Sugars are not only metabolites but also signals that gate plant growth, fruit ripening, and stress responses. Carbon-sensing pathways (HEXOKINASE 1, TOR-SnRK1, and the sucrose Trehalose-6-phosphate 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.

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