The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with transcript accumulation in sesame (original) (raw)
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In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants
Plants, 2021
Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their gro...
The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress
Plant Physiology, 2017
Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epialleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.
Bulgarian Journal of Agricultural Science, 2019
Vassileva, V., Vaseva, I. & Dimitrova, A. (2019). Expression profi ling of DNA methyltransferase genes in wheat genotypes with contrasting drought tolerance. Bulgarian Journal of Agricultural Science, 25(5), 845–851 DNA methylation is a reversible epigenetic mechanism that affects important developmental processes and stress-related events in living organisms. The process of cytosine methylation is catalysed by DNA methyltransferases that are structurally and functionally conserved in all eukaryotes. This study assessed the effect of drought stress and subsequent rewatering on the transcription of DNA methyltransferase coding genes (TaMET1, TaMET2a, TaMET2b and TaMET3) in wheat genotypes with contrasting drought tolerance. The applied drought stress led to changes in leaf water defi cit in a variety-specifi c manner. Two of the wheat genotypes, Farmer and Bojana, performed as sensitive to drought, the other two, Yoana and Guinness, were considered as drought tolerant. Under drought ...
Journal of Experimental Botany, 2011
An indica pyramiding line, DK151, and its recurrent parent, IR64, were evaluated under drought stress and nonstress conditions for three consecutive seasons. DK151 showed significantly improved tolerance to drought. The DNA methylation changes in DK151 and IR64 under drought stress and subsequent recovery were assessed using methylation-sensitive amplified polymorphism analysis. Our results indicate that drought-induced genome-wide DNA methylation changes accounted for ;12.1% of the total site-specific methylation differences in the rice genome. This drought-induced DNA methylation pattern showed three interesting properties. The most important one was its genotypic specificity reflected by large differences in the detected DNA methylation/demethylation sites between DK151 and IR64, which result from introgressed genomic fragments in DK151. Second, most droughtinduced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of the sites at which drought-induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought-induced DNA demethylation/methylation changes remain even after recovery. Third, the drought-induced DNA methylation alteration showed a significant level of developmental and tissue specificity. Together, these properties are expected to have contributed greatly to rice response and adaptation to drought stress. Thus, induced epigenetic changes in rice genome can be considered as a very important regulatory mechanism for rice plants to adapt to drought and possibly other environmental stresses.
DNA Methylation and Plants Response to Biotic and Abiotic Stress
Trends in Sciences
DNA methylation is a conserved epigenetic modification that regulates, stabilizes, and maintains genomic integrity. Loss of DNA methylation or aberrant patterns of DNA methylation causes abnormalities in the gene regulation of plants. DNA methylation in plants is regulated by the combined action of de novo methylation, maintenance of methylation, and demethylation. The enzymes that regulate DNA methylation in plants are different but have some homology to that of mammalian DNA methylation enzymes. DNA methylation helps to develop adaptation mechanisms towards various biotic and abiotic stresses. This paper provides a comprehensive review of the DNA methylation pathway and its role in biotic and abiotic stress tolerances in plants. HIGHLIGHTS Plants responds to the changing climatic condition via epigenetic changes - changing the gene expression patterns, without changing the DNA sequences Abiotic and biotic stress leads to the differential expression of genes; furthermore, plants ha...
bioRxiv (Cold Spring Harbor Laboratory), 2024
• Premise of the study. Mounting evidence supports the view that the responses of plants to environmental stress are mediated by epigenetic factors, including DNA methylation. Understanding the relationships between DNA methylation, plant development and individual fitness under contrasting environments is key to uncover the potential impact of epigenetic regulation on plant adaptation. Experimental approaches that combine a controlled alteration of epigenetic features with exposure to some relevant stress factor can contribute to this end. • Methods. We combined the experimental application of a demethylating agent (5azacytidine) with recurrent drought, and recorded their effects on above-and below-ground phenotypic traits related to early development, phenology and fitness in Erodium cicutarium from two provenances. • Key results. We found that 5-azacytidine significantly reduced DNA methylation in leaf and root tissues. Moreover, it slowed plant development, delayed flowering, and reduced the number of inflorescences produced, and such detrimental effects occurred independently of water regime. Recurrent drought reduced final above-and below-ground biomass and total inflorescence production, and such negative effects were unaffected by artificial changes in DNA methylation. Increased fruit and seed-set were the only adaptive responses to drought observed in E. cicutarium, together with an increased number of flowers per inflorescence recorded in water stressed plants previously treated with 5-azacytidine. • Conclusion. Epigenetic effects can desynchronize plant growth, flowering and senescence among individual plants in both favourable and adverse environments. Future studies should focus on understanding intraspecific variation in the ability to change plant methylome in response to stress. .
Drought is one of the most important abiotic stresses that impair sesame (Sesamum indicum L.) productivity mainly when it occurs at flowering stage. However up to now, very few studies have attempted to investigate the molecular responses of sesame to drought stress. In this experiment, two genotypes having contrasting responses to drought (tolerant and sensitive) were submitted to progressive drought followed by recovering stage at flowering stage. RNAs were isolated from roots of plants before drought stress, at 3-time points during progressive drought, after rewatering, and sequenced using Illumina HiSeq 4000 platform. These RNA-Seq resources (BioSample IDs: SAMN06130606 and SAMN06130607) provided an opportunity to elucidate the molecular responses of sesame to drought and find out some candidate genes for drought tolerance improvement.
Responsive changes of DNA methylation in wheat (Triticum aestivum) under water deficit
Scientific Reports, 2020
DnA methylation plays an important role in the growth and development of plant, and would change under different environments. In this study, 5-methyl cytosine (5mC) content and methylation level exhibited tissue specificity in genomic DNA of wheat seedling, and increased significantly in leaf along with the increase of water deficit, which was especially significant in leaf of wheat AK58. Fullmethylation might dominate in genomic DNA of wheat seedling, the increase of full-methylation level under water deficit was significantly higher than that of hemi-methylation level. Under water deficit, DNA methylation of wheat seedling showed significant polymorphism, this polymorphism was always higher in root, especially was higher in root of wheat AK58. Further analysis appeared that changes of DnA methylation in wheat seedling took methylation as principle and demethylation as supplement under water deficit. Therefore, under water deficit, the degree, level and polymorphism of DNA methylation in wheat seedling showed tissue specificity and species specificity, and were higher in wheat AK58 compared with those of wheat XM13, perhaps wheat AK58 could more rapidly respond to water deficit by changes of DNA methylation, which would contribute to reveal molecular mechanism of wheat adapting to water deficit. Growth and development of plant are often influenced by environment, yet some studies indicated that plant could rapidly respond to the change of environment by epigenetic modification 1. As one important mode of epigenetic modifications, DNA methylation could regulate gene expression by changing chromatin structure, DNA conformation, DNA stability, DNA-protein interaction and so on 2. In nuclear genome of plant, about 20-30% cytosines are methylated, and levels of DNA methylation are different in all kinds of tissues, organs or stages 3-5. If DNA methylation is insufficient or increases in plant, growth and phenotype of plant might be aberrant 6-8 , for example, Arabidopsis thaliana would exhibit dwarf plant, smaller leaf, clump growth or maturity decline because of the reduction of DNA methylation, and these aberrant traits may be inherited to filial generation 9. Manning et al. found that DNA hyper-methylation of Cnr point in Tomato would inhibit the maturation of fruit and cause appearance variation of fruit, such as colorless fruit, pericarp absence, etc 6. Furthermore, level and status of DNA methylation might change under stress conditions, such as salt 10-12 , drought 13-15 , low temperature 16 , heavy metal 17 , pathogen 18 , and so on 19. Water deficit could lead to hyper-methylation in Pea and methylation level of second C in CCGG sequence increases by 40% 20 , low temperature would cause methylation and demethylation at some points of CCGG sequence in Oryza sativa 21. Under salt stress, methylation level of cytosine in CCGG sequence would increase by 0.2-17.6% in Rape seed 22 , and methylation level in Manioc would increase significantly 23. Tang et al. also found that drought might cause methylation level decrease by 10% in Ryegrass 13. Therefore, methylation state of plant could be influenced by environment, and plant can respond to different environments by the change of DNA methylation. Wheat belongs to one of important crops in the world, the quality and yield of wheat are seriously influenced by drought, some studies also showed that DNA methylation of plant would change under drought stress 13-15 , yet the relationship between DNA methylation and drought-tolerant mechanism is unclear in wheat. In order to study the response of DNA methylation to water deficit, common wheat genotype XinMai 13 (XM13) and resistant wheat genotype AiKang 58 (AK58) were selected as experimental materials in this study, the change of DNA methylation in wheat seedling under water deficit was analyzed with High Performance Liquid Chromatography (HPLC) and Methylation Sensitive Amplification Polymorphism (MSAP), which would provide reference to
One important function of cytosine methylation in plant genomes is to provide protection against the activation of harmful , transposable, and repeated sequence elements. 2 Under certain stressful conditions, the maintenance of methylated sites can become weakened, allowing elements to become activated, leading to increased retrotransposition and newly created, environmental sensitivity. 3 DNA methylation is therefore not permanently fixed, but is dynamic and reversible with abiotic stress. Cytosine methylation is usually located away from the 5 prime of Arabidopsis thaliana gene coding regions to protect important endogenes from transcriptional silencing. 4 However, where methylation exists in promoter regions, presumably primarily to suppress the expression of harmful elements, the presence of this methylation can also act to silence expression of the endogenous gene. 5 Release, imposition, and spread of methylation under adverse environmental conditions around harmful elements can also influence proximal gene expression 6 as we recently reported for 2 gene loci in the stomatal development pathway (SPCH and FAMA) in plants grown under increased evaporative demand. 1 As methylation is heritable through cell divisions, this mechanism might provide a " memory " of adverse conditions that allows for altered gene expression patterns over time and so lead to the generation of more tolerant phenotypes. 7 In our plants, increased methylation in and around the SPCH and FAMA loci was associated with decreased expression of both target genes and a reduction in Stomatal Index (SI; stomata as a percentage of epidermal cells), although not in their stomatal density (stomata.mm −2). We hypothesized that these transcrip-tional and phenotypic changes, mediated by methylation, could increase the tolerance of our plants to more severe water stress. Epigenetic " priming " against biotic stress leads to enhanced resistance in the progeny compared with the parental generation 8 and the progeny of plants salt-stressed at 25 or 75 mM NaCl also show increased tolerance to 125–150 mM NaCl. 9 We found that constant exposure to high vpd protected A. thaliana 'Landsberg erecta' from the negative effect on leaf chlorophyll content of a 4-day periodic drought experienced 40 d post-germination (Fig. 1A) and also from the final drought-induced reduction in Epigenetic modification of the genome via cytosine methylation is a dynamic process that responds to changes in the growing environment. this modification can also be heritable. the combination of both properties means that there is the potential for the life experiences of the parental generation to modify the methylation profiles of their offspring and so potentially to " precondition " them to better accommodate abiotic conditions encountered by their parents. We recently identified high vapor pressure deficit (vpd)-induced Dna methylation at 2 gene loci in the stomatal development pathway and an associated reduction in leaf stomatal frequency. 1 here, we test whether this epigenetic modification pre-conditioned parents and their offspring to the more severe water stress of periodic drought. We found that 3 generations of high vpd-grown plants were better able to withstand periodic drought stress over 2 generations. this resistance was not directly associated with de novo methylation of the target stomata genes, but was associated with the cmt3 mutant's inability to maintain asymmetric sequence context methylation. if our finding applies widely, it could have significant implications for evolutionary biology and breeding for stressful environments.