Melatonin-induced DNA demethylation of metal transporters and antioxidant genes alleviates lead stress in radish plants

Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response

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

Underlying mechanism of Dendrobium huoshanense resistance to lead stress using the quantitative proteomics method

Lead affects photosynthesis and growth and has serious toxic effects on plants. Here, the differential expressed proteins (DEPs) in D. huoshanense were investigated under different applications of lead acetate solutions. Using label-free quantitative proteomics methods, more than 12,000 peptides and 2,449 proteins were identified. GO and KEGG functional annotations show that these differential proteins mainly participate in carbohydrate metabolism, energy metabolism, amino acid metabolism, translation, protein folding, sorting, and degradation, as well as oxidation and reduction processes. A total of 636 DEPs were identified, and lead could induce the expression of most proteins. KEGG enrichment analysis suggested that proteins involved in processes such as homologous recombination, vitamin B6 metabolism, flavonoid biosynthesis, cellular component organisation or biogenesis, and biological regulation were significantly enriched. Nearly 40 proteins are involved in DNA replication and repair, RNA synthesis, transport, and splicing. The effect of lead stress on D. huoshanense may be achieved through photosynthesis, oxidative phosphorylation, and the production of excess antioxidant substances. The expression of 9 photosynthesis-related proteins and 12 oxidative phosphorylation-related proteins was up-regulated after lead stress. Furthermore, a total of 3 SOD, 12 POD, 3 CAT, and 7 ascorbate-related metabolic enzymes were identified. Under lead stress, almost all key enzymes involved in the synthesis of antioxidant substances are up-regulated, which may facilitate the scavenging of oxygen-free radical scavenging. The expression levels of some key enzymes involved in sugar and glycoside synthesis, the phenylpropanoid synthesis pathway, and the terpene synthesis pathway also increased. More than 30 proteins involved in heavy metal transport were also identified. Expression profiling revealed a significant rise in the expression of the ABC-type multidrug resistance transporter, copper chaperone, and P-type ATPase with exposure to lead stress. Our findings lay the basis for research on the response and resistance of D. huoshanense to heavy metal stress.

Epigenetic changes induced by chronic and acute chromium stress treatments in Arabidopsis thaliana identified by the MSAP-Seq

Chromium (Cr) is an highly toxic metal to plants and causes severe damage to their growth, development, and reproduction. Plant exposure to chronic and acute Cr stress treatments results in significant changes at short time in the gene expression profile and at long time in the genomic DNA methylation profile at a transgenerational level and, consequently, in gene expression. These epigenetic modifications and their implications imposed by the Cr stress are not yet completely known in plants. Herein, were identified the epigenetic changes induced by chronic and acute Cr stress treatments in Arabidopsis thaliana plants using Methylation Sensitive Amplification Polymorphism coupled with next-generation sequencing (MSAP-Seq). First-generation Arabidopsis plants (termed F0 plants) kept under hoagland solution were subjected to Cr stress treatments. For chronic Cr stress, plants were treated through hoagland solution with 2.5 μM Cr during the entire cultivation period until seed harvest. Meanwhile, for acute Cr stress, plants were treated with 5 μM Cr during the first three weeks and returned to unstressful control condition until seed harvest. Seeds from F0 plants were sown and F1 plants were re-submitted to the same Cr stress treatments. The seed germination rate was evaluated from F-2 seeds harvested of F1 plants kept under different Cr stress treatments (0, 10, 20, and 40 μM) compared to the unstressful control condition. These data showed significant changes in the germination rate of F-2 seeds originating from stressed F1 plants compared to F-2 seeds harvested from unstressful control plants. Given this data, F1 plants kept under these chronic and acute Cr stress treatments and unstressful control condition were evaluated for the transgenerational epigenetic modifications using MSAP-Seq. The MSAP-Seq data showed that several genes were modified in their methylation status as a consequence of chronic and acute Cr stress treatment to maintain plant defenses activated. In particular, RNA processing, protein translation, photorespiration, energy production, transmembrane transport, DNA transcription, plant development, and plant resilience were the major biological processes modulated by epigenetic mechanisms identified in F1 plants kept under chronic and acute Cr stress. Therefore, collective data suggested that Arabidopsis plants kept under Cr stress regulate their epigenetic status over generations based on DNA methylation to modulate defense and resilience mechanisms.

Melatonin: The Multifaceted Molecule in Plant Growth and Defense

Melatonin (MEL), a hormone primarily known for its role in regulating sleep and circadian rhythms in animals, has emerged as a multifaceted molecule in plants. Recent research has shed light on its diverse functions in plant growth and defense mechanisms. This review explores the intricate roles of MEL in plant growth and defense responses. MEL is involved in plant growth owing to its influence on hormone regulation. MEL promotes root elongation and lateral root formation and enhances photosynthesis, thereby promoting overall plant growth and productivity. Additionally, MEL is implicated in regulating the circadian rhythm of plants, affecting key physiological processes that influence plant growth patterns. MEL also exhibits antioxidant properties and scavenges reactive oxygen species, thereby mitigating oxidative stress. Furthermore, it activates defense pathways against various biotic stressors. MEL also enhances the production of secondary metabolites that contribute to plant resistance against environmental changes. MEL's ability to modulate plant response to abiotic stresses has also been extensively studied. It regulates stomatal closure, conserves water, and enhances stress tolerance by activating stress-responsive genes and modulating signaling pathways. Moreover, MEL and nitric oxide cooperate in stress responses, antioxidant defense, and plant growth. Understanding the mechanisms underlying MEL's actions in plants will provide new insights into the development of innovative strategies for enhancing crop productivity, improving stress tolerance, and combating plant diseases. Further research in this area will deepen our knowledge of MEL's intricate functions and its potential applications in sustainable agriculture.

Multicontamination Toxicity Evaluation in the Model Plant Lactuca sativa L

Many contaminated soils contain several toxic elements (TEs) in elevated contents, and plant-TE interactions can differ from single TE contamination. Therefore, this study investigated the impact of combined contamination (As, Cd, Pb, Zn) on the physiological and metabolic processes of lettuce. After 45 days of exposure, TE excess in soil resulted in the inhibition of root and leaf biomass by 40 and 48%, respectively. Oxidative stress by TE accumulation was indicated by markers-malondialdehyde and 5-methylcytosine-and visible symptoms of toxicity (leaf chlorosis, root browning) and morpho-anatomical changes, which were related to the change in water regime (water potential decrease). An analysis of free amino acids (AAs) indicated that TEs disturbed N and C metabolism, especially in leaves, increasing the total content of free AAs and their families. Stress-induced senescence by TEs suggested changes in gas exchange parameters (increase in transpiration rate, stomatal conductance, and intercellular CO2 concentration), photosynthetic pigments (decrease in chlorophylls and carotenoids), a decrease in water use efficiency, and the maximum quantum yield of photosystem II. These results confirmed that the toxicity of combined contamination significantly affected the processes of lettuce by damaging the antioxidant system and expressing higher leaf sensitivity to TE multicontamination.

Exogenous 5-Aminolevulinic acid improved low-temperature tolerance tomato seedling by regulating starch content and phenylalanine metabolism

Tomato is an important horticultural cash crop, and low-temperature stress has seriously affected the yield and quality of tomato. 5-Aminolevulinic acid (ALA) is widely used in agriculture as an efficient and harmless growth regulator. It is currently unclear whether exogenous ALA can cope with low-temperature stress by regulating tomato starch content and phenylalanine metabolism. In this study, exogenous ALA remarkably improved the low-temperature tolerance of tomato seedlings. RNA-sequencing results showed that exogenous ALA affected starch metabolism and phenylalanine metabolism in tomato seedling leaves under low-temperature stress. Subsequently, we used histochemical staining, observation of chloroplast microstructure, substance content determination, and qRT-PCR analysis to demonstrate that exogenous ALA could improve the low-temperature tolerance of tomato seedlings by regulating starch content and phenylalanine metabolism (SlPAL, SlPOD1, and SlPOD2). Simultaneously, we found that exogenous ALA induced the expression of SlMYBs and SlWRKYs under low-temperature stress. In addition, dual luciferase, yeast one hybrid, and electrophoretic mobility shift assays indicate that SlMYB4 and SlMYB88 could regulate the expression of SlPOD2 in phenylalanine metabolism. We demonstrated that exogenous ALA could improve the low-temperature tolerance of tomato seedlings by regulating starch content and phenylalanine metabolism.

Sulfonamide-induced DNA hypomethylation disturbed sugar metabolism in rice (Oryza sativa L.)

DNA methylation is well-accepted as a bridge to unravel the complex interplay between genome and environmental exposures, and its alteration regulated the cellular metabolic responses towards pollutants. However, the mechanism underlying site-specific aberrant DNA methylation and metabolic disorders under pollutant stresses remained elusive. Herein, the multilevel omics interferences of sulfonamides (i.e., sulfadiazine and sulfamerazine), a group of antibiotics pervasive in farmland soils, towards rice in 14 days of 1 mg/L hydroponic exposure were systematically evaluated. Metabolome and transcriptome analyses showed that 57.1-71.4 % of mono- and disaccharides were accumulated, and the differentially expressed genes were involved in the promotion of sugar hydrolysis, as well as the detoxification of sulfonamides. Most differentially methylated regions (DMRs) were hypomethylated ones (accounting for 87-95 %), and 92 % of which were located in the CHH context (H = A, C, or T base). KEGG enrichment analysis revealed that CHH-DMRs in the promoter regions were enriched in sugar metabolism. To reveal the significant hypomethylation of CHH, multi-spectroscopic and thermodynamic approaches, combined with molecular simulation were conducted to investigate the molecular interaction between sulfonamides and DNA in different sequence contexts, and the result demonstrated that sulfonamides would insert into the minor grooves of DNA, and exhibited a stronger affinity with the CHH contexts of DNA compared to CG or CHG contexts. Computational modeling of DNA 3D structures further confirmed that the binding led to a pitch increase of 0.1 Å and a 3.8° decrease in the twist angle of DNA in the CHH context. This specific interaction and the downregulation of methyltransferase CMT2 (log2FC = -4.04) inhibited the DNA methylation. These results indicated that DNA methylation-based assessment was useful for metabolic toxicity prediction and health risk assessment.

5-Aminolevulinic acid improves cold resistance through regulation of SlMYB4/SlMYB88-SlGSTU43 module to scavenge reactive oxygen species in tomato

Cold stress severely affects the growth and quality of tomato. 5-Aminolevulinic acid (ALA) can effectively improve tomato's cold stress tolerance. In this study, a tomato glutathione S-transferase gene, SlGSTU43, was identified. Results showed that ALA strongly induced the expression of SlGSTU43 under cold stress. SlGSTU43-overexpressing lines showed increased resistance to cold stress through an enhanced ability to scavenge reactive oxygen species. On the contrary, slgstu43 mutant lines were sensitive to cold stress, and ALA did not improve their cold stress tolerance. Thus, SlGSTU43 is a key gene in the process of ALA improving tomato cold tolerance. Through yeast library screening, SlMYB4 and SlMYB88 were preliminarily identified as transcription factors that bind to the SlGSTU43 promoter. Electrophoretic mobility shift, yeast one-hybrid, dual luciferase, and chromatin immunoprecipitation assays experiments verified that SlMYB4 and SlMYB88 can bind to the SlGSTU43 promoter. Further experiments showed that SlMYB4 and SlMYB88 are involved in the process of ALA-improving tomato's cold stress tolerance and they positively regulate the expression of SlGSTU43. The findings provide new insights into the mechanism by which ALA improves cold stress tolerance. SlGSTU43, as a valuable gene, could be added to the cold-responsive gene repository. Subsequently, it could be used in genetic engineering to enhance the cold tolerance of tomato.

Melatonin modulates the tolerance of plants to water stress: morphological response of the molecular mechanism

Water stress (drought and waterlogging) leads to an imbalance in plant water distribution, disrupts cell homeostasis, and severely inhibits plant growth. Melatonin is a growth hormone that plants synthesise and has been shown to resist adversity in many plants. This review discusses the biosynthesis and metabolism of melatonin, as well as the changes in plant morphology and physiological mechanisms caused by the molecular defence process. Melatonin induces the expression of related genes in the process of plant photosynthesis under stress and protects the structural integrity of chloroplasts. Exogenous melatonin can maintain the dynamic balance of root ion exchange under waterlogging stress. Melatonin can repair mitochondria and alleviate damage caused by reactive oxygen species and reactive nitrogen species; and has a wide range of uses in the regulation of stress-specific genes and the activation of antioxidant enzyme genes. Melatonin improves the stability of membrane lipids in plant cells and maintains osmotic balance by regulating water channels. There is crosstalk between melatonin and other hormones, which jointly improve the ability of the root system to absorb water and breathe and promote plant growth. Briefly, as a multifunctional molecule, melatonin improves the tolerance of plants under water stress and promotes plant growth and development.

Modulation of plant photosynthetic processes during metal and metalloid stress, and strategies for manipulating photosynthesis-related traits

Metals constitute vital elements for plant metabolism and survival, acting as essential co-factors in cellular processes which are indispensable for plant growth and survival. Excess or deficient provision of metal/metalloids puts plant's life and survival at risk, thus considered a potent stress for plants. Chloroplasts as an organelle with a high metal demand form a pivotal site within the metal homeostasis network. Therefore, the metal-mediated electron transport chain (ETC) in chloroplasts is a primary target site of metal/metalloid-induced stresses. Both excess and deficient availability of metal/metalloids threatens plant's photosynthesis in several ways. Energy demands from the photosynthetic carbon reactions should be in balance with energy output of ETC. Malfunctioning of ETC components as a result of metal/metalloid stress initiates photoinhiition. A feedback inhibition from carbon fixation process also impedes the ETC. Metal stress impairs antioxidant enzyme activity, pigment biosynthesis, and stomatal function. However, genetic manipulations, nutrient management, keeping photostasis, and application of phytohormones are among strategies for coping with metal stress. Consequently, a comprehensive understanding of the underlying mechanisms of metal/metalloid stress, as well as the exploration of potential strategies to mitigate its impact on plants are imperative. This review offers a mechanistic insight into the disruption of photosynthesis regulation by metal/metalloids and highlights adaptive approaches to ameliorate their effects on plants. Focus was made on photostasis, nutrient interactions, phytohormones, and genetic interventions for mitigating metal/metalloid stresses.

Toxic effects of lead on plants: integrating multi-omics with bioinformatics to develop Pb-tolerant crops

MAIN CONCLUSION

Lead disrupts plant metabolic homeostasis and key structural elements. Utilizing modern biotechnology tools, it's feasible to develop Pb-tolerant varieties by discovering biological players regulating plant metabolic pathways under stress. Lead (Pb) has been used for a variety of purposes since antiquity despite its toxic nature. After arsenic, lead is the most hazardous heavy metal without any known beneficial role in the biological system. It is a crucial inorganic pollutant that affects plant biochemical and morpho-physiological attributes. Lead toxicity harms plants throughout their life cycle and the extent of damage depends on the concentration and duration of exposure. Higher levels of lead exposure disrupt numerous key metabolic activities of plants including oxygen-evolving complex, organelles integrity, photosystem II connectivity, and electron transport chain. This review summarizes the detrimental effects of lead toxicity on seed germination, crop growth, and yield, oxidative and ultra-structural alterations, as well as nutrient absorption, transport, and assimilation. Further, it discusses the Pb-induced toxic modulation of stomatal conductance, photosynthesis, respiration, metabolic-enzymatic activity, osmolytes accumulation, and antioxidant activity. It is a comprehensive review that reports on omics-based studies along with morpho-physiological and biochemical modifications caused by lead stress. With advances in DNA sequencing technologies, genomics and transcriptomics are gradually becoming popular for studying Pb stress effects in plants. Proteomics and metabolomics are still underrated and there is a scarcity of published data, and this review highlights both their technical and research gaps. Besides, there is also a discussion on how the integration of omics with bioinformatics and the use of the latest biotechnological tools can aid in developing Pb-tolerant crops. The review concludes with core challenges and research directions that need to be addressed soon.

The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals

Contamination of the soil with non-essential metals and metalloids is a serious problem in many regions of the world. These non-essential metals and metalloids are toxic to all organisms impacting crop yields and human health. Crop plants exposed to high concentrations of these metals leads to perturbed mineral homeostasis, decreased photosynthesis efficiency, inhibited cell division, oxidative stress, genotoxic effects and subsequently hampered growth. Plants can activate epigenetic and epitranscriptomic mechanisms to maintain cellular and organism homeostasis. Epigenetic modifications include changes in the patterns of cytosine and adenine DNA base modifications, changes in cellular non-coding RNAs, and remodeling histone variants and covalent histone tail modifications. Some of these epigenetic changes have been shown to be long-lasting and may therefore contribute to stress memory and modulated stress tolerance in the progeny. In the emerging field of epitranscriptomics, defined as chemical, covalent modifications of ribonucleotides in cellular transcripts, epitranscriptomic modifications are postulated as more rapid modulators of gene expression. Although significant progress has been made in understanding the plant's epigenetic changes in response to biotic and abiotic stresses, a comprehensive review of the plant's epigenetic responses to metals is lacking. While the role of epitranscriptomics during plant developmental processes and stress responses are emerging, epitranscriptomic modifications in response to metals has not been reviewed. This article describes the impact of non-essential metals and metalloids (Cd, Pb, Hg, Al and As) on global and site-specific DNA methylation, histone tail modifications and epitranscriptomic modifications in plants.

RsPDR8, a member of ABCG subfamily, plays a positive role in regulating cadmium efflux and tolerance in radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is one of the most vital root vegetable crops worldwide. Cadmium (Cd), a non-essential and toxic heavy metal, can dramatically restrict radish taproot quality and safety. Although the Peiotrpic Drug Resistance (PDR) genes play crucial roles in heavy metal accumulation and transport in plants, the systematic identification and functional characterization of RsPDRs remain largely unexplored in radish. Herein, a total of 19 RsPDR genes were identified from the radish genome. A few RsPDRs, including RsPDR1, RsPDR8 and RsPDR12, showed significant differential expression under Cd and lead (Pb) stress in the 'NAU-YH' genotype. Interestingly, the plasma membrane-localized RsPDR8 exhibited significantly up-regulated expression and enhanced promoter activity under Cd exposure. Ectopic expression of RsPDR8 conferred Cd tolerance via reducing Cd accumulation in yeast cells. Moreover, the transient transformation of RsPDR8 revealed that it positively regulated Cd tolerance by promoting ROS scavenging and enhancing membrane permeability in radish. In addition, overexpression of RsPDR8 increased root elongation but deceased Cd accumulation compared with the WT plants in Arabidopsis, demonstrating that it could play a positive role in mediating Cd efflux and tolerance in plants. Together, these results would facilitate deciphering the molecular mechanism underlying RsPDR8-mediated Cd tolerance and detoxification in radish.

DNA methylation mediates overgrazing-induced clonal transgenerational plasticity

Overgrazing generally induces dwarfism in grassland plants, and these phenotypic traits could be transmitted to clonal offspring even when overgrazing is excluded. However, the dwarfism-transmitted mechanism remains largely unknown, despite generally thought to be enabled by epigenetic modification. To clarify the potential role of DNA methylation on clonal transgenerational effects, we conducted a greenhouse experiment with Leymus chinensis clonal offspring from different cattle/sheep overgrazing histories via the demethylating agent 5-azacytidine. The results showed that clonal offspring from overgrazed (by cattle or sheep) parents were dwarfed and the auxin content of leaves significantly decreased compared to offspring from no-grazed parents'. The 5-azaC application generally increased the auxin content and promoted the growth of overgrazed offspring while inhibited no-grazed offspring growth. Meanwhile, there were similar trends in the expression level of genes related to auxin-responsive target genes (ARF7, ARF19), and signal transduction gene (AZF2). These results suggest that DNA methylation leads to overgrazing-induced plant transgenerational dwarfism via inhibiting auxin signal pathway.

Exogenous melatonin enhances the tolerance of tiger nut (Cyperus esculentus L.) via DNA damage repair pathway under heavy metal stress (Cd2+) at the sprout stage

Heavy metal (HM) stress is a non-negligible abiotic stress that seriously restricts crop yield and quality, while the sprout stage is the most sensitive to stress and directly impacts the growth and development of the later stage. Melatonin (N-acetyl-5-methoxytryptamine), as an exogenous additive, enhances stress resistance due to its ability to oxidize and reduce. However, few reports on exogenous melatonin to tiger nuts under HM stress have explored whether exogenous melatonin enhances plants' resistance to heavy metals. Here, "Jisha 2″ was used as material, with a stress concentration of 5 mg/L and 100 μmol/L of CdCl2 to explore whether exogenous melatonin enhances plant resistance and molecular mechanism. The result revealed that stress limits growth, while melatonin alleviated the sprout damage under stress from the phenotypes. Moreover, stress-enhanced reactive oxygen species (ROS) accumulation and membrane lipid peroxidation, while melatonin-increased ROS reduce damage via the analysis of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) and malondialdehyde (MDA) content, hydrogen peroxide (H2O2), superoxide anion (O2-), and Electrolyte leakage (El). Further results indicated that HM leads to DNA damage while exogenous melatonin will repair the damage by analyzing random amplified polymorphic DNA (RAPD), DNA cross-linking, 8-hydroxy-20-deoxyguanine level, and relative density of apurinic sites. Furthermore, gene expression in the DNA-repaired pathway exhibited similar results. These results applied that exogenous melatonin released the hurt caused by HM stress, with DNA repair and ROS balance serving as candidate pathways. This study elucidated the mechanism of melatonin's influence and provided theoretical insights into its application in tiger nuts.

Epigenetic Control of Plant Response to Heavy Metals

Plants are sessile organisms that must adapt to environmental conditions, such as soil characteristics, by adjusting their development during their entire life cycle. In case of low-distance seed dispersal, the new generations are challenged with the same abiotic stress encountered by the parents. Epigenetic modification is an effective option that allows plants to face an environmental constraint and to share the same adaptative strategy with their progeny through transgenerational inheritance. This is the topic of the presented review that reports the scientific progress, up to date, gained in unravelling the epigenetic response of plants to soil contamination by heavy metals and metalloids, collectively known as potentially toxic elements. The effect of the microbial community inhabiting the rhizosphere is also considered, as the evidence of a transgenerational transfer of the epigenetic status that contributes to the activation in plants of response mechanisms to soil pollution.

Exogenous glutathione can alleviate chromium toxicity in kenaf by activating antioxidant system and regulating DNA methylation

Glutathione (GSH) participates in plant response to heavy metals (HMs) stress, however, the epigenetic regulating mechanisms of GSH in HMs detoxification remains unclear. In this study, to reveal the potential epigenetic regulating mechanisms, kenaf seedlings were treated with/without GSH under chromium (Cr) stress. A comprehensive physiological, genome-wide DNA methylation and gene functional analysis were performed. Results showed that external GSH obviously recovered Cr-induced growth inhibition, significantly decreased H₂O₂, O₂^.- and MDA accumulation, increased the activities of antioxidant enzymes (SOD, CAT, GR and APX) in kenaf exposed to Cr. In addition, the expression level of the main DNA methyltransferase (MET1, CMT3 and DRM1) and demethylase (ROS1, DEM, DML2, DML3 and DDM1) genes were investigated by qRT-PCR. The result indicated that Cr stress decreased DNA methyltransferase genes expression while increased demethylase genes expression; however, apply exogenous GSH led to the recovery trend. These indicating exogenous GSH alleviation Cr stress on kenaf seedlings by increasing DNA methylation level. At the same time, the MethylRAD-seq genome-wide DNA methylation analysis showed the DNA methylation level was significantly increased after GSH treatment compared with Cr treatment alone. The differentially methylated genes (DMGs) were uniquely enriched in DNA repair, flavin adenine dinucleotide binding and oxidoreductase activity. Furthermore, a ROS homeostasis-associated DMG, HcTrx, was selected for further functional analysis. Results showed that the knock-down of HcTrx kenaf seedlings displayed yellow-green phenotype and impaired antioxidant enzyme activity; in contrast, the overexpression lines of HcTrx improved chlorophyll levels and enhanced Cr tolerance in Arabidopsis. Taken together, our results illustrate the novel role of GSH-mediated Cr detoxification in kenaf by modulating the DNA methylation, and thus further affect the activation of antioxidant defense systems. The present characterized Cr tolerant gene resource could be further used for kenaf Cr tolerant breeding via genetic improvement.

Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection

The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.

Melatonin alleviates chromium toxicity by altering chromium subcellular distribution and enhancing antioxidant metabolism in wheat seedlings

The endogenous stimulating molecule melatonin (N-acetyl-5-methoxytryptamine, MT) has an important function in mitigating the impact of multiple abiotic stressors. However, the ameliorating effect of MT on chromium (Cr) stress and its mechanisms remains unclear. Therefore, the present study aimed to clarify the mitigating effect of exogenous MT (0 μM and 100 μM) on wheat seedlings under Cr (0 μM and 50 μM) stress stemming from the growth and physiological characteristics, phytochelatin (PC) biosynthesis, Cr subcellular distribution, and antioxidant system of the plants in these treatments. The results showed that endogenous MT application significantly promoted plant growth and improved root morphology of wheat seedlings under Cr stress due to decreased Cr and reactive oxygen species (ROS) accumulation in both roots and leaves. Accumulation and transport of Cr from roots to leaves were reduced by MT, because enhanced vacuolar sequestration via upregulated PC accumulation, took place, derived from the fact that MT upregulated the expression of key genes for PC synthesis (TaPCS and Taγ-ECS). Furthermore, MT pre-treatment alleviated Cr-induced oxidative damage by diminishing lipid peroxidation and cell apoptosis, profiting from the enhanced scavenging ability of ROS as a result of the MT-induced increase in the activities of superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase, and the related encoding gene expression levels of TaSOD2, TaCAT, TaAPX, and TaGR. In conclusion, endogenous MT application improved the growth traits, antioxidant system, and decreased Cr accumulation especially at the leaf level in wheat seedlings under Cr stress mainly through enhancing antioxidant enzyme activities and altering Cr subcellular distribution via strengthening PC biosynthesis. The mechanisms of MT-induced plant tolerance to Cr stress could help develop new strategies for secure crop production in Cr-polluted soils.

Melatonin: Current status and future perspectives in horticultural plants

Global warming in this century increases incidences of various abiotic stresses, restricting plant growth and productivity and posing a severe threat to global food production and security. Different phytohormones are produced by plants to mitigate the adverse effects of these stresses. One such phytohormone is melatonin (MEL), which, being a potential bio-stimulator, helps to govern a wide array of functions in horticultural crops. Recent advancements have determined the role of MEL in plants' responses to abiotic stresses. MEL enhances physiological functions such as seed germination, growth and development, seedling growth, root system architecture, and photosynthetic efficiency. The potential function of MEL in stressful environments is to regulate the enzymatic and non-enzymatic antioxidant activity, thus playing a role in the substantial scavenging of reactive oxygen species (ROS). Additionally, MEL, as a plant growth regulator and bio-stimulator, aids in promoting plant tolerance to abiotic stress, mainly through improvements in nutrient uptake, osmolyte production, and cellular membrane stability. This review, therefore, focuses on the possible functions of MEL in the induction of different abiotic stresses in horticultural crops. Therefore, this review would help readers learn more about MEL in altered environments and provide new suggestions on how this knowledge could be used to develop stress tolerance.

RsERF40 contributes to cold stress tolerance and cell expansion of taproot in radish (Raphanus sativus L.)

The growth and development of taproots are inhibited by cold stress in radish (Raphanus sativus L.). Ethylene-responsive element binding factors (ERF) are key participators in the cold stress response and growth regulation of plants. However, the function of ERF genes in cold tolerance and root development in radish remains elusive. Here, we showed that the secondary growth of radish taproots was inhibited by cold stress. Comparative transcriptome analysis demonstrated that the RsERF40 gene is an important regulator of the cold stress response and root growth regulation. The cold tolerance of transgenic Arabidopsis plants overexpressing the RsERF40 gene was significantly improved. Overexpressing RsERF40 in the cold-sensitive radish genotype and silencing RsERF40 in the cold-tolerant radish genotype indicated that RsERF40 was beneficial for alleviating oxidative damage under cold stress in radish. Transgenic Arabidopsis seedlings showed an increase in the elongation and radial growth of dark-grown roots. RT-qPCR analysis showed that the expression of the cold-related genes (CORs) RsCOR78 and RsCOR413PM1 and the cell wall strengthening-related genes RsCESA6 and RsEXPB3 was upregulated in transgenic Arabidopsis seedlings. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays (DLA) revealed that RsERF40 directly regulates RsCOR78, RsCOR413PM1, RsCESA6 and RsEXPB3 expression, illustrating that RsERF40 enhances cold tolerance and taproot growth by modulating osmotic adjustment and cell wall mechanical strength in radish. In this study, the RsERF40-regulon was firstly found to be a new cold response pathway independent of the CBF-COR pathway conferring cold stress tolerance with increasing radish taproot growth. These results provided novel insight into the molecular mechanism underlying cold stress response and would facilitate the genetic improvement of cold tolerance in radish and other root vegetable crops.

Functions of Melatonin during Postharvest of Horticultural Crops

Melatonin, a tryptophan-derived molecule, is endogenously generated in animal, plant, fungal and prokaryotic cells. Given its antioxidant properties, it is involved in a myriad of signaling functions associated with various aspects of plant growth and development. In higher plants, melatonin (Mel) interacts with plant regulators such as phytohormones, as well as reactive oxygen and nitrogen species including hydrogen peroxide (H2O2), nitric oxide (NO) and hydrogen sulfide (H2S). It shows great potential as a biotechnological tool to alleviate biotic and abiotic stress, to delay senescence and to conserve the sensory and nutritional quality of postharvest horticultural products which are of considerable economic importance worldwide. This review provides a comprehensive overview of the biochemistry of Mel, whose endogenous induction and exogenous application can play an important biotechnological role in enhancing the marketability and hence earnings from postharvest horticultural crops.

Exogenous melatonin improved the growth and development of naked oat seedlings under cadmium stress

Heavy metal pollution has become a global problem, which affect more and more crop yields. Melatonin (MT) is widely used in plant stress resistance to alleviate the toxicity caused by heavy metals and other stresses. In this paper, the effects of exogenous 50 μM and 100 μM MT on the growth and development of naked oat seedlings under cadmium stress (25 mg L^-1) were studied. The results showed that different concentrations of MT could promote the growth of naked oat seedlings under 25-mg L^-1 cadmium stress. The application of exogenous melatonin could significantly increase the plant height, fresh weight, dry weight, chlorophyll, and proline contents of naked oats. MT could also reduce the contents of hydrogen peroxide, superoxide anion, and malondialdehyde in the cells of naked oat seedlings, and increase the activities of SOD, POD, and CAT. In addition, exogenous melatonin could affect the gene expression of LOX, POX, and Asmap1 in MAPK family and NAC and WRKY1 in TFS family in naked oat seedlings, thus promoting the growth and development of naked oat seedlings. In conclusion, this study is the first to demonstrate that MT is able to alleviate the negative effects to treat naked oat seedlings with cadmium stress. Therefore, melatonin has the potential to be applied in crops threatened by heavy metals.

DNA hypermethylation promotes the flowering of orchardgrass during vernalization

Vernalization, influenced by environmental factors, is an essential process associated with the productivity of temperate crops, during which epigenetic regulation of gene expression plays an important role. Although DNA methylation is one of the major epigenetic mechanisms associated with the control of gene expression, global changes in DNA methylation in the regulation of gene expression during vernalization-induced flowering of temperate plants remain largely undetermined. To characterize vernalization-associated DNA methylation dynamics, we performed whole-genome bisulfite-treated sequencing and transcriptome sequencing in orchardgrass (Dactylis glomerata) during vernalization. The results revealed that increased levels of genome DNA methylation during the early vernalization of orchardgrass were associated with transcriptional changes in DNA methyltransferase and demethylase genes. Upregulated expression of vernalization-related genes during early vernalization was attributable to an increase in mCHH in the promoter regions of these genes. Application of an exogenous DNA methylation accelerator or overexpression of orchardgrass NUCLEAR POLY(A) POLYMERASE (DgPAPS4) promoted earlier flowering, indicating that DNA hypermethylation plays an important role in vernalization-induced flowering. Collectively, our findings revealed that vernalization-induced hypermethylation is responsible for floral primordium initiation and development. These observations provide a theoretical foundation for further studies on the molecular mechanisms underlying the control of vernalization in temperate grasses.

DNA Methylation in Plant Responses and Adaption to Abiotic Stresses

Due to their sessile state, plants are inevitably affected by and respond to the external environment. So far, plants have developed multiple adaptation and regulation strategies to abiotic stresses. One such system is epigenetic regulation, among which DNA methylation is one of the earliest and most studied regulatory mechanisms, which can regulate genome functioning and induce plant resistance and adaption to abiotic stresses. In this review, we outline the most recent findings on plant DNA methylation responses to drought, high temperature, cold, salt, and heavy metal stresses. In addition, we discuss stress memory regulated by DNA methylation, both in a transient way and the long-term memory that could pass to next generations. To sum up, the present review furnishes an updated account of DNA methylation in plant responses and adaptations to abiotic stresses.

An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes

This study presents an improved genome of Raphanus sativus cv. WK10039 uncovering centromeres and differentially methylated regions of radish chromosomes. Comprehensive genome comparison of radish and diploid Brassica species of U's triangle reveals that R. sativus arose from the Brassica B genome lineage and is a sibling species of B. nigra. Radish (Raphanus sativus L.) is a key root vegetable crop closely related to the Brassica crop species of the family Brassicaceae. We reported a draft genome of R. sativus cv. WK10039 (Rs1.0), which had 54.6 Mb gaps. To study the radish genome and explore previously unknown regions, we generated an improved genome assembly (Rs2.0) by long-read sequencing and high-resolution genome-wide mapping of chromatin interactions. Rs2.0 was 434.9 Mb in size with 0.27 Mb gaps, and the N50 scaffold length was 37.3 Mb (40-fold larger assembly compared to Rs1.0). Approximately 38% of Rs2.0 was comprised of repetitive sequences, and 52,768 protein-coding genes and 4845 non-protein-coding genes were predicted and annotated. The improved contiguity and coverage of Rs2.0, along with the detection of highly methylated regions, enabled localization of centromeres where R. sativus-specific centromere-associated repeats, full-length OTA and CRM LTR-Gypsy retrotransposons, hAT-Ac, CMC-EnSpm and Helitron DNA transposons, and sequences highly homologous to B. nigra centromere-specific CENH3-associated CL sequences were enriched. Whole-genome bisulfite sequencing combined with mRNA sequencing identified differential epigenetic marks in the radish genome related to tissue development. Synteny comparison and genomic distance analysis of radish and three diploid Brassica species of U's triangle suggested that the radish genome arose from the Brassica B genome lineage through unique rearrangement of the triplicated ancestral Brassica genome after splitting of the Brassica A/C and B genomes.

Melatonin-Mediated Abiotic Stress Tolerance in Plants

Melatonin is a multi-functional molecule that is ubiquitous in all living organisms. Melatonin performs essential roles in plant stress tolerance; its application can reduce the harmful effects of abiotic stresses. Plant melatonin biosynthesis, which usually occurs within chloroplasts, and its related metabolic pathways have been extensively characterized. Melatonin regulates plant stress responses by directly inhibiting the accumulation of reactive oxygen and nitrogen species, and by indirectly affecting stress response pathways. In this review, we summarize recent research concerning melatonin biosynthesis, metabolism, and antioxidation; we focus on melatonin-mediated tolerance to abiotic stresses including drought, waterlogging, salt, heat, cold, heavy metal toxicity, light and others. We also examine exogenous melatonin treatment in plants under abiotic stress. Finally, we discuss future perspectives in melatonin research and its applications in plants.

DNA methylation and histone modifications induced by abiotic stressors in plants

BACKGROUND

A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants.

DISCUSSION

Plant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications.

CONCLUSIONS

Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.

The Role of Membrane Transporters in Plant Growth and Development, and Abiotic Stress Tolerance

The proteins of membrane transporters (MTs) are embedded within membrane-bounded organelles and are the prime targets for improvements in the efficiency of water and nutrient transportation. Their function is to maintain cellular homeostasis by controlling ionic movements across cellular channels from roots to upper plant parts, xylem loading and remobilization of sugar molecules from photosynthesis tissues in the leaf (source) to roots, stem and seeds (sink) via phloem loading. The plant's entire source-to-sink relationship is regulated by multiple transporting proteins in a highly sophisticated manner and driven based on different stages of plant growth and development (PG&D) and environmental changes. The MTs play a pivotal role in PG&D in terms of increased plant height, branches/tiller numbers, enhanced numbers, length and filled panicles per plant, seed yield and grain quality. Dynamic climatic changes disturbed ionic balance (salt, drought and heavy metals) and sugar supply (cold and heat stress) in plants. Due to poor selectivity, some of the MTs also uptake toxic elements in roots negatively impact PG&D and are later on also exported to upper parts where they deteriorate grain quality. As an adaptive strategy, in response to salt and heavy metals, plants activate plasma membranes and vacuolar membrane-localized MTs that export toxic elements into vacuole and also translocate in the root's tips and shoot. However, in case of drought, cold and heat stresses, MTs increased water and sugar supplies to all organs. In this review, we mainly review recent literature from Arabidopsis, halophytes and major field crops such as rice, wheat, maize and oilseed rape in order to argue the global role of MTs in PG&D, and abiotic stress tolerance. We also discussed gene expression level changes and genomic variations within a species as well as within a family in response to developmental and environmental cues.

Melatonin in Plant Defense against Abiotic Stress

Abiotic stress adversely affects plant growth and metabolism and as such reduces plant productivity. Recognized as a major contributor in the production of reactive oxygen species (ROS), it hinders the growth of plants through induction of oxidative stress. Biostimulants such as melatonin have a multifunctional role, acting as a defense strategy in minimizing the effects of oxidative stress. Melatonin plays important role in plant processes ranging from seed germination to senescence, besides performing the function of a biostimulant in improving the plant’s productivity. In addition to its important role in the signaling cascade, melatonin acts as an antioxidant that helps in scavenging ROS, generated as part of different stresses among plants. The current study was undertaken to elaborate the synthesis and regulation of melatonin in plants, besides emphasizing its function under various abiotic stress namely, salt, temperature, herbicides, heavy metals, and drought. Additionally, a special consideration was put on the crosstalk of melatonin with phytohormones to overcome plant abiotic stress.