Epigenetic and Epitranscriptomic Antiviral Responses in Plants for Disease Management

Plant viral diseases cause significant agricultural losses worldwide and are shaped by complex virus-host and virus-virus interactions. Unlike fungal or bacterial pathogens, viruses cannot be directly controlled with chemicals, and their management relies on insect vector control and the development of virus-resistant plant varieties. Plants deploy endogenous epigenetic (DNA/chromatin-based) and epitranscriptomic (RNA-based) mechanisms to limit viral infections. RNA silencing pathways, particularly post-transcriptional gene silencing (PTGS) mediated by small RNAs, restrict viral replication and shape viral populations. Additional layers, including RNA-directed DNA methylation (RdDM), N6-methyladenosine (m⁶A) RNA modifications, histone modifications and chromatin remodeling, further modulate host–virus interactions. DNA methylation can be inherited and may confer resistance to future generations, although its stability is partial and context-dependent. Virus-derived 24-nt small interfering RNAs (siRNAs) act as mobile signals, inducing systemic gene silencing and potentially influencing viral population dynamics. Understanding these epigenetic and epitranscriptomic mechanisms can improve virus diagnosis, pathogenesis studies and disease management, while also providing insights into viral diversity and co-infection dynamics. This review synthesizes current knowledge of these mechanisms and discusses their implications for developing sustainable antiviral strategies.