Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.© 2024. The Author(s).

表观遗传是DNA序列不变而基因表达发生可遗传改变的生物现象，包括DNA甲基化、组蛋白修饰及变体、RNA修饰、染色质重塑和非编码RNA等。表观遗传主要在转录和转录后水平调控基因表达及转座子活性，在作物重要农艺性状形成和倍性育种等方面发挥重要调控作用。综述了目前与作物育种直接相关表观遗传调控研究的重要进展，并分析了其应用于作物育种上的潜力及途径方法，以期加快和推动植物表观遗传调控的基础与应用研究。

作物表型的多样性受到多方面因素的影响，其中表观遗传变异可以通过表观修饰调控基因表达来控制作物性状及胁迫响应，进而影响农作物产量。影响玉米产量的主要农艺性状包括株高、叶夹角、根系等株型因素。此外，生物胁迫和非生物胁迫、种质资源也是影响玉米产量的关键因素。作物中主要的表观调控方式包括组蛋白修饰、DNA修饰、RNA修饰、非编码RNA及染色质重构。本综述重点总结了表观遗传修饰对玉米主要产量性状的调控机制及表观遗传变化在作物品种改良中的重要性，并结合表观遗传编辑技术提出了提高玉米产量的表观育种新途径。

Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.Copyright © 2017 Elsevier Ltd. All rights reserved.

Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a "histone code" that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.

Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. The methylation marks are written on lysine or arginine by distinct enzymes, namely, histone lysine methyltransferases (HKMTs) or protein arginine methyltransferases (PRMTs). Once established, the methylation marks are specifically recognized by the proteins that act as readers and are interpreted into specific biological outcomes. Histone methylation status is dynamic; methylation marks can be removed by eraser enzymes, the histone demethylases (HDMs). The proteins responsible for writing, reading, and erasing the methylation marks are known mostly in animals. During the past several years, a growing body of literature has demonstrated the impact of histone methylation on genome management, transcriptional regulation, and development in plants. The aim of this review is to summarize the biochemical, genetic, and molecular action of histone methylation in two plants, the dicot Arabidopsis and the monocot rice.

Epigenetics is the epi-information beyond the DNA sequence that can be inherited from parents to offspring. From years of studies, people have found that histone modifications, DNA methylation, and RNA-based mechanism are the main means of epigenetic control. In this chapter, we will focus on the general introductions of epigenetics, which is important in the regulation of chromatin structure and gene expression. With the development and expansion of high-throughput sequencing, various mutations of epigenetic regulators have been identified and proven to be the drivers of tumorigenesis. Epigenetic alterations are used to diagnose individual patients more accurately and specifically. Several drugs, which are targeting epigenetic changes, have been developed to treat patients regarding the awareness of precision medicine. Emerging researches are connecting the epigenetics and cancers together in the molecular mechanism exploration and the development of druggable targets.

In eukaryotes, the genome does not exist as a linear molecule but instead is hierarchically packaged inside the nucleus. This complex genome organization includes multiscale structural units of chromosome territories, compartments, topologically associating domains, which are often demarcated by architectural proteins such as CTCF and cohesin, and chromatin loops. The 3D organization of chromatin modulates biological processes such as transcription, DNA replication, cell division and meiosis, which are crucial for cell differentiation and animal development. In this Review, we discuss recent progress in our understanding of the general principles of chromatin folding, its regulation and its functions in mammalian development. Specifically, we discuss the dynamics of 3D chromatin and genome organization during gametogenesis, embryonic development, lineage commitment and stem cell differentiation, and focus on the functions of chromatin architecture in transcription regulation. Finally, we discuss the role of 3D genome alterations in the aetiology of developmental disorders and human diseases.

Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.

In plants, restoring intercellular communication is required for cell activity in buds during the growth transition from slow to fast growth after dormancy release. However, the epigenetic regulation of this phenomenon is far from understood. Here we demonstrate that lily VERNALIZATION INSENSITIVE 3-LIKE 1 (LoVIL1) confers growth transition by mediating plasmodesmata opening via epigenetic repression of CALLOSE SYNTHASE 3 (LoCALS3). Moreover, we found that a novel transcription factor, NUCLEAR FACTOR Y, SUBUNIT A7 (LoNFYA7), is capable of recruiting the LoVIL1-Polycomb Repressive Complex 2 (PRC2) and enhancing H3K27me3 at the LoCALS3 locus by recognizing the CCAAT cis-element (Cce) of its promoter. The LoNFYA7-LoVIL1 module serves as a key player in orchestrating the phase transition from slow to fast growth in lily bulbs. These studies also indicate that LoVIL1 is a suitable marker for the bud-growth-transition trait following dormancy release in lily cultivars.© 2023. The Author(s), under exclusive licence to Springer Nature Limited.

Flower color is an important character of ornamental plants and one of the main target traits for variety innovation. We previously identified a CmMYB6 epigenetic allele that affects the flower color in chrysanthemum, and changes in flower color are caused by the DNA methylation level of this gene. However, it is still unknown which DNA methyltransferases are involved in modifying the DNA methylation levels of this gene. Here, we used dead Cas9 (dCas9) together with DNA methyltransferases that methylate cytosine residues in the CHH context to target the CmMYB6 promoter through transient and stable transformation methods. We found that CmDRM2a increased the DNA methylation level of the CmMYB6 promoter, the expression of CmMYB6 decreased and a lighter flower color resulted. By contrast, both CmDRM2b and CmCMT2 enhanced DNA methylation levels of the CmMYB6 promoter, the expression of CmMYB6 increased and a deeper flower color resulted. Furthermore, the regulatory mechanism of DNA methyltransferase in the formation of chrysanthemum flower color was investigated, pointing to a new strategy for silencing or activating CmMYB6 epiallele to regulate anthocyanin synthesis. This lays a solid foundation for regulating flower color in chrysanthemum through epigenetic breeding.© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.

The petals of rose (Rosa sp.) flowers determine the ornamental and industrial worth of this species. The number of petals in roses was previously shown to be subject to fluctuations in ambient temperature. However, the mechanisms by which rose detects and responds to temperature changes are not entirely understood. In this study, we identified short interstitial telomere motifs (telo boxes) in the second intron of AGAMOUS (RcAG) from China rose (Rosa chinensis) that play an essential role in precise temperature perception. The second intron of RcAG harbors two telo boxes that recruit telomere repeat binding factors (RcTRBs), which interact with CURLY LEAF (RcCLF) to compose a repressor complex. We show that this complex suppresses RcAG expression when plants are subjected to low temperatures via depositing H3K27me3 marks (trimethylation of lysine 27 on histone H3) over the RcAG gene body. This regulatory mechanism explains the low-temperature-dependent decrease in RcAG transcript levels, leading to the production of more petals under these conditions. Our results underscore an interesting intron-mediated regulatory mechanism governing RcAG expression, enabling rose plants to perceive temperature cues and establish petal numbers.© 2024 Society for Experimental Biology and John Wiley & Sons Ltd.

Taxon-specific small RNA loci are widespread in eukaryotic genomes, yet their role in lineage-specific adaptation, phenotypic diversification, and speciation is poorly understood. Here, we report that a speciation locus in monkeyflowers (), (), contains an inverted repeat region that produces small interfering RNAs (siRNAs) in a phased pattern. Although the inverted repeat is derived from a partial duplication of a protein-coding gene that is not involved in flower pigmentation, one of the siRNAs targets and represses a master regulator of floral carotenoid pigmentation. emerged with two protein-coding genes that control other aspects of flower coloration as a "superlocus" in a subclade of and has contributed to subsequent phenotypic diversification and pollinator-mediated speciation in the descendant species.

As one of the ten most famous flowers in China, the chrysanthemum has rich germplasm with a variety of flowering induction pathways, most of which are photoperiod-induced. After treatment with DNA methylation inhibitors, it was found that DNA methylation plays an important role in flowering regulation, but the mechanism of action remains unclear. Therefore, in this study, curcumin, 5-azaC, their mixed treatment, and MET1 lines were used for transcriptome sequencing to find out how different treatments affected gene expression in chrysanthemums at different stages of flowering.Genomic DNA methylation levels were measured using HPLC technology. The methylation level of the whole genome in the vegetative growth stage was higher than that in the flowering stage. The methylation level of DNA in the vegetative growth stage was the lowest in the curcumin and mixed treatment, and the methylation level of DNA in the transgenic line, mixed treatment, and curcumin treatment was the lowest in the flowering stage. The flowering rate of mixed treatment and curcumin treatment was the lowest. Analysis of differentially expressed genes in transcriptomes showed that 5-azaC treatment had the most differentially expressed genes, followed by curcumin and transgenic lines, and mixed treatment had the fewest. In addition, 5-azaC treatment resulted in the differential expression of multiple DNA methylation transferases, which led to the differential expression of many genes. Analysis of differentially expressed genes in different treatments revealed that different treatments had gene specificity. However, the down-regulated GO pathway in all 4 treatments was involved in the negative regulation of the reproductive process, and post-embryonic development, and regulation of flower development. Several genes associated with DNA methylation and flowering regulation showed differential expression in response to various treatments.Both DNA methylase reagent treatment and targeted silencing of the MET1 gene can cause differential expression of the genes. The operation of the exogenous application is simple, but the affected genes are exceedingly diverse and untargeted. Therefore, it is possible to construct populations with DNA methylation phenotypic diversity and to screen genes for DNA methylation regulation.© 2023. The Author(s).

<p class="MsoNormal" style="text-align:justify;"> <br></p><p class="MsoNormal" style="text-align:justify;"> Flowering is one of the most important phenological periods, as it determines the timing of fruit maturation and seed dispersal. &nbsp;To date, both nitric oxide (NO) and DNA demethylation have been reported to regulate flowering in plants. &nbsp;However, there is no compelling experimental evidence for a relationship between NO and DNA demethylation during plant flowering. &nbsp;In this study, an NO donor and a DNA methylation inhibitor were used to investigate the involvement of DNA demethylation in NO-mediated tomato (<i>Solanum</i>&nbsp;<i>lycopersicum</i>&nbsp;cv. Micro-Tom) flowering. &nbsp;The results showed that the promoting effect of NO on tomato flowering was dose-dependent, with the greatest positive effect observed at 10&nbsp;μmol L^{<span>–1</span>}&nbsp;of the NO donor S-nitrosoglutathione (GSNO). &nbsp;Treatment with 50&nbsp;μmol L^{<span>–1</span>}&nbsp;of the DNA methylation inhibitor 5-azacitidine (5-AzaC) also significantly promoted tomato flowering. &nbsp;Moreover, GSNO and 5-AzaC increased the peroxidase (POD) and catalase (CAT) activities and cytokinin (CTK) and proline contents, while they reduced the gibberellic acid (GA3) and indole-3-acetic acid (IAA) contents. &nbsp;Co-treatment with GSNO and 5-AzaC accelerated the positive effects of GSNO and 5-AzaC in promoting tomato flowering. &nbsp;Meanwhile, compared with a GSNO or 5-AzaC treatment alone, co-treatment with GSNO+5-AzaC significantly increased the global DNA demethylation levels in different tissues of tomato. &nbsp;The results also indicate that DNA demethylation may be involved in NO-induced flowering. &nbsp;The expression of flowering genes was significantly altered by the GSNO+5-AzaC treatment. &nbsp;Five of these flowering induction genes, <i>ARGONAUTE</i>&nbsp;<i>4</i>&nbsp;(<i>AGO4A</i>), <i>SlSP3D/SINGLE</i>&nbsp;<i>FLOWER</i>&nbsp;<i>TRUSS</i>&nbsp;(<i>SFT</i>), <i>MutS</i>&nbsp;<i>HOMOLOG</i>&nbsp;<i>1</i>&nbsp;(<i>MSH1</i>), <i>ZINC</i>&nbsp;<i>FINGER</i>&nbsp;<i>PROTEIN</i>&nbsp;<i>2</i>&nbsp;(<i>ZFP2</i>), and <i>FLOWERING</i>&nbsp;<i>LOCUS</i>&nbsp;<i>D</i>&nbsp;(<i>FLD</i>), were selected as candidate genes for further study. &nbsp;An McrBC-PCR analysis showed that DNA demethylation of the <i>SFT</i>&nbsp;gene in the apex and the <i>FLD</i>&nbsp;gene in the stem might be involved in NO-induced flowering. &nbsp;Therefore, this study shows that NO might promote tomato flowering by mediating the DNA demethylation of flowering induction genes, and it provides direct evidence for a synergistic effect of NO and DNA demethylation in promoting tomato flowering.</p><p> <br></p>

Age, as a threshold of floral competence acquisition, prevents precocious flowering when there is insufficient biomass, and ensures flowering independent of environmental conditions; however, the underlying regulatory mechanisms are largely unknown. In this study, silencing the expression of a nuclear factor gene, CmNF-YB8, from the short day plant chrysanthemum (Chrysanthemum morifolium), results in precocious transition from juvenile to adult, as well as early flowering, regardless of day length conditions. The expression of SQUAMOSA PROMOTER BINDING-LIKE (SPL) family members, SPL3, SPL5, and SPL9, is upregulated in CmNFYB8-RNAi plants, while expression of the microRNA, cmo-MIR156, is downregulated. In addition, CmNF-YB8 is shown to bind to the promoter of the cmo-MIR156 gene. Ectopic expression of cmo-miR156, using a virus-based microRNA expression system, restores the early flowering phenotype caused by CmNF-YB8 silencing. These results show that CmNF-YB8 influences flowering time through directly regulating the expression of cmo-MIR156 in the aging pathway.

Ripening of tomato fruits is triggered by the plant hormone ethylene, but its effect is restricted by an unknown developmental cue to mature fruits containing viable seeds. To determine whether this cue involves epigenetic remodeling, we expose tomatoes to the methyltransferase inhibitor 5-azacytidine and find that they ripen prematurely. We performed whole-genome bisulfite sequencing on fruit in four stages of development, from immature to ripe. We identified 52,095 differentially methylated regions (representing 1% of the genome) in the 90% of the genome covered by our analysis. Furthermore, binding sites for RIN, one of the main ripening transcription factors, are frequently localized in the demethylated regions of the promoters of numerous ripening genes, and binding occurs in concert with demethylation. Our data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening. Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenome.

DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown.Here, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening.Our study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.© 2024. The Author(s).

Dynamic DNA methylation regulatory networks are involved in many biological processes. However, how DNA methylation patterns change during flower senescence and their relevance with gene expression and related molecular mechanism remain largely unknown. Here, we used whole genome bisulfite sequencing to reveal a significant increase of DNA methylation in the promoter region of genes during natural and ethylene-induced flower senescence in carnation (Dianthus caryophyllus L.), which was correlated with decreased expression of DNA demethylase gene DcROS1. Silencing of DcROS1 accelerated while overexpression of DcROS1 delayed carnation flower senescence. Moreover, among the hypermethylated differentially expressed genes during flower senescence, we identified two amino acid biosynthesis genes, DcCARA and DcDHAD, with increased DNA methylation and reduced expression in DcROS1 silenced petals, and decreased DNA methylation and increased expression in DcROS1 overexpression petals, accompanied by decreased or increased amino acids content. Silencing of DcCARA and DcDHAD accelerates carnation flower senescence. We further showed that adding corresponding amino acids could largely rescue the senescence phenotype of DcROS1, DcCARA and DcDHAD silenced plants. Our study not only demonstrates an essential role of DcROS1-mediated remodeling of DNA methylation in flower senescence but also unravels a novel epigenetic regulatory mechanism underlying DNA methylation and amino acid biosynthesis during flower senescence.© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation.

Fruit ripening and disease resistance are two essential biological processes for quality formation and maintenance. DNA methylation, in the form of 5-methylcytosine (5mC), has been elucidated to modulate fruit ripening, but its role in regulating fruit disease resistance remains poorly understood. In this study, we show that mutation of SlDML2, the DNA demethylase gene essential for fruit ripening, affects multiple developmental processes of tomato besides fruit ripening, including seed germination, leaf length and width and flower branching. Intriguingly, loss of SlDML2 function decreased the resistance of tomato fruits against the necrotrophic fungal pathogen Botrytis cinerea. Comparative transcriptomic analysis revealed an obvious transcriptome reprogramming caused by SlDML2 mutation during B. cinerea invasion. Among the thousands of differentially expressed genes, SlβCA3 encoding a β-carbonic anhydrase and SlFAD3 encoding a ω-3 fatty acid desaturase were demonstrated to be transcriptionally activated by SlDML2-mediated DNA demethylation and positively regulate tomato resistance to B. cinerea probably in the same genetic pathway with SlDML2. We further show that the pericarp tissue surrounding B. cinerea infection exhibited a delay in ripening with singnificant decrease in expression of ripening genes that are targeted by SlDML2 and increase in expression of SlβCA3 and SlFAD3. Taken together, our results uncover an essential layer of gene regulation mediated by DNA methylation upon B. cinerea infection and raise the possible that the DNA demethylase gene SlDML2, as a multifunctional gene, participates in modulating the trade-off between fruit ripening and disease resistance.© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

DNA methylation is an important epigenetic marker for the suppression of transposable elements (TEs) and the regulation of plant immunity. However, little is known how RNA viruses counter defense such antiviral machinery. In this study, the change of DNA methylation in turnip mosaic virus (TuMV)-infected cells was analyzed by whole genome bisulfite sequencing. Results showed that the total number of methylated sites of CHH and CHG increased in TuMV-infected cells, the majority of differentially methylated regions (DMRs) in the CHH and CHG contexts were associated with hypermethylation. Gene expression analysis showed that the expression of two methylases (DRM2 and CMT3) and three demethylases (ROS3, DML2, DML3) was significantly increased and decreased in TuMV-infected cells, respectively. Pathogenicity tests showed that the enhanced resistance to TuMV of the loss-of-function mutant of DRM2 is associated with unregulated expression of several defense-related genes. Finally, we found TuMV-encoded NIb, the viral RNA-dependent RNA polymerase, was able to induce the expression of DRM2. In conclusion, this study discovered that TuMV can modulate host DNA methylation by regulating the expression of DRM2 to promote virus infection.© 2022. The Author(s).

<div style="text-align:justify;"> Salt stress is a typical abiotic stress in plants that causes slow growth, stunting, and reduced yield and fruit quality. &nbsp;Fertilization is necessary to ensure proper crop growth. &nbsp;However, the effect of fertilization on salt tolerance in grapevine is unclear. &nbsp;In this study, we investigated the effect of nitrogen fertilizer (0.01 and 0.1 mol L^–1&nbsp;NH₄NO₃) application on the salt (200 mmol L^–1&nbsp;NaCl) tolerance of grapevine based on physiological indices, and transcriptomic and metabolomic analyses. &nbsp;The results revealed that 0.01 mol L^–1&nbsp;NH₄NO₃&nbsp;supplementation significantly reduced the accumulation of superoxide anion (O₂^–·), enhanced the activities of superoxide dismutase (SOD) and peroxidase (POD), and improved the levels of ascorbic acid (AsA) and glutathione (GSH) in grape leaves compared to salt treatment alone. &nbsp;Specifically, joint transcriptome and metabolome analyses showed that the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were significantly enriched in the flavonoid biosynthesis pathway (ko00941) and the flavone and flavonol biosynthesis pathway (ko00944). &nbsp;In particular, the relative content of quercetin (C00389) was markedly regulated by salt and nitrogen. &nbsp;Further analysis revealed that exogenous foliar application of quercetin improved the SOD and POD activities, increased the AsA and GSH contents, and reduced the H₂O₂and O₂^–· contents. &nbsp;Meanwhile, 10 hub DEGs, which had high Pearson correlations (<i>R</i>²>0.9) with quercetin, were repressed by nitrogen. &nbsp;In conclusion, all the results indicated that moderate nitrogen and quercetin application under salt stress enhanced the antioxidant system defense response, thus providing a new perspective for improving salt tolerance in grapes.</div><p> <br></p>

Tea plant is a thermophilic cash crop and contains a highly duplicated and repeat-rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single-base resolution DNA methylation map of tea plants under chilling stress. We found that compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG, and CHH (H = A, T, or C), which is further proved to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, while non-CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element-mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. DNA methylation and expression divergence of tea plant duplicated genes increase with their evolutionary ages and selective pressure. Besides, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly down-regulated, while demethylase genes are up-regulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well-known cold-responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into the duplicated gene evolution and chilling tolerance in tea plants.This article is protected by copyright. All rights reserved.