Epigenetic Regulation of Stress Tolerance and Fruit Quality in Fruit Crops

Epigenetic regulation and ROS signaling in plant stress adaptation: an integrated framework

Epigenetic Memory and Hormonal Crosstalk in Plant Drought Adaptation: Mechanisms, miRNAs, and Technological Advances

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.

Unravelling the Epigenetic Roles of Long Non-Coding RNAs in Plant Drought Resistance.

Drought stress is one of the most severe abiotic constraints limiting plant growth, productivity, and global food security, with its impact intensifying under climate change. Plants adapt to drought through complex physiological, transcriptional, and epigenetic regulatory networks. Among these, long non-coding RNAs (lncRNAs) have emerged as critical regulators that integrate transcriptional control with chromatin-level modulation. Once considered transcriptional noise, lncRNAs are now recognised as dynamic molecular regulators that fine-tune drought-responsive gene expression through chromatin remodelling, histone modifications, DNA methylation, RNA-directed DNA methylation (RdDM), and lncRNA-microRNA crosstalk. These mechanisms regulate key adaptive pathways, including abscisic acid (ABA) signalling, reactive oxygen species (ROS) homeostasis, osmotic adjustment, and root system plasticity. Emerging evidence further highlights the role of lncRNAs in epigenetic stress memory, enabling plants to maintain a primed transcriptional state and respond more efficiently to recurrent drought episodes. This review summarises recent advances in the epigenetic functions of lncRNAs in plant drought adaptation, with particular emphasis on chromatin dynamics, stress memory, and lncRNA-mediated regulatory networks. We also discuss insights from integrated omics approaches and highlight the translational potential of drought-responsive lncRNAs for developing climate-resilient crops.

THE EPIGENETIC LANDSCAPE OF THERMOTOLERANCE: HISTONE MODIFICATIONS AND DNA METHYLATION IN PLANT ADAPTATION TO HEAT STRESS

This abstract discusses the crucial role of epigenetic mechanisms in mediating plant adaptation and acquired thermotolerance to detrimental heat stress. The sensing of heat by plants activates complex signaling cascades that rapidly alter the chromatin landscape. Key histone modifications, such as the activating H3K4me3, are required for the transcriptional poising that enables the fast and robust induction of key heat stress-responsive genes. Simultaneously, histone modifications with repressive roles, as well as dynamic changes in DNA methylation, are indispensable for fine-tuning the transcriptional response via the silencing of non-essential or harmful genes and thereby conserving energy. Success in immediate acclimatization depends on their integrated action-epigenetic crosstalk. Moreover, these epigenetic changes are contributing to epigenetic memory, a stable cellular state that provides priming for enhanced defense upon subsequent episodes of heat stress. Intriguingly, transmission of some of these adaptive marks from parents could represent a mechanism for transgenerational epigenetic inheritance of thermo tolerance. Elucidation of this complex epigenetic architecture will therefore open promising avenues for biotechnological translation in the development of climate-resilient crops with enhanced heat stress adaptation.

Epigenetic Stress Memory and Adaptive Responses in Plants: Metabolic Reprogramming, Organelle Signalling and Systemic Acclimation.

Plants frequently encounter recurring, sequential and combined environmental stresses, yet their adaptive capacity cannot be explained solely by immediate signalling and short-term acclimation. Increasing evidence indicates that prior stress exposure can leave molecular, metabolic and physiological imprints that alter the magnitude, speed and quality of later responses, thereby giving rise to stress memory and adaptive plasticity. In plants, these persistent states are increasingly linked to epigenetic regulation, including changes in chromatin accessibility, histone modifications, DNA methylation, RNA-directed DNA methylation and non-coding RNA-mediated control. However, stress memory is not determined by chromatin regulation alone. It is also shaped by metabolic and cellular reprogramming involving osmolyte accumulation, redox buffering, energy redistribution, protein quality control, autophagy, selective protein turnover and membrane remodelling, all of which help sustain cellular homeostasis during stress and recovery. In parallel, chloroplasts, mitochondria and the endoplasmic reticulum act as stress-sensitive organelles that relay their functional state to the nucleus through retrograde signalling, while long-distance systemic communication mediated by reactive oxygen species, calcium waves, electrical and hydraulic signals, hormones and peptides coordinates whole-plant acclimation. This review synthesizes these layers into a unified framework and argues that plant resilience under fluctuating environments depends on the interaction between stress memory, metabolic plasticity, organelle-derived signalling and systemic acquired acclimation. Particular attention is given to the distinction between transient acclimation and true memory, the balance between maintenance and resetting of stress-induced states and the developmental and fitness trade-offs associated with persistent preparedness. This review also highlights major gaps that continue to limit the field, including the lack of standardized criteria for defining stress memory, insufficient causal validation of epigenetic marks, weak integration of chromatin and metabolic states with whole-plant phenotypes, and the limited translation of memory-associated mechanisms into crop performance under realistic field conditions. Overall, this review provides a comprehensive framework for understanding how plants not only respond to stress, but also encode, retain and deploy information from prior exposure to optimize subsequent adaptation.

Regulation of lipid metabolism by epigenetic mechanisms. Application to microalgae.

Microalgae are emerging as valuable model systems for studying epigenetic regulation in unicellular eukaryotes and as promising platforms for biotechnological lipid production. In these organisms, DNA and RNA methylation, histone modifications, and non-coding RNAs form interconnected regulatory layers that shape chromatin structure, genome stability, transcriptional responses, and metabolic plasticity. This review synthesizes current knowledge on epigenetic mechanisms in microalgae, with particular emphasis on environmental responsiveness, and links to lipid metabolism. The major epigenetic pathways will be described in model species, including cytosine and adenine DNA methylation, RNA methylation, histone post-translational modifications, and RNA-guided silencing mediated by small and long non-coding RNAs. Then it will be reported how environmental drivers such as salinity, nutrient limitation, light, temperature, and carbon availability remodel the microalgal epigenome. Finally, the evidence connecting epigenetic regulation to lipid accumulation will be presented, including methylation-dependent carbon reallocation, histone-modification dynamics under nutrient stress, and RNA-based regulation of lipid-related genes. Chemical perturbation and emerging epigenome-editing approaches further support the functional relevance of these pathways, although interpretation remains complicated by stress-associated secondary effects and strong lineage dependence. Overall, available studies indicate that epigenetic regulation contributes to both environmental acclimation and metabolic rewiring in microalgae, but direct causal links to lipid productivity remain limited to a small number of systems. A better mechanistic understanding of these processes will be essential for exploiting epigenetic regulation as a lever for strain improvement and sustainable lipid biotechnology.