DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications

Abstract

Abiotic stresses such as drought, salinity, extreme temperatures, and heavy metal contamination severely limit global crop productivity and threaten food security. Plants have evolved epigenetic strategies, particularly DNA methylation, to perceive, adapt to, and memorize environmental challenges. This review systematically elucidates the dynamic regulatory mechanisms of DNA methylation-including establishment via RNA-directed DNA methylation (RdDM), maintenance by methyltransferases (MET1, CMT), and active removal by demethylases (ROS1)-in plant responses to diverse abiotic stresses. We highlight how stress-induced methylation reprogramming modulates gene expression, chromatin states, and physiological adaptations, contributing to both somatic and transgenerational stress memory. Furthermore, we discuss advanced detection technologies for profiling methylation patterns and evaluate their applications in epigenetic breeding, such as exploiting heritable epialleles, RdDM-based gene silencing, and methylation markers for heterosis prediction. Despite significant progress, translating epigenetic insights into predictable breeding tools remains challenging. Future efforts should focus on establishing causal links between methylation changes and stress phenotypes, improving epigenome editing precision, and integrating multi-omics approaches for the development of climate-resilient crops. This work provides a comprehensive epigenetic perspective for enhancing crop adaptability and sustainable agriculture.