Search Results (80)

Soil salinization is increasingly threatening global agricultural productivity and food security, currently affecting over 6% of the world’s land and one-third of irrigated areas. Tomato (Solanum lycopersicum L.), a major vegetable crop worldwide, exhibits moderate sensitivity to salinity, which limits both its yield and fruit quality. In recent years, epigenetic regulation has gained attention as a key mechanism enabling flexible and reversible control of gene expression without altering DNA sequences. This review synthesizes current knowledge on the epigenetic control of salt stress responses in tomato, focusing on three interconnected levels: DNA methylation dynamics, RNA-directed DNA methylation (RdDM), and histone modifications. We explore how DNA methyltransferases reshape the methylome under salinity, using examples such as PKE1 and SlGI to illustrate functional gene-body methylation. The RdDM pathway is discussed with emphasis on the unexpected role of SlAGO4A as a negative modulator of stress tolerance and the growing evidence for RdDM-mediated regulation of transcription factors. We also examine the balanced regulation of histone acetylation and deacetylation, highlighting the conserved role of GCN5 in maintaining cell wall integrity and the diverse functions of histone deacetylases, such as SlHDA1, SlHDA3, and SlHDA5, in stress adaptation. Additionally, insights from wild tomato species and grafting-induced epigenetic changes are presented, revealing new dimensions of stress memory. Collectively, these epigenetic mechanisms constitute a complex regulatory framework that integrates stress responses with growth and development, providing potential targets for epigenetic breeding of salt-tolerant tomatoes. Full article

Root knot nematodes (RKNs) induce galls, containing multinucleated giant cells (GCs) to nourish them. The differentiation of precursor cells to galls/GCs involves extensive cellular reprogramming with multiple layers of regulation. Epigenetic regulation during the early stages of infection indicates that RNA-directed DNA methylation (RdDM) and microRNA-dependent gene silencing contribute to transcriptional and post-transcriptional reprogramming during gall organogenesis. Although later stages of galls/GC development are crucial for nematode life-cycle maintenance, epigenetic reprogramming events remain largely unexplored. An integrative analysis of sRNAs, DNA methylation, and transcriptomic dynamics in galls induced by Meloidogyne javanica revealed that enrichment of 24 nt sRNAs represents a gall hallmark across early and late developmental stages. Fewer gall-distinctive sRNAs were detected at mid-to-late stages than at early stages, alongside a pronounced spatial reorganization of rasiRNA accumulation. At early stages, gall-distinctive rasiRNAs preferentially accumulated in pericentromeric retrotransposon-rich regions, whereas, at mid-to-late stages, they predominantly localized to chromosome arms, matching DNA transposons, promoters, and gene bodies. A decline in the regulatory influence of miRNAs was observed as infection progressed, possibly reflecting a transition toward specialized regulatory states associated with gall maintenance. Moreover, three regulatory modules, miR2111-5p/HOLT, miR172/AP2, and miR156/SPL10, were tightly but oppositely regulated at 3 and 14 days post-infection. Furthermore, miR156/SPL10 showed crucial functions during gall formation and/or maintenance, possibly influenced by hormonal cues involving ARF8 among other ARFs. Our results highlight stage-specific patterns involving sRNA dynamics, DNA methylation, and transcriptomic changes underlying nematode feeding site development and maintenance. Full article

Epigenetic regulation plays a central role in modulating plant immune responses and interactions with beneficial microbes. In this study, we investigated the contribution of RNA-directed DNA methylation (RdDM) components—DCL3; AGO9; DCL1; and the de novo DNA methyltransferases CMT3, DRM1, and DRM2—to the interaction between Arabidopsis thaliana, Trichoderma atroviride, and foliar pathogens. We show that DCL3 and AGO9 differentially regulate basal and inducible immunity, negatively affecting resistance to the necrotrophic fungus Botrytis cinerea, while promoting defense against the hemibiotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Transcriptional analyses revealed that RdDM components modulate the balance between jasmonic acid/ethylene (JA/ET) and salicylic acid (SA) signaling pathways, influencing the amplitude and coordination of defense responses. In addition, DCL3 and DCL1 appear to be required for the full expression of T. atroviride-mediated systemic resistance, whereas AGO9 and DNA methyltransferases contribute to efficient root colonization. Notably, mutants in these pathways displayed enhanced basal resistance but impaired responsiveness to beneficial microbial signals, revealing a trade-off between constitutive defense activation and inducible systemic protection. Consistent with this, alterations in RdDM components were also associated with changes in plant growth dynamics under specific conditions, supporting a role for epigenetic regulation in coordinating growth–defense trade-offs. Together, our findings support a model in which epigenetic regulation controls defense responsiveness, enabling plants to balance immune activation, growth and compatibility toward beneficial microbes. Full article

Potato cultivars are inherently sensitive to high temperatures, and dissecting the mechanisms underlying heat response and tolerance has long been a central focus in potato research. However, the molecular mechanisms governing the short-term heat stress response in potato, as well as the regulatory role of DNA methylation in heat adaptation, remain largely unclear. In this study, we identified breeding line D187 as heat-tolerant and cultivar Q9 as heat-sensitive through microtuber induction under heat stress. We further confirmed that heat-sensitive cultivar Q9 exhibited distinct physiological responses in leaves following 6 h of heat treatment. Comparative transcriptome analysis of leaves exposed to 6 h of heat stress revealed distinct molecular response patterns between D187 and Q9. D187 specifically upregulated genes enriched in heat and other stress response pathways to enhance heat adaptation, whereas Q9 relied on pathways related to RNA modification and splicing, presumably adapting to high temperatures via post-transcriptional regulation. Notably, genes involved in the RdDM pathway were differentially upregulated in both genotypes, and heat stress correspondingly enhanced CHH methylation levels in the vicinity of functional genes in the heat-sensitive cultivar Q9. Treatment with 5-Azacytidine, a DNA methylation inhibitor, exacerbated the inhibition of in vitro tuber formation under high temperatures, indicating that maintaining and enhancing DNA methylation is essential for heat adaptation in potato. Furthermore, overexpression of StAGO4a/b in Nicotiana benthamiana modestly improved heat tolerance, suggesting that StAGO4s act as positive regulators of heat tolerance in potato. Collectively, our results suggest that heat-induced CHH methylation near functional genes via the RdDM pathway contributes positively to heat stress response and tolerance in Q9, providing new insights for identifying heat tolerance regulators from a DNA methylation perspective. Full article

The SARS-CoV-2 Omicron variant and its descendants accumulated unprecedented numbers of spike substitutions yet remained transmissible, implying compensatory mechanisms that preserve entry while eroding humoral immunity. We analyzed 32 variants for sequence-level mutation, physicochemical profiling, and epitope disruption; 25 had growth-advantage estimates, and 18 underwent molecular dynamics/MM-PBSA simulations. We applied a systems-virology framework to the SARS-CoV-2 receptor-binding domain (RBD), integrating immunodominance-weighted epitope conservation (567 B-cell and 97 T-cell epitopes) across variants (Wuhan-Hu-1 to KP.3) with molecular dynamics, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) binding energetics, and deep mutational scanning (DMS) benchmarking. B-cell epitope conservation declined from a median of 72.7% in pre-Omicron variants to 28.8% in BA.1 and 10.6% in KP.3, and was strongly inversely associated with a breakthrough-infection proxy (Spearman ρ = −0.8246, p < 0.001), whereas RBD T-cell epitopes remained comparatively conserved (91.5% to 87.2%). Despite the loss of the ancestral K417–ACE2 D30 salt bridge, Omicron reconfigured the interface via alternative electrostatic contacts (Q493R–E35 and Q498R–D38), producing compensatory interactions captured by MM-PBSA, but with only modest agreement with DMS affinity changes (r = 0.682, p = 0.007), consistent with enthalpy–entropy compensation. Finally, mutation tolerance shifted toward stronger epistatic buffering in Omicron (two-fold higher epistasis than pre-Omicron; p = 0.0093), enabling extensive antigenic change without structural collapse. Together, these results support a multi-objective evolutionary strategy—epitope erosion, interface rewiring, and epistatic compensation—that can be operationalized to prioritize emerging lineages for surveillance and to inform vaccine designs that emphasize conserved T-cell targets. Full article

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. Full article

RNA-directed DNA methylation (RdDM), a new plant breeding technology, induces epigenetic modifications that can be inherited even after segregation of the responsible transgene. The transgene-free descendants (null segregants) are potentially exempt from the regulation of genetically modified plants. To evaluate the risks of potential unintended molecular changes in the null segregants of RdDM-positive plants, we produced null segregants (S44end2-null) from a transgenic tobacco line in which RdDM targeting the promoter of the transgene was introduced. Comprehensive multi-omics analyses, including transcriptomics, proteomics, and metabolomics, were conducted using S44end2-null and wild-type (WT) plants. Principal component analysis demonstrated clear separation of the transcriptomic and proteomic profiles of the two groups. The metabolomic profiles of S44end2-null plants exhibited considerable overlap with those of WT plants. Proteomic analysis of the null segregants of tobacco plants transformed with an empty vector demonstrated distinct cluster separation from WT plants. Because only sporadic DNA methylation on the tobacco genome was expected by the RdDM construct used in this study, the observed differences in omics profiles are considered to be significantly influenced by genetic variation accumulated during the transformation and regeneration processes (somaclonal variation). The safety assessment points for null segregants using RdDM technology are discussed. Full article

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. Full article

Precision agriculture, including sensors and artificial intelligence, is transforming agricultural monitoring. This study developed predictive models for fresh and dry forage mass, canopy height, forage density, dry matter (%DM), and crude protein (%CP) concentrations in signalgrass [Urochloa decumbens (Stapf) R.D. Webster] pastures using machine learning and UAV-based multispectral imagery. The experiment was conducted at the Federal University of Viçosa (2019–2020), applying nitrogen doses after each harvest to promote variability. Multiple Linear Regression (MLR), Support Vector Regressor (SVR), and Random Forest Regressor (RFR) models were trained with multispectral and meteorological data. The best results were obtained for fresh forage mass with RFR (R² = 0.82, RMSE = 2894.10 kg ha⁻¹), dry forage mass with SVR (R² = 0.68, RMSE = 719.87 kg ha⁻¹), and dry matter concentration with MLR (R² = 0.64, RMSE = 3.83%). Forage density showed moderate performance (R² = 0.56), while canopy height demonstrated limited accuracy (R² = 0.44). Crude protein was not adequately predicted by any model, highlighting multispectral sensor limitations and suggesting hyperspectral sensors usage. Results demonstrate the applicability of remote sensing combined with machine learning in forage management, but indicate the need to expand temporal and spatial data variability and integrate different sensor types to increase model robustness. Full article

Plants have evolved a complex, multilayered immune system that integrates molecular recognition, signaling pathways, epigenetic regulation, and small RNA-mediated control. Recent studies have shown that DNA-level regulatory mechanisms, such as RNA-directed DNA methylation (RdDM), histone modifications, and chromatin remodeling, are critical for modulating immune gene expression, allowing for rapid and accurate pathogen-defense responses. The epigenetic landscape not only maintains immunological homeostasis but also promotes stress-responsive transcription via stable chromatin modifications. These changes contribute to immunological priming, a process in which earlier exposure to pathogens or abiotic stress causes a heightened state of preparedness for future encounters. Small RNAs, including siRNAs, miRNAs, and phasiRNAs, are essential for gene silencing before and after transcription, fine-tuning immune responses, and inhibiting negative regulators. These RNA molecules interact closely with chromatin features, influencing histone acetylation/methylation (e.g., H3K4me3, H3K27me3) and guiding DNA methylation patterns. Epigenetically encoded immune memory can be stable across multiple generations, resulting in the transgenerational inheritance of stress resilience. Such memory effects have been observed in rice, tomato, maize, and Arabidopsis. This review summarizes new findings on short RNA biology, chromatin-level immunological control, and epigenetic memory in plant defense. Emerging technologies, such as ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing), ChIP-seq (Chromatin Immunoprecipitation followed by Sequencing), bisulfite sequencing, and CRISPR/dCas9-based epigenome editing, are helping researchers comprehend these pathways. These developments hold an opportunity for establishing epigenetic breeding strategies that target the production of non-GMO, stress-resistant crops for sustainable agriculture. Full article

The RNA-directed DNA methylation (RdDM) pathway is a crucial epigenetic mechanism governing plant responses to environmental stress. While the RdDM pathway has been extensively studied in Arabidopsis thaliana, the comprehensive understanding of its components in cucumber (Cucumis sativus L.) remains lacking. In this study, we performed a genome-wide identification and characterization of RdDM pathway genes in cucumber, followed by an analysis of their expression patterns across various tissues and under multiple abiotic stress conditions. A total of 67 putative CsRdDM genes were identified, which are unevenly distributed across the cucumber’s chromosomes. Phylogenetic and gene structure analyses revealed considerable evolutionary divergence, particularly within the key Argonaute gene family (CsAGO). Crucially, the promoter regions of CsRdDM genes were found to contain cis-regulatory elements associated with abiotic stress, light signaling, and development, suggesting their potential involvement in complex regulatory networks. RT-qPCR assays confirmed that CsRdDM genes exhibit distinct and stress-specific transcriptional patterns. Notably, several genes such as CsAGO4 and CsIDN2 showed antagonistic expression between roots and leaves under drought (PEG-6000) stress, implying a sophisticated, tissue-specific defense mechanism. Among them, CsAGO4 emerged as a candidate gene responsive to abiotic stress. Those findings provide new insights into the regulatory roles of CsRdDM genes under abiotic stress and highlight candidate genes for the genetic improvement of stress tolerance in cucumber. Full article

Background/Objectives: Long-term cognitive outcomes after carotid surgery are influenced by diabetes and intraoperative changes. We aimed to analyze the postoperative cognitive changes in diabetic patients and nondiabetic patients after carotid endarterectomy (CEA). Additionally, major cardiovascular and cerebrovascular events (MACCEs) and the incidence of mortality at two years after surgery were assessed. Methods: We enrolled 37 diabetic and 67 nondiabetic patients undergoing elective carotid surgery. Intraoperatively, routine monitoring was completed with NIRS (near-infrared spectroscopy) and an Entropy monitor was used for neuromonitoring. The lowest cerebral tissue saturation levels during the cross-clamp period (rSO_2lowestclamp) and the degree of desaturation were calculated. We used MMSE (Mini-Mental State Examination) and MoCA (Montreal Cognitive Assessment) to assess cognitive function. Cognitive change was defined as one standard deviation (SD) change from the preoperative test scores. Results: The MMSE and MoCA were available for 103 patients at three months and for 90 patients at 12 months after discharge. Compared with nondiabetic patients, diabetic patients exhibited greater decreases in MoCA scores (p = 0.028 and p = 0.042 at the 3rd and 12th months, respectively). Cognitive improvement was lower in the DM group than in the control group at the 12th month (18.75% vs. 42.86%, respectively; p = 0.029). The mean rSO₂ in the pre-clamping period (67.4% vs. 74.6% in diabetic and in nondiabetic patients, respectively; p = 0.011) was lower in diabetic patients. Furthermore, MACCEs at the 24th month were observed at a higher rate in diabetic patients (p = 0.040). Conclusions: Diabetic patients demonstrated greater risks for cognitive decline, MACCEs, and mortality at two years after surgery. Full article

Electroencephalography (EEG) communication technology with ultra-low power consumption, high transmission data rates, and low latency plays a significant role in mHealth, telemedicine, and Internet of Medical Things (IoMT). In this paper, generalized frequency division multiplexing (GFDM)-based direct mapping (DM) multi-input—multi-output (MIMO) mobile EEG communication technology (MECT) is proposed for implementation with the above-mentioned applications. The (2000, 1000) low-density parity-check (LDPC) code, four-quadrature amplitude modulation (4-QAM), a power assignment mechanism, and the 3rd Generation Partnership Project (3GPP) cluster delay line (CDL) channel model D were integrated into the proposed EEGCT. The transmission bit error rates (BERs), mean square errors (MSEs), and Pearson-correlation coefficients (PCCs) of the original and received EEG signals were evaluated. Simulation results show that, with a signal to noise ratio (SNR) of 14.51 dB, with a channel estimation error (CEE) of 5%, the BER, MSE, and PCC of the original and received EEG signals were 9.9777 × 10⁻⁸, 1.440 × 10⁻⁵ and 0.999999998, respectively, whereas, with an SNR of 15.0004 dB and a CEE of 10%, they were 9.9777 × 10⁻⁸, 1.4368 × 10⁻⁵, and 0.999999997622151, respectively. As the BER value, and PS saving are 9.9777 × 10⁻⁸, and 40%, respectively. With the CEE changes from 0% to 5%, and 5% to 10%, the N₀ values of the proposed MECT decrease by approximately 0.0022 and 0.002, respectively. The MECT has excellent EEG signal transmission performance. Full article

RNA-directed DNA methylation (RdDM) is an epigenetic mechanism involved in several biological processes in plants, requiring complex machinery including the chromatin remodeling protein CLASSY (CLSY). The CLSY family regulates global and locus-specific DNA methylation and was initially identified in Arabidopsis thaliana. Despite reports in other plants, detailed knowledge about CLSY proteins in soybean is scarce. In this work, we used profile hidden Markov models (profile HMMs) specifically constructed for CLSY detection to identify new members in soybean and to analyze their phylogenetic relationships across bryophyte, basal angiosperm, basal eudicot, monocots, and eudicots. We identified two new candidates for CLSY1-2 and one for DRD1 in soybean and, for the first time, detected CLSY and DRD1 genes in Aquilegia coerulea. Phylogenetic analysis indicated two main CLSY groups: one similar to Arabidopsis CLSY1-2 and another to CLSY3-4. Gene duplication analysis demonstrated that whole-genome duplication/segmental duplication events contributed to CLSY family expansion in soybean. RT-qPCR analysis showed that CLSY and five other epigenetic regulator genes had stress-modulated expression during soybean germination under salt and osmotic stress, with variation among cultivars. Our findings enhance comprehension of the evolutionary dynamics of the CLSY family and furnish insights into their response to abiotic stress in soybean. Full article

Abiotic stress can reprogram the gametophytic pathway; the mechanisms by which floral bud pre-treatment influences microspore embryogenesis initiation remain unclear. In this study, we use bisulfite sequencing, sRNA-seq, and RNA-seq to analyze the dynamic changes in rice microspores under different cold treatment durations. Our results showed that a 10-day cold treatment is essential for CXJ microspore embryogenesis initiation. DNA methylation levels showed a slight change at CG, CHG, and CHH sites under cold treatment. The number of both hyper- and hypomethylated DMRs increased over cold treatment, with more hypermethylated DMRs at 5 and 10 dpt. Hypermethylated DMRs were more frequently in the TSS region compared to hypomethylated DMRs. The proportion of 24 nt sRNAs increased upon cold stress, with more downregulated than upregulated sRNAs at 10 dpt. The number of DMR target DEGs increased from 5 to 10 dpt. Promoter hypomethylation at the CHH site was more frequently associated with DEGs. These outcomes suggested that the RdDM pathway participates in the initiation of rice ME. GO analysis indicated that DMR target DEGs at 10 dpt were enriched in responses to chemical stimuli, biological processes, and stress responses. An auxin-related gene, OsHOX28, was further identified. Its upregulation, potentially mediated by the RdDM pathway, may play a crucial role in the initiation of rice ME. This study provides more information on epigenetic mechanisms during rice ME. Full article