Epitranscriptomic modulations optimize crop traits via messenger RNA modifications

Rising global demand for food quantity and quality requires precision strategies on fine-tuning trait-related gene expression targeting crop improvement. Dynamic covalent modifications on mRNA add a reversible layer of post-transcriptional regulation on gene expression, yet their trait-level logic in crops remains fragmented. Recent studies connect epitranscriptomic enzymes and readers to yield components, quality traits and stress resilience. Here, we summarize regulatory mechanisms of covalent modifications emerging from 13 functionally validated crop cases across cereals, fiber and horticultural species, focusing on how m⁶A, m⁵C, m¹A, ac⁴C, and Ψ reprogramme mRNA molecular functions, such as stability, translation, and RNA compartmentalization. We further discuss the sufficiency and insufficiency of applying current Arabidopsis-based mechanisms to crop improvements, where whole-genome duplication and paralog specialization diversify writer-eraser-reader repertoires and enable species-specific control circuits. Finally, we highlight future directions to transform descriptive maps into predictive breeding tools, emphasizing the need for quantitative, base-resolution profiling with stoichiometric accuracy and the development of programmable, site-specific perturbation systems that can test causal relationships in defined tissues and developmental stages. These advances position epitranscriptomic reprogramming as a complementary route to precision engineering of crop yield and quality.