Environmental stress significantly affects plant growth, development, and survival. Plants respond to stressors such as temperature fluctuations, water scarcity, nutrient deficiencies, and pathogen attacks through intricate molecular and physiological adaptations. Epigenetic mechanisms are crucial in regulating gene expression in response to environmental stress. This review explores the current understanding of epigenetic modifications, including DNA methylation, and their roles in modulating gene expression patterns under environmental stress conditions. The dynamic nature of epigenetic modifications, their crosstalk with stress-responsive pathways, and their potential implications for plant adaptation and crop improvement are highlighted in the face of changing environmental conditions.

Rice (Oryza sativa L.) is a staple food for over half the global population and a model organism for monocot plant research. However, it is susceptible to salinity, with most cultivated varieties showing reduced growth at salt levels above 3 dS/m. Despite numerous efforts to improve its salt tolerance, little progress has been made. A promising area of research lies in the study of epigenetic regulation, which encompasses DNA methylation, histone modifications, and chromatin remodelling. These processes play a crucial role in mediating how plants respond to salt stress by modulating gene expression. This often results in heritable changes that can be used as molecular markers. Studies in rice and other cereals have demonstrated a clear association between histone alterations, shifts in DNA methylation patterns, and the expression of salt-responsive genes. Furthermore, epigenetic mechanisms contribute to the development of stress memory, enabling plants to respond more effectively to recurring stressful conditions. Understanding these regulatory pathways offers new opportunities for breeding or engineering salt-tolerant rice varieties, potentially leading to improved crop resilience and productivity under saline conditions.

Heavy metal and metalloid stress, particularly from toxic elements like cadmium (Cd), poses a growing threat to plant ecosystems, crop productivity, and global food security. Elevated concentrations of these contaminants can trigger cytotoxic and genotoxic effects in plants, severely impairing growth, development, and reproduction. In recent years, epigenetic mechanisms have emerged as crucial regulators of plant responses to heavy metal stress, offering novel insights and strategies for enhancing plant resilience in contaminated environments. This review synthesises current advances in the field of plant epigenetics, focusing on key modifications such as DNA methylation, histone acetylation and remodelling, chromatin dynamics, and small RNA-mediated regulation. These processes not only influence gene expression under metal-induced stress but also hold promise for long-term adaptation through transgenerational epigenetic memory. Recent developments in high-throughput sequencing and functional genomics have accelerated the identification of epigenetic markers associated with stress tolerance, enabling the integration of these markers into breeding programs and targeted epigenome editing strategies. Special attention is given to cadmium stress responses, where specific epigenetic traits have been linked to enhanced tolerance. As plant epigenomic research progresses, its application in sustainable agriculture becomes increasingly evident offering environmentally friendly solutions to mitigate the impact of heavy metal pollution. This review provides a foundation for future research aimed at leveraging epigenetic tools to engineer crops capable of thriving under metal stress, thereby contributing to resilient agricultural systems and sustainable food production.

Non-CG DNA methylation plays a critical role in regulating root development and stress responses in Arabidopsis thaliana under cadmium (Cd²⁺) exposure. We compared wild type (WT) plants with the ddc triple mutant (deficient in DRM1, DRM2, and CMT3) to assess how epigenetic modifications affect the root apical meristem (RAM) under 100 µM and 150 µM CdCl₂ treatments. Cd²⁺ exposure led to RAM disorganization, reduced cortical cell number, and quiescent center (QC) cell loss in WT roots, while ddc mutants maintained meristem integrity and exhibited QC cell expansion. Auxin signaling, assessed via pDR5::GFP, was disrupted in WT roots at high Cd²⁺ levels but remained stable in ddc mutants. Similarly, WT roots showed elevated reactive oxygen species accumulation under stress, whereas ddc mutants displayed a reduced oxidative response. These results suggest that non-CG DNA methylation suppresses key regulators of stem cell maintenance, hormonal balance, and redox homeostasis during heavy metal stress. Loss of this methylation in the ddc mutant confers enhanced resilience to Cd²⁺ toxicity, highlighting an epigenetic mechanism underlying root stress adaptation.

DNA methylation regulates plant growth by modulating gene expression; however, its contribution to hormone responsiveness and photomorphogenesis remains only partially understood. We examined Arabidopsis thaliana DNA methylation mutants met1 and drm1, drm2, and cmt3 (ddc) under defined light regimes and following exogenous treatments with auxin, gibberellin, and the auxin transport inhibitor TIBA. Hypocotyl elongation and cotyledon expansion exhibited strong light dependency across all genotypes, with met1 seedlings developing a consistently reduced cotyledon area and ddc seedlings displaying impaired hypocotyl elongation under specific light qualities. Exogenous auxin inhibited growth in all genotypes, whereas GA₃ promoted elongation in hypocotyls and roots (by approximately 75–80% and 15–35%, respectively, in Col0 and met1), with ddc exhibiting delayed and non-linear dose-dependent sensitivity. Quantitative RT–PCR analysis revealed differential expression of genes involved in auxin transport (PIN1, PIN3, PIN7), auxin signalling (ARF7, IAA3, LAX3), circadian regulation (TOC1, LHY, CCA1), and light signalling (PIFs, HY5, HYH), supporting a link between DNA methylation status and coordinated regulation of hormone-, light-, and clock-controlled transcriptional networks. Together, these findings demonstrate that MET1- and DRM/CMT-dependent methylation pathways integrate epigenetic regulation with environmental and hormonal cues, modulating the intensity, timing, and organ specificity of growth responses, thereby fine-tuning growth plasticity during early Arabidopsis seedling development.

Drought poses a major threat to global food security, making it critical to understand the molecular mechanisms underlying plant responses to water scarcity. Epigenetic modifications, including DNA methylation and histone alterations, play central roles in regulating genes and hormonal pathways essential for drought adaptation. MicroRNAs, while primarily functioning as post-transcriptional regulators, can also influence epigenetic pathways and contribute to chromatin remodelling, suggesting a role in modulating epigenetic memory. Investigating these interactions is essential for understanding how plants integrate epigenetic and post-transcriptional regulation during stress. Epigenetic memory in drought-adapted plants provides insights into the transgenerational inheritance of adaptive traits and reveals how plants balance genome stability with flexibility. The crosstalk between epigenetic mechanisms and hormonal signalling is crucial for fine-tuning gene expression, promoting drought resilience. This review proposes a conceptual framework integrating epigenetic, hormonal, and miRNA-mediated regulation of drought responses. It emphasizes the impact of advanced technologies, such as bisulfite sequencing and CRISPR-Cas9, in dissecting plant epigenetic responses to drought. These approaches improve our understanding of drought tolerance mechanisms and offer promising strategies for developing resilient crops for sustainable agriculture. However, direct evidence linking epitranscriptomic modifications to long-term drought memory remains limited, and this emerging regulatory layer requires further experimental validation.