKINASE 1 perception, TOR-SnRK1, and the sucrose-trehalose-6-phosphate (T6P) pathway) reprogram gene expression by engaging DNA methylation, histone modification, chromatin remodeling, regulatory RNAs, and RNA modifications. Cutting-edge quantitative epigenomic and epitranscriptomic methods, integrated with novel bioinformatics tools, are driving unprecedented resolution in epigenetic landscape analysis. Benefitting from state-of-the-art technologies, we summarize epigenetic control points for pigmentation, softening, sugar-acid balance, and stress acclimation (e.g., SlDML2, PH5, RdDM-ABA modules). This synthesis underscores that decoding the sugar-epigenome interplay is key to understanding plant phenotypic plasticity and improving crop performance. Finally, we explore how leveraging epigenetic regulation via CRISPR-based epigenome editing, transgenerational inheritance patterns, and epigenomic biomarker-based (epibreeding) approaches holds promise for improving crop resilience and productivity.