DNA methylation regulates gene expression under abiotic stress conditions by regulating TE. Under abiotic stress, WGBS reveals TE hypomethylation that reactivates nearby stress-responsive genes, promoting phenotypic plasticity (Ramakrishnan et al., 2022). These patterns are illustrated in Figure 1, showing TE-gene interactions under stress. Stress-induced hypomethylation reactivates Ty1 and Ty3 retrotransposons in Moso bamboo, producing lncRNAs and circRNAs that target stress genes, to correlative evidenced by bisulfite sequencing (Ding et al., 2024). These dynamic methylation changes contribute to both immediate responses and stress memory. However, causal validation requires TE-specific epigenome editing, which remains limited (Ma et al., 2024).

Environmental stress can also cause variations in methylation forms that affect the expression of stress-responsive and plant growth-regulating genes. In rice, bisulfite sequencing revealed promoter hypomethylation of OsGLP8–10 and OsGLP12 under salinity, which correlated with upregulation, though no functional mutants have been reported (Anum et al., 2023). Chickpea gene-body CG hypermethylation under salinity inversely correlates with expression (correlative; WGBS data), while foxtail millet demethylase upregulation suggests active adaptation (Gupta and Garg, 2023; Sun et al., 2024). DNA methylation thus modulates ABA signaling pathway genes during drought stress. Figure 2 illustrates the epigenetic regulation of stress-responsive genes under various abiotic stresses, including drought, cold, heat, and salinity, highlighting key modifications such as DNA methylation, histone modifications, and small RNAs. Targeted demethylation through dCas9-TET1 could enable breeding (Yin et al., 2024). Table 1 integrates DNA methylation with histone modifications discussed in Section 2.2, offering a summary of the key mechanisms involved.

Histone acetylation and deacetylation are crucial processes that govern the expression of genes by modulating the chromatin structure to enhance transcriptional activation of stress-responsive genes under abiotic circumstances (Wang et al., 2024). The histone acetyltransferases (HATs) are mainly responsible for the mechanisms of histone acetylation that involve the linking of an acetyl group to the lysine chain on the histone end, namely H3K9 and H3K14. This modification stops this molecular protein from interacting with DNA and produces a more accessible, unstructured chromatin that encourages transcription, as it reduces the positive charge in histone. Rice salt stress increases H3K9ac and H3K14ac at OsPP2C49 (ChIP-seq), enhancing tolerance with causal evidence from HAT overexpression lines (Liu et al., 2023). The function of histone acetylation in stress adaptation is demonstrated by the distinct transcriptional and metabolic behaviors shown in Arabidopsis plants that express the histone acetyltransferase HAC1 from Medicago truncatula across salt and cold (Ivanova et al., 2023). In contrast, histone deacetylases (HDACs) regulate the expression of genes by eliminating acetyl groups. These cause chromatin condensation and transcriptional repression in adaptation to stress (Vincent et al., 2022). However, HDA6 (Histone Deacetylase 6) and its homolog HDA19 mediate stress-responsive deacetylation (Ueda and Seki, 2020). H3K27ac, a well-established activation mark at enhancers and promoters, differs from acetylation in gene bodies (Huang and Irish, 2024; Wang et al., 2025b). hda6 exhibits jasmonate hypersensitivity and stress-related defects, confirming that HDA6 plays a causal role in repressing stress genes through deacetylation, as demonstrated by ChIP-qPCR analyses (Chang et al., 2020; Vincent et al., 2022; Sun, 2025).

Histone methylation modifications on particular lysine residues can promote or inhibit gene expression. It contributes to the determination of memory of stress and controls metabolism, which in turn increases the resistance of plants to drought, salinity, and extreme temperatures (Shi et al., 2024). Trimethylation of H3 at lysine 4 (H3K4me3) is generally associated with transcriptional activation, whereas trimethylation at lysine 27 (H3K27me3) is associated to gene silencing. ChIP-seq reveals that H3K27me3 represses cold-responsive genes before stress, with repression alleviated upon stress induction. This relationship is confirmed by clf/swn mutants, which affect H3K27 methyltransferases (Wang et al., 2025b). These modifications are crucial for immediate stress responses and also for establishing epigenetic stress memory, which helps plants withstand recurring stresses (Jin et al., 2024). A specific histone modification genes that respond to various abiotic stresses has been identified in Brassicaceae, revealing their potential for developing stress-tolerant crops (Hu et al., 2023). Moreover, histone methylation regulates the expression of stress adaptive genes through interacting with other epigenetic processes such as DNA methylation and chromatin remodeling (Dar et al., 2022; Grgić et al., 2025). Table 1 summarizes the regulation of histone modifications (H3K4me3 activation and H3K27me3 repression) across various abiotic stress contexts, integrating these with the effects of DNA methylation. In fruits, a critical agricultural organ, heat stress induces histone acetylation (H3K9ac and H3K27ac) at the promoters of HSPs in tomatoes (Kumar et al., 2021) and triggers dynamic chromatin remodeling in strawberries (López et al., 2024), similar to the responses observed in roots.

In plants, the small non-coding RNAs (ncRNAs) mediate the regulatory response for the genes that respond to abiotic stress (Figure 1). These ncRNAs are involved in diverse regulatory interactions that determine how adaptable a plant might be to environmental stimuli. miRNAs (20–24 nucleotides; small RNA-seq + degradome) promote target mRNA degradation and inhibit translation, regulating heat shock proteins (HSPs) and NF-Y factors to maintain cellular homeostasis. Target mimics confirm the causal role of miRNAs in this process (Basso et al., 2019; Samat et al., 2024). Similarly, miRNAs actively participate in cross-kingdom interactions and may play a key role in influencing plant stress responses and agronomic traits through their interactions with other plants and microorganisms (Ding et al., 2024). siRNAs (lisiRNAs, nat-siRNAs; small RNA-seq) target and degrade stress-related mRNAs, facilitating adaptation. AGO1/4 mutants exhibit defects in this process. These interactions suggest highly complex ncRNA regulatory networks that provide resilience to abiotic stress. Additionally, the regulation of non-coding RNAs regarding anthocyanin biosynthesis and their function as ROS scavengers and stress tolerance enhancers (Zhou et al., 2023).

RNA-seq and chromatin isolation revealed lncRNAs regulating chromatin remodeling, histone modification, and stress memory (Magar et al., 2024). lncRNAs act at multiple layers (RNA-seq + RIP-seq), associating with chromatin modifiers (ChIP assays) to alter DNA/histone marks (Hazra et al., 2023). lncRNAs employ various mechanisms to affect this role, most importantly, the alteration of chromatin structures, which adjusts the chromatin structure to be more or less condensed. lncRNAs perform this function through the association of chromatin-modifying proteins and agents that affect histone and DNA methylation changes.

For instance, lncRNAs help tether chromatin remodelers to precise genomic locations. This results in modifications to the structural chromatin that enable the activation of gene transcription during stressful conditions (Hazra et al., 2023). Hence, lncRNAs control the activation of which fundamental stress-responsive gene pathways are regulated by the phytohormones ABA and salicylic acid, both of which are crucial to the stress adaptation response in plants (Jin et al., 2024). ceRNA networks act as sponges for miRNAs that regulate stress-related genes, as revealed by RNA-seq and luciferase assays (Rakhi et al., 2024). Other regulatory lncRNAs might act as competing endogenous RNA (ceRNA) in concert with these miRNAs to influence the expression of a target mRNA (Xiao et al., 2022). For example, suitable lncRNAs, which act as ceRNAs for miRNAs and affect the expression of intricate genes involved in the stress response, have been reported in Oryza sativa (Rakhi et al., 2024). Similarly, lncRNAs and generic circRNAs interact with miRNAs via ceRNA networks that regulate important drought tolerance-associated genes, such as starch synthase 4 in switch grass (Guan et al., 2024). In addition, lncRNAs mediate the mechanisms through which plants develop stress memory to allow them to “remember” stressful events from the past and respond effectively to subsequent disturbances (Traubenik et al., 2024). This multifarious function of lncRNAs with regard to chromatin remodeling and stress responses raises much hope for using lncRNAs as targets in emerging crop varieties that can resist stress, in light of the avenues it opens up for agricultural innovation in climate change scenarios (Yang et al., 2023).

RNA modifications such as methylation and acetylation play a major role in regulating plant performance under abiotic stress. However, they run through an overall broader area of epitranscriptomics, which includes all chemical changes that occur among RNA molecules and modify the gene expression and adaptation of plants against various environmental stresses. m⁶A-seq revealed that RNA methylation regulates mRNA stability, splicing, and translation under stress (Cai et al., 2024). Such an epigenetic modification does not alter the DNA sequence itself. However, it can be inherited and has been proposed as a mechanism for transgenerational stress memory, enhancing plant resilience across generations (Essemine et al., 2025). This integration of modifications into breeding strategies holds a bright future in terms of developing stress-resistant crops, as it provides a method for enhancing adaptability without altering the genetics within plants (Rao et al., 2024). Such improvements in high-throughput sequencing skills have greatly contributed to identifying and understanding these modifications and their ability to improve crop yield and quality under adverse environmental conditions (Essemine et al., 2025). The elaborate interaction system, which emerges among important ncRNAs, such as miRNAs, siRNAs, and lncRNAs themselves, forms a highly sophisticated regulatory network for perceptive response-behavior patterns of plants against all possible environmental stresses for an improved capacity to endure and acclimate to threatening conditions (Yang et al., 2023).

Chromatin remodelers dynamically reposition nucleosomes at stress-responsive loci, facilitating rapid transcriptional responses. SWI/SNF complexes (BRAHMA subunit) and DDM1 play essential roles in maintaining chromatin accessibility under abiotic stress, as demonstrated by ATAC-seq profiling. The brahma mutants exhibit severe drought sensitivity, with reduced root growth and impaired gene activation, confirming the complex causal involvement in ABA-responsive loci as ChIP-seq H3K4me3 (Venkatesh and Workman, 2015). DDM1 prevents TEs reactivation under salinity stress, and ddm1 mutants show genome instability and salt hypersensitivity, with WGBS and RNA-seq providing evidence of context-specific hypomethylation (Pecinka et al., 2010; Zemach et al., 2013). ISWI remodelers, such as CHR3, regulate flowering time under heat stress, with chr3 mutants exhibiting early flowering (Kang et al., 2022).

Hormonal signaling pathways, including ABA, JA and auxin, which are intricately linked with epigenetic regulation to coordinate stress responses. The ABA signaling pathway requires H3K27me3 demethylation by JMJ30/KDM4C at ABI5 and RAB18 promoters. AtJmj30 mutants show ABA insensitivity and increased drought susceptibility, further supporting the epigenetic regulation of ABA responses (ChIP-seq) (Ay et al., 2009; Yamaguchi et al., 2021). Jasmonic acid (JA) signaling recruits HDA6 to deacetylate JAZ repressors and stress-related genes, with hda6 mutants displaying defects in jasmonate-mediated defense and stress crosstalk (ChIP-qPCR) (Liu et al., 2010; Chang et al., 2020). Auxin homeostasis is repressed by RdDM under drought stress through promoter hypermethylation of GH3 auxin genes (WGBS); ros1 demethylase mutants show ectopic auxin accumulation and reduced stress tolerance (Yu et al., 2013; Hayashi et al., 2021). Ethylene response factors (ERFs) require H3K36 demethylation by SDG8 for heat stress tolerance, with sdg8 mutants showing enhanced heat tolerance (ChIP-seq) (Chang et al., 2020).

Tissue-specific epigenetic regulation is revealed through spatial epigenomics techniques. Single-cell ATAC-seq (scATAC-seq) in roots shows drought-induced changes in chromatin accessibility, specifically in the stele versus cortex, correlating with aquaporin expression. This finding is validated by scWGBS (Ma et al., 2025). Guard cell bisulfite sequencing reveals CG hypomethylation linked to stomatal aperture regulation, supported by live-cell imaging and WGBS (Siqueira et al., 2021). Long-read nanopore sequencing enables the resolution of polyploid crop epialleles, such as wheat homologs, identifying subgenome-specific stress marks through ONT WGBS (Angeloni et al., 2022). The meristem-specific scRNA-seq and scATAC-seq analyses have uncovered progenitor-specific H3K27me3 bivalency, enabling rapid cold acclimation (Theler et al., 2014).

Integration of chromatin remodelers (SWI, SNF and DDM1), hormone signaling (ABA, JA and auxin), and spatial epigenomics (scATAC and WGBS) reveals the convergence of these mechanisms at stress hubs. The functional validation through brahma, hda6, ros1 and jmj30 mutants establishes causality beyond correlative relationships. Moreover, epiallele editing using dCas9-TET1 at SWI/SNF loci improves rice drought tolerance (Gallego-Bartolomé et al., 2018), and dCas9-KRAB in wheat enhances salinity resilience (Mccarty et al., 2020).

Tolerant genotypes exhibit controlled epigenomic plasticity, distinguishing them from sensitive varieties across crops (Sun, 2025)WGBS/BS-seq; (Yang et al., 2025). Maize and cotton tolerant lines exhibit stable global methylation, with targeted promoter hypomethylation at ABA biosynthesis (NCED3), ROS scavenging (SOD and CAT) and osmoprotectant synthesis (P5CS), enabling the rapid activation of stress-responsive genes. In contrast, sensitive genotypes display erratic genome-wide hyper- and hypomethylation patterns that correlate with poor acclimation and yield loss, offering potential for actionable epiallele selection (Zhang et al., 2024a).

ChIP-seq profiling reveals that H3K4me3 and H3K9ac are rapidly established at osmoprotectant and LEA gene promoters within hours in drought-tolerant maize, sorghum and cotton, while sensitive lines show delayed or absent chromatin opening (Prasad et al. (2024). miR169g represses NF-YA transcription factors more efficiently in tolerant varieties, leading to reduced stomatal aperture and enhanced water conservation, as validated by degradome analysis and transgenics (Rao et al., 2024). Ca²⁺ and Na⁺ fluxes trigger scATAC-seq identified open chromatin specific to root responses in tolerant genotypes, highlighting ion-epigenome crosstalk (Miryeganeh, 2025). These epigenomic patterns provide deployable epialleles for marker-assisted selection.

Root system architecture (RSA) plasticity is a key target for epigenetic engineering aimed at enhancing drought avoidance in field conditions (Nguyen et al., 2022). WGBS reveals ABA-responsive promoter demethylation at the DRO1 (deep rooting) and PLT1 (lateral root density) loci, which control adaptive RSA phenotypes. Dro1 mutants exhibit defective deep rooting, highlighting the role of this loci in root plasticity (Sun et al., 2022). In barley, root tissues show organ-specific hypermethylation, with stele tissues exhibiting elevated CG methylation compared to the cortex under water deficit conditions. ChIP-seq analysis confirms the exclusion of H3K27me3 from aquaporin and hydraulic conductivity genes, linking chromatin modifications to root function under drought stress (Chwialkowska et al., 2016).

Hormonal signaling pathways, including ethylene and JA, amplify epigenetic regulation of RSA. These pathways require H3K36me3 deposition by SDG8 at root hair development and suberization genes. SdG8 mutants produce shallow, poorly suberized roots, underscoring the importance of H3K36me3 in root adaptation (Ranjan et al., 2022; Gao et al., 2025). Wheat QTL-methylation overlap analyses across diverse panels have identified breeding targets, linking natural epiallele variation to RSA ideotypes. These epialleles confer a 15-20% yield advantage under terminal drought conditions (Siddiqui et al., 2023). Single-cell ATAC-seq reveals compartment-specific changes in chromatin accessibility, coordinating the responses of the stele, cortex and endodermis. Figure 2 shows the multi-layered coordination of DNA, histone modifications, and non-coding RNAs (ncRNAs) in driving adaptive RSA under progressive water deficit. These findings position epigenetic markers as complementary tools for classical RSA QTL breeding.

The C-repeat binding factor-cold-regulated (CBF-COR) pathway demonstrates the epigenetic regulation of cold acclimation (ChIP-seq/ATAC-seq) (Kwon et al., 2009). Cold exposure triggers the dynamic removal of H3K27me3 from COR15A, RD29A and LEA promoter regions through the antagonism of Polycomb Repressive Complex 2 (PRC2) with clf and swn double mutants exhibiting cold hypersensitivity. The PKL and SWR1 chromatin remodeling complex mediates RdDM-independent activation at CBF and DREB1 loci, with pkl mutants showing hypersensitivity to cold stress (Yang et al., 2019; Carter et al., 2018). The PWR-HOS15-HD2C complex deposits H4 acetylation at COR promoters during cold acclimation, and hd2c mutants exhibit defects in freezing tolerance (Lim et al., 2020).

Histone deacetylase HDA6 is transcriptionally induced by cold, establishing basal repression that allows for rapid de-repression upon stress, with hda6 mutants showing increased sensitivity to cold (To et al., 2011; Park et al., 2018). Long non-coding RNA (lncRNA) CRIR1 recruits DRM2 demethylase to alter cold-responsive methylation patterns in cassava, as confirmed by WGBS validation (Li et al., 2024). The SWI and SNF chromatin remodeler, specifically the LFR subunit, activates transcription at the CBF3 and ICE1 loci, with lfr mutants showing defects in cold response (Ma et al., 2023). Histone variant H2A.Z eviction, accompanied by H3K4me3 gain, occurs at cold memory loci, enabling recurrent cold tolerance (Grgić et al., 2025). These epigenetic modifications contribute to the establishment of cold memory and stress resilience (Table 1).

The transcriptional memory of heat shock proteins (HSPs) is governed by persistent chromatin marks as demonstrated by ChIP-seq and MNase-seq analyses (Pratx et al., 2023; Arıkan et al., 2025). The continuous enrichment of H3K4me3, coupled with low nucleosome turnover at the promoters of HSP22, HSP70, and sHSP, enables rapid re-induction during recurrent heat waves, contributing to developed thermotolerance. JUMONJI C-domain demethylases (JMJ30 and 32) actively remove repressive H3K27me3 from HSP promoters, with jmj mutants showing impaired heat acclimation (Yamaguchi et al., 2021, Yamaguchi et al., 2020). In wheat, hypomethylation of the HSP17.6 promoter correlates with stronger heat induction across genotypes, as revealed by WGBS profiling (El-Shehawi, 2020).

In barley, DNA demethylation integrates with H3K9ac deposition at heat-responsive loci, a process confirmed by ChIP-seq (Li et al., 2022). miR398 targets Cu and Zn-SOD, and miR156 targets HSFA2, regulating ROS detoxification and heat shock factor amplification, as demonstrated by degradome analysis and transgenic studies (Meiri and Breiman, 2009; Samanta and Thakur, 2015). ONSEN retrotransposon-derived siRNAs enhance HSF1 binding and prevent genome instability (Cavrak et al., 2014). The H3K36me3 reader EBS plays a critical role in maintaining HSP memory across cell divisions. In maize, genome-wide changes in H3K4me2 and H3K9ac are accompanied by HsfA2 binding, further illustrating the coordinated role of chromatin and non-coding RNA regulation in heat stress response (Friedrich et al., 2021). This coordinated chromatin-ncRNA regulation establishes thermos-memory, which can be leveraged for breeding heat-resilient varieties in response to climate warming.

The whole-genome bisulfite sequencing (WGBS) conducted across chickpea, wheat, and rice has identified hypomethylation at the SOS1 and HKT1;5 promoters as a key feature of salt-tolerant genotypes. The accumulation of toxic Na⁺ in HKT1;5 mutants further underscores the importance of these epigenetic modifications in salt tolerance (Gupta and Garg, 2023; Baek et al., 2011). Histone acetyltransferase GCN5 is involved in mediating H3K9 and H3K14 acetylation at cell wall remodeling genes such as PGX3, CTL1 and MYB54, with gcn5 mutants showing increased sensitivity to salt stress (Zheng et al., 2019). In soybeans, salt priming induces global hypomethylation that activates ABA-dependent LEA and osmolyte genes, thereby providing cross-protection (Boyko and Kovalchuk, 2011; Yung et al., 2024).

In maize, the transcription factor ZmKTF1 directs RdDM-mediated CHH methylation at oxidoreductase loci in response to salinity (Law and Jacobsen, 2010; Wang et al., 2025a). Figure 2 illustrates RdDM-TE silencing across stresses, with heat-induced ONSEN transgenerational activation making heritable stress memory (Kang et al., 2022). m⁶A-seq analysis reveals that FIONA1 and MTA methyltransferases stabilize aquaporin PIP1 and SOS1 mRNAs, with fio1 mutants displaying impaired stabilization (Cai et al., 2024). Altered DNA methylation patterns at salt-resilience loci are observed in wild wheat introgression lines, highlighting the role of epiallele flow during breeding (Hoseini et al., 2024). In rice, OsBISAMT1 facilitates salt-induced RNA m6A modifications at stress-responsive transcripts (Amara et al., 2022). These multi-omics datasets collectively reveal deployable epialleles that link DNA methylation dynamics to ion homeostasis, osmoprotection, and hormonal signaling, offering valuable targets for marker-assisted selection of salt-tolerant cultivars.

Dynamic histone modifications play a crucial role in reshaping chromatin at genes involved in the salinity response, as demonstrated by ChIP-seq analysis (Shi et al., 2024). Enrichment of H3K4me3 at ion transporters (NHX1), ROS scavengers (APX2), and transcription factors (WRKY) characterizes salt-tolerant genotypes, while repressive H3K27me3 and H3K9me2 decline enables activation (Chen and Wu, 2010; Wan et al., 2024). In rice, the histone deacetylase OsHDA706 targets H4K5 and H4K5 deacetylation at the OsPP2C49 promoter, integrating ABA signaling with salt response. The oshda706 mutant exhibits defective salt stress responses (Liu et al., 2023).

In soybean, NF-Y transcription factor complexes recruit H3K9ac to salt-responsive genes, while the GmHDA13-GmFVE complex maintains repression under non-stress conditions, as validated by ChIP-qPCR (Lu et al., 2021). The histone variant H2A.Z modulates transcriptional flexibility at stress loci through thermosensitive deposition and eviction (Miao et al., 2024). Overexpression of Arabidopsis HAC1 reprograms the transcriptome and metabolome under salinity, upregulating proline and polyamine biosynthesis pathways (Ivanova et al., 2023). Trithorax ATX1 deposits H3K4me3 at NHX antiporters, with atx1 mutants showing impaired salt tolerance (Ding et al., 2011). The dynamic balance between active and repressive histone modifications, coordinated with DNA methylation and m⁶A RNA modifications, drives variation in genotypic tolerance. Table 1 synthesizes these mechanisms for potential breeding applications.

Tonoplast sequestration serves as a prime example of high-value epigenetic engineering targets. In rice, overexpression of OsHMA3 reduces Cd accumulation in grains by 10-fold through vacuolar compartmentalization, coordinated with ZIP-family transporter regulation under combined Zn, Cu and Cd stress. Oshma3 mutants, however, are defective in root sequestration (Sasaki et al., 2014). WGBS profiling reveals that hypomethylation of the OsZIP1 promoter specifically excludes Cd, Cu and Zn from shoots, while maintaining essential nutrient levels. Oszip1 mutants, on the other hand, enhance metal uptake (Liu et al., 2019).

Cd stress induces H3K9ac and H3K4me3 deposition at key detoxification loci, including phytochelatin synthase PCS1, glutathione S-transferase GST, and metallothionein genes, as validated by ChIP-seq (Guarino et al., 2024). The histone deacetylases HDA6 and HDA19 maintain basal repression, enabling rapid activation upon metal exposure; hda6 single and double mutants exhibit increased metal accumulation (Niekerk et al., 2021). miR390 and miR393 target TIR1 and AFB2 auxin receptors, modulating root exclusion and lateral root suppression, as demonstrated by degradome analysis and transgenic studies (Niekerk et al., 2021). scATAC-seq identifies chromatin opening at NRAMP and IRT1 influx loci, specifically in salt-tolerant genotypes, highlighting epigenetic regulation of metal influx (Wang et al., 2025b). These findings suggest breeding targets across legumes, cereals, and brassicas, with potential for a 20% improvement in grain safety.

Transgenerational epigenetic memory in rice persists across 1 to 3 generations after exposure to Cd or mercury (Hg) with heritable hypomethylation at the OsHMA4 and PCS2 detoxification loci enhancing tolerance in progeny, as tracked by WGBS inheritance profiling (Cong et al., 2019, Cong et al., 2024). This memory resets in clean soil after the F3 generation, balancing adaptation with plasticity (Iqbal et al., 2024). QTL-methylation overlap analyses across diverse rice and wheat panels have linked MET1 and DRM2 variants to Cd exclusion phenotypes, with potential for a 15-25% improvement in grain safety (Sharma et al., 2025). CRISPR-dCas9 targeting of OsZIP1 and OsHMA3 promoters enables reversible editing of metal exclusion traits without genetic load (Feng et al., 2023). Wild rice and wheat introgressions carry pre-adapted methylation states at metal homeostasis loci, offering a foundation for breeding (Hoseini et al., 2024).

Locus-specific siRNAs maintain silencing of TEs across F2 populations, as demonstrated by RdDM validation (Lancíková et al., 2023). m⁶A modifications, mediated by FIONA1 and MTA complexes, stabilize detoxification mRNAs transgenerationally, enhancing stress resilience (Cai et al., 2024). Inheritance of H3K27me3 at NRAMP5 reinforces metal exclusion, contributing to salt tolerance (Ding et al., 2011). Figure 1 demonstrates the integrated DNA-histone-ncRNA memory circuit. Dual genetic-epigenetic selection schemes position epialleles as powerful breeding tools for developing metal-safe cultivars.