Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae)

The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress. We analysed leaf cytosine methylation changes in adult plants of the annual Mediterranean herb, Erodium cicutarium, in a greenhouse, after seed demethylation with 5-Azacytidine and/or recurrent water stress. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2 × 2 factorial design, controlling for plant relatedness. In the long term, 5-Azacytidine treatment alone caused both hypo- and hyper-methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5-Azacytidine increased DNA methylation level by ca. 5%. Seed demethylation and recurrent drought produced a highly significant interaction in terms of global and context-specific cytosine methylation. Most methylation changes occurred around genic regions and within Transposable Elements. The annotation of these Differentially Methylated Regions associated with genes included several with a potential role in stress responses (e.g., PAL, CDKC, and ABCF), confirming an epigenetic contribution in response to stress at the molecular level.

Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms

Epigenetics research in evolutionary biology encompasses a variety of research areas, from regulation of gene expression to inheritance of environmentally mediated phenotypes. Such divergent research foci can occasionally render the umbrella term "epigenetics" ambiguous. Here I discuss several areas of contemporary epigenetics research in the context of evolutionary biology, aiming to provide balanced views across timescales and molecular mechanisms. The importance of epigenetics in development is now being assessed in many nonmodel species. These studies not only confirm the importance of epigenetic marks in developmental processes, but also highlight the significant diversity in epigenetic regulatory mechanisms across taxa. Further, these comparative epigenomic studies have begun to show promise toward enhancing our understanding of how regulatory programs evolve. A key property of epigenetic marks is that they can be inherited along mitotic cell lineages, and epigenetic differences that occur during early development can have lasting consequences on the organismal phenotypes. Thus, epigenetic marks may play roles in short-term (within an organism's lifetime or to the next generation) adaptation and phenotypic plasticity. However, the extent to which observed epigenetic variation occurs independently of genetic influences remains uncertain, due to the widespread impact of genetics on epigenetic variation and the limited availability of comprehensive (epi)genomic resources from most species. While epigenetic marks can be inherited independently of genetic sequences in some species, there is little evidence that such "transgenerational inheritance" is a general phenomenon. Rather, molecular mechanisms of epigenetic inheritance are highly variable between species.

Heat-stress memory enhances the acclimation of a migratory insect pest to global warming

In the face of rising global temperatures, the mechanisms behind an organism's ability to acclimate to heat stress remain enigmatic. The rice leaf folder, Cnaphalocrocis medinalis, traditionally viewed as temperature-sensitive, paradoxically exhibits robust larval acclimation to heat stress. This study used the heat-acclimated strain HA39, developed through multigenerational exposure to 39°C during the larval stage, and the unacclimated strain HA27 reared at 27°C to unravel the transgenerational effects of heat acclimation and its regulatory mechanisms. Heat acclimation for larvae incurred a fitness cost in pupae when exposed to high temperature, yet a significant transgenerational effect surfaced, revealing heightened fitness benefit in pupae from HA39, even without additional heat exposure during larval recovery at 27°C. This transgenerational effect exhibited a short-term memory, diminishing after two recovery generations. Moreover, the effect correlated with increased superoxide dismutase (SOD) enzyme activity and expression levels of oxidoreductase genes, representing physiological and molecular foundations of heat acclimation. Heat-acclimated larvae displayed elevated DNA methylation levels, while pupae from HA39, in recovery generations, exhibited decreased methylation indicated by the upregulation of a demethylase gene and downregulation of two methyltransferase genes at high temperatures. In summary, heat acclimation induces DNA methylation, orchestrating heat-stress memory and influencing the expression levels of oxidoreductase genes and SOD activity. Heat-stress memory enhances the acclimation of the migratory insect pest to global warming.

Epigenetic Modifications of Hormonal Signaling Pathways in Plant Drought Response and Tolerance for Sustainable Food Security

Drought significantly challenges global food security, necessitating a comprehensive understanding of plant molecular responses for effective mitigation strategies. Epigenetic modifications, such as DNA methylation and histone modifications, are key in regulating genes and hormones essential for drought response. While microRNAs (miRNAs) primarily regulate gene expression post-transcriptionally, they can also interact with epigenetic pathways as potential effectors that influence chromatin remodeling. Although the role of miRNAs in epigenetic memory is still being explored, understanding their contribution to drought response requires examining these indirect effects on epigenetic modifications. A key aspect of this exploration is epigenetic memory in drought-adapted plants, offering insights into the transgenerational inheritance of adaptive traits. Understanding the mechanisms that govern the maintenance and erasure of these epigenetic imprints provides nuanced insights into how plants balance stability and flexibility in their epigenomes. A major focus is on the dynamic interaction between hormonal pathways-such as those for abscisic acid (ABA), ethylene, jasmonates, and salicylic acid (SA)-and epigenetic mechanisms. This interplay is crucial for fine-tuning gene expression during drought stress, leading to physiological and morphological adaptations that enhance plant drought resilience. This review also highlights the transformative potential of advanced technologies, such as bisulfite sequencing and CRISPR-Cas9, in providing comprehensive insights into plant responses to water deficit conditions. These technologies pave the way for developing drought-tolerant crops, which is vital for sustainable agriculture.

DNA Methylation Dynamics in Response to Drought Stress in Crops

Drought is one of the most hazardous environmental factors due to its severe damage on plant growth, development and productivity. Plants have evolved complex regulatory networks and resistance strategies for adaptation to drought stress. As a conserved epigenetic regulation, DNA methylation dynamically alters gene expression and chromosome interactions in plants' response to abiotic stresses. The development of omics technologies on genomics, epigenomics and transcriptomics has led to a rapid increase in research on epigenetic variation in non-model crop species. In this review, we summarize the most recent findings on the roles of DNA methylation under drought stress in crops, including methylating and demethylating enzymes, the global methylation dynamics, the dual regulation of DNA methylation on gene expression, the RNA-dependent DNA methylation (RdDM) pathway, alternative splicing (AS) events and long non-coding RNAs (lnc RNAs). We also discuss drought-induced stress memory. These epigenomic findings provide valuable potential for developing strategies to improve crop drought tolerance.

The evolutionary consequences of interactions between the epigenome, the genome and the environment

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics

Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.

DNA methylation: an emerging paradigm of gene regulation under drought stress in plants

Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.

Correlation of genome methylation of fig tree accessions with natural nematode and rust incidence

Abstract Commercial fig tree cultivation in Brazil involves a single cultivar, ‘Roxo-de-Valinhos’. The use of a single cultivar results in serious diseases and related problems. The aim of this study was to characterize fig accessions by analyzing the natural root-knot nematode and leaf rust incidence in relation to the epigenomic profile of the plant, since epigenetic variations affect plant–pathogen interactions. All plants were attacked by nematodes, indicating susceptibility; Meloidogyne incognita was the root-knot nematode species involved. Joint analysis of data showed that methylation and leaf rust incidence were correlated when observed in the same phenological phase, presenting initial evidence of the same factorial pressure loads in genotypes, suggesting similar behavior within these genotypes.

Global methylation in 'Valencia' orange seedlings associated with rootstocks and Huanglongbing

Citrus farming is one of the main activities that contributed to the Brazilian trade balance, with citrus seedling being the most important input in the formation of orchards to guarantee high productivity and fruit quality, which fundamentally depends on the chosen genetics. The present study aimed to analyze the existence of epigenetic variability in 'Valencia' orange plants on rootstocks, associated or not with HLB, through the quantification of the global methylation of its genome, in order to support works on genetic improvement and crop production. For this purpose, this work was carried out in greenhouse in a completely randomized experimental design, with 5 treatments and 6 replicates per treatment, each seedling being considered a replicate, namely: T1 = "Valencia" orange grafted onto "Rangpur" lemon, inoculated with HLB; T2 = "Valencia" orange grafted onto "Swingle" citrumelo, inoculated with HLB; T3 = "Valencia" orange grafted onto "Rangpur" lemon, without HLB inoculation ; T4 = "Valencia" orange grafted onto "Swingle" citrumelo, without HLB inoculation ; T5 = "Valencia" orange in free standing. The DNA was extracted from leaves and the ELISA test (Enzyme-Linked Immunosorbent Assay) was carried out, based on the use of receptors sensitive to 5-mC., to measure the relative quantification of global methylation between genomic orange DNAs . Since the control treatment (T5) consists of "Valencia" orange in free standing, it could be inferred that both the normal grafting technique in the seedling formation process and the inoculation of buds infected with HLB are external factors capable of changing the methylation pattern in the evaluated plants, including the DNA demethylation process, causing an adaptive response in association with the expression of genes previously silenced by genome methylation.

Evolutionary roles of polyploidization-derived structural variations in the phenotypic diversification of Panax species

Genomic structural variations (SVs) are widespread in plant and animal genomes and play important roles in phenotypic novelty and species adaptation. Frequent whole genome duplications followed by (re)diploidizations have resulted in high diversity of genome architecture among extant species. In this study, we identified abundant genomic SVs in the Panax genus that are hypothesized to have occurred through during the repeated polyploidizations/(re)diploidizations. Our genome-wide comparisons demonstrated that although these polyploidization-derived SVs have evolved at distinct evolutionary stages, a large number of SV-intersecting genes showed enrichment in functionally important pathways related to secondary metabolites, photosynthesis and basic cellular activities. In line with these observations, our metabolic analyses of these Panax species revealed high diversity of primary and secondary metabolites both at the tissue and interspecific levels. In particular, genomic SVs identified at ginsenoside biosynthesis genes, including copy number variation and large fragment deletion, appear to have played important roles in the evolution and diversification of ginsenosides. A further herbivore deterrence experiment demonstrated that, as major triterpenoidal saponins found exclusively in Panax, ginsenosides provide protection against insect herbivores. Our study provides new insights on how polyploidization-derived SVs have contributed to phenotypic novelty and plant adaptation.

Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

DNA methylation is an important epigenetic marker, yet its diversity and consequences in tomato breeding at the population level are largely unknown. We performed whole-genome bisulfite sequencing (WGBS), RNA sequencing, and metabolic profiling on a population comprising wild tomatoes, landraces, and cultivars. A total of 8,375 differentially methylated regions (DMRs) were identified, with methylation levels progressively decreasing from domestication to improvement. We found that over 20% of DMRs overlapped with selective sweeps. Moreover, more than 80% of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms (SNPs), and DMRs had strong linkages with adjacent SNPs. We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs. We detected 971 and 711 large-effect loci via SNP and DMR markers, respectively. Combined with multi-omics, we identified 13 candidate genes and updated the polyphenol biosynthetic pathway. Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity. Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.

Intergenerational and transgenerational effects of drought stress on winter wheat (Triticum aestivum L.)

The environments where the progenitors are grown have the potential to affect the expression of traits in their offspring. Currently, there are various hypotheses regarding the evolutionary and ecological importance of stress memory effects. There is uncertainty regarding its occurrence, persistence, predictability, and adaptive value. In this study, 15 winter wheat cultivars were grown under drought and well-watered (control) treatments for two seasons to produce seeds with all possible combinations of drought exposure histories. A comprehensive analysis to estimate transgenerational (grandparental effects), intergenerational (parental effects), and their combined memory effects on offspring traits under both control and drought moisture treatments, was performed. There were significant memory effects in most of the evaluated traits ranging from +787% to -39.0% changes in both seed quality and plant traits. The expression of stress memory was highly dependent on the generation and number of exposures, traits, and seasons. Under drought treatment, the combination of grandparental and parental stress memories was additive in all traits, but their strengths were variable when considered separately. Stress memory enhanced the performance of offspring under similar stressful conditions: increased plant height, above-ground biomass, number of grains per plant, grain weight per plant and water potential. This study offers valuable new insights into the occurrence of drought stress memory, the complexities of the effects, possible physiological and metabolic alterations explaining the detected differences, and impacts toward a clearer understanding of their generation and context-dependency.

Developing Functional Relationships between Soil Moisture Content and Corn Early-Season Physiology, Growth, and Development

Drought is a severe threat to agriculture production that affects all growth stages of plants, including corn (Zea mays L.). Any factor affecting early seedling growth and development will significantly impact yield. Despite the recurrence of low rainfall during the growing seasons, corn responses to different early-season soil moisture content levels have not been investigated. In this study, we investigated how corn morpho-physiological and biomass traits responded to varied soil moisture content during the early vegetative stage. Two corn hybrids were grown in a pot-culture facility under five different soil moisture treatments (0.15, 0.12, 0.09, 0.06, and 0.03 m³ m^-3 volumetric water content, VWC) to assess the growth and developmental responses to varied soil moisture content during early-season growth (V2 to V7) stage. Sub-optimal soil moisture content limited plant growth and development by reducing physiological and phenotypic expression. Stomatal conductance and transpiration were decreased by an average of 65% and 59% across stress treatments relative to optimum conditions. On average, soil moisture deficit reduced the total leaf area by 71% and 72% compared to the control in 'A6659VT2RIB' and 'P1316YHR', respectively. Shoot and root dry weights were reduced by 74% and 43% under 0.03 m³ m^-3 VWC. An increase in the root-to-shoot ratio was noticed under low VWC conditions compared to the control. Based on the stress tolerance index, the physiology and leaf growth parameters were more sensitive to soil moisture deficit. Our results highlight the impact of sub-optimal soil moisture on physiology and morphological traits during early-season growth. 'P1316YHR' demonstrated better physiological performance under stress conditions, while 'A6659VT2RIB' produced relatively better root growth. The findings suggest that biomass partitioning between shoot and root components is dynamic and depends on stress intensity. The current findings can help to prioritize traits associated with the early-season drought tolerance in corn. The functional relationships developed between soil moisture content and growth and developmental responses can be integrated into corn crop modeling to allow better irrigation management decisions.

Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Drought adaptation of plants is closely related to resistance and tolerance to drought stress as well as the ability to recover after the elimination of the stress. Glycyrrhiza uralensis Fisch is a commonly applied herb whose growth and development are greatly affected by drought. Here, we provide the first comprehensive analysis of the transcriptomic, epigenetic, and metabolic responses of G. uralensis to drought stress and rewatering. The hyper-/hypomethylation of genes may lead to up-/downregulated gene expression, and epigenetic changes can be regarded as an important regulatory mechanism of G. uralensis under drought stress and rewatering. Moreover, integrated transcriptome and metabolome analysis revealed that genes and metabolites involved in pathways of antioxidation, osmoregulation, phenylpropanoid biosynthesis, and flavonoid biosynthesis may regulate the drought adaptation of G. uralensis. This work provides crucial insights into the drought adaptation of G. uralensis and offers epigenetic resources for cultivating G. uralensis with high drought adaptation.

A Genome-Wide Association Study to Identify Novel Candidate Genes Related to Low-Nitrogen Tolerance in Cucumber (Cucumis sativus L.)

Cucumber is one of the most important vegetables, and nitrogen is essential for the growth and fruit production of cucumbers. It is crucial to develop cultivars with nitrogen limitation tolerance or high nitrogen efficiency for green and efficient development in cucumber industry. To reveal the genetic basis of cucumber response to nitrogen starvation, a genome-wide association study (GWAS) was conducted on a collection of a genetically diverse population of cucumber (Cucumis sativus L.) comprising 88 inbred and DH accessions including the North China type, the Eurasian type, the Japanese and South China type mixed subtype, and the South China type subtype. Phenotypic evaluation of six traits under control (14 mM) and treatment (3.5 mM) N conditions depicted the presence of broad natural variation in the studied population. The GWAS results showed that there were significant differences in the population for nitrogen limitation treatment. Nine significant loci were identified corresponding to six LD blocks, three of which overlapped. Sixteen genes were selected by GO annotation associated with nitrogen. Five low-nitrogen stress tolerance genes were finally identified by gene haplotype analysis: CsaV3_3G003630 (CsNRPD1), CsaV3_3G002970 (CsNRT1.1), CsaV3_4G030260 (CsSnRK2.5), CsaV3_4G026940, and CsaV3_3G011820 (CsNPF5.2). Taken together, the experimental data and identification of candidate genes presented in this study offer valuable insights and serve as a useful reference for the genetic enhancement of nitrogen limitation tolerance in cucumbers.

Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.

Stress memory and its regulation in plants experiencing recurrent drought conditions

Developing stress-tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation is not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This ability could enable training of plants to face future challenges that increase in frequency and intensity. A better understanding of stress memory-associated mechanisms leading to alteration in gene expression and how they link to physiological, biochemical, metabolomic and morphological changes would initiate diverse opportunities to breed stress-tolerant genotypes through molecular breeding or biotechnological approaches. In this perspective, this review discusses different stress memory types and gives an overall view using general examples. Further, focusing on drought stress, we demonstrate coordinated changes in epigenetic and molecular gene expression control mechanisms, the associated transcription memory responses at the genome level and integrated biochemical and physiological responses at cellular level following recurrent drought stress exposures. Indeed, coordinated epigenetic and molecular alterations of expression of specific gene networks link to biochemical and physiological responses that facilitate acclimation and survival of an individual plant during repeated stress.

Impact of climate perturbations on seeds and seed quality for global agriculture

In agriculture, seeds are the most basic and vital input on which croplands productivity depends. These implies a good starting material, good production lines and good storage options. High-quality seed lots must be free of pests and pathogens and contain a required degree of genetic purity. Seeds need also to be stored in good condition between harvest and later sowing, to insure later on the field a good plant density and higher crop yield. In general, these parameters are already widely accepted and considered in many countries where advanced technologies evaluate them. However, the more and more frequently devastating climate changes observed around the world has put seed quality under threat, and current seeds may not be adapted to hazardous and unpredictable conditions. Climate-related factors such as temperature and water availability directly affect seed development and later germination. For these reasons, investigating seed quality in response to climate changes is a step to propose new crop varieties and practices that will bring solutions for our future.

Local diversity of drought resistance and resilience in Populus tomentosa correlates with the variation of DNA methylation

Little information is known about DNA methylation variation in shaping environment-specific drought resistance and resilience for tree adaptation. In this study, we leveraged RNA sequencing and whole-genome bisulfite sequencing data to dissect the distinction of epigenetic regulation under drought stress and rewater condition of Populus tomentosa accessions from three geographical regions. We demonstrated low resistance and high resilience for accessions from South. Non-CG methylation levels in promoter regions of Southern accessions were lower than accessions from higher latitudes and negatively regulated gene expression. CHH context methylation was more sensitive to drought stress, and the geographical-specific differentially methylated regions were scarcely changed by environmental fluctuation. We identified 60 conserved hub genes within the co-expression networks that correlate with photosynthetic and stomatal morphological traits. Epigenome-wide association studies and genome-wide association studies of these 60 hub genes revealed the interdependency between genetic and epigenetic variation in GATA9 and LECRK-VIII.2, which was associated with stomatal morphology and chlorophyll content. The natural epigenetic variation in GATA9 was also faithfully transmitted to progenies in two family-based F1 populations. This study indicates a functional relationship of DNA methylation diversity with drought resistance and resilience which offers new insights into plants' local adaptation to a stressful environment.

Deep inside the epigenetic memories of stressed plants

Recent evidence sheds light on the peculiar type of plant intelligence. Plants have developed complex molecular networks that allow them to remember, choose, and make decisions depending on the stress stimulus, although they lack a nervous system. Being sessile, plants can exploit these networks to optimize their resources cost-effectively and maximize their fitness in response to multiple environmental stresses. Even more interesting is the capability to transmit this experience to the next generation(s) through epigenetic modifications that add to the classical genetic inheritance. In this opinion article, we present concepts and perspectives regarding the capabilities of plants to sense, perceive, remember, re-elaborate, respond, and to some extent transmit to their progeny information to adapt more efficiently to climate change.

DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures

Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may therefore be more conducive to long-term inheritance of epigenetic marks. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we hypothesize that long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulphite sequencing approach (epiGBS), we show that temperature stress induces DNA hypermethylation at many CG and CHG cytosine contexts but not CHH. Additionally, differential methylation in CHG context that was observed was still detected in a subset of cytosines, even after 3-12 generations of culturing in a common environment. This demonstrates a memory effect of stress reflected in the methylome and that persists over multiple clonal generations. Structural annotation revealed that this memory effect in CHG methylation was enriched in transposable elements. The observed epigenetic stress memory is probably caused by stable transgenerational persistence of temperature-induced DNA methylation variants across clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants.

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.

Active DNA demethylation in plants: 20 years of discovery and beyond

Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.

Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants

Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.

Will epigenetics be a key player in crop breeding?

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.

Nutrient Inputs Alleviate Negative Effects of Early and Subsequent Flooding on Growth of Polygonum hydropiper With the Aid of Adventitious Roots

Riparian plants are exposed to harmful stress induced by flooding, which is often accompanied by eutrophication in the Three Gorges Reservoir Region. The phenomenon is mainly caused by domestic sewage discharges, slow water flow, and agricultural fertilizer pollution. Simulating abiotic stress, such as flooding at the initial period, can act as a signal and induce positive responses of plants to subsequent severe stress. In addition, eutrophication supplies nutrients, provides a favorable environment in the early stages of plant, and facilitates good performance in later development. However, whether early flooding (with or without eutrophication) acts as positive cue or as stress on plants at different developmental stages remains unclear. To address this question, seeds of Polygonum hydropiper were collected from low and high elevations in the hydro-fluctuation belt of the Three Gorges Reservoir Region. Plants germinated from these seeds were subjected to shallower and shorter early flooding treatments with or without eutrophication. Subsequently, plants were subjected to deeper and longer flooding treatments with or without eutrophication. Early flooding and eutrophic flooding significantly induced generation of adventitious roots, suggesting morphological adaptation to flooding. Although early flooding and eutrophic flooding treatments did not increase plant biomass in subsequent treatments compared with control, stem length, length and width of the 1st fully expanded leaf, and biomass of plants in the early eutrophic treatment were higher than these of the early flooding treatment plants. These results suggest a negative lag-effect of early flooding, and also indicate that nutrient inputs can alleviate such effects. Similarly, subsequent eutrophic flooding also enhanced plant growth compared with subsequent flooding, showing significantly higher values of leaf traits and adventitious root number. Plants originated from low elevation had significantly higher functional leaf length and stem biomass compared with those from high elevation. These results suggest that nutrient inputs can alleviate negative effects of early and subsequent flooding on growth of P. hydropiper with the generation of adventitious roots.

Transcriptome and DNA methylome provide insights into the molecular regulation of drought stress in sea buckthorn

Sea buckthorn is a typical drought-resistant tree species. However, there is a general lack of understanding of the pattern of DNA methylation linked with sea buckthorn responses to drought, and its relationship with drought tolerance mechanisms. In this study, we performed whole-transcriptome RNA sequencing and methylome sequencing in response to drought stress to explore differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs in sea buckthorn leaves. Based on predicted DE pairs, we constructed a competitive endogenous RNA network, which revealed potential transcriptional regulatory roles in response to drought stress. The results of methylome sequencing revealed that the DNA methylation level was increased in sea buckthorn leaves under drought stress. We identified 13,405 differentially methylated regions between CK and TR. We found one DMR-associated DEG (Vacuolar-sorting receptor 6) involved in the ABA accumulation pathway. In addition, two DNA methyltransferases (HrMET1 and HrDRM1) were closely associated with drought-induced hypermethylation in sea buckthorn. Together, we firstly conducted a comprehensive transcriptomic and epigenetic analysis of sea buckthorn under drought stress, providing a resource for further study of the potential functions of genes, miRNAs, lncRNAs, circRNAs and DNA methyltransferases.

Crosstalk of DNA Methylation Triggered by Pathogen in Poplars With Different Resistances

DNA methylation plays crucial roles in responses to environmental stimuli. Modification of DNA methylation during development and abiotic stress responses has been confirmed in increasing numbers of plants, mainly annual plants. However, the epigenetic regulation mechanism underlying the immune response to pathogens remains largely unknown in plants, especially trees. To investigate whether DNA methylation is involved in the response to infection process or is related to the resistance differences among poplars, we performed comprehensive whole-genome bisulfite sequencing of the infected stem of the susceptible type Populus × euramerican ‘74/76’ and resistant type Populus tomentosa ‘henan’ upon Lonsdalea populi infection. The results revealed that DNA methylation changed dynamically in poplars during the infection process with a remarkable decrease seen in the DNA methylation ratio. Intriguingly, the resistant P. tomentosa ‘henan’ had a much lower basal DNA methylation ratio than the susceptible P. × euramerican ‘74/76’. Compared to mock-inoculation, both poplar types underwent post-inoculation CHH hypomethylation; however, significant decreases in mC and mCHH proportions were found in resistant poplar. In addition, most differentially CHH-hypomethylated regions were distributed in repeat and promoter regions. Based on comparison of DNA methylation modification with the expression profiles of genes, DNA methylation occurred in resistance genes, pathogenesis-related genes, and phytohormone genes in poplars during pathogen infection. Additionally, transcript levels of genes encoding methylation-related enzymes changed during pathogen infection. Interestingly, small-regulator miRNAs were subject to DNA methylation in poplars experiencing pathogen infection. This investigation highlights the critical role of DNA methylation in the poplar immune response to pathogen infection and provides new insights into epigenetic regulation in perennial plants in response to biotic stress.

Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance

Plant response to drought stress includes systems for intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps entire plants acquire stress resistance. Plants sense water-deficit conditions both via the stomata of leaves and roots, and transfer water-deficit signals from roots to shoots via inter-organ signaling. Abscisic acid is an important phytohormone involved in the drought stress response and adaptation, and is synthesized mainly in vascular tissues and guard cells of leaves. In leaves, stress-induced abscisic acid is distributed to various tissues by transporters, which activates stomatal closure and expression of stress-related genes to acquire drought stress resistance. Moreover, the stepwise stress response at the whole-plant level is important for proper understanding of the physiological response to drought conditions. Drought stress is sensed by multiple types of sensors as molecular patterns of abiotic stress signals, which are transmitted via separate parallel signaling networks to induce downstream responses, including stomatal closure and synthesis of stress-related proteins and metabolites. Peptide molecules play important roles in the inter-organ signaling of dehydration from roots to shoots, as well as signaling of osmotic changes and reactive oxygen species/Ca²⁺ . In this review, we have summarized recent advances in research on complex plant drought stress responses, focusing on inter-tissue signaling in leaves and inter-organ signaling from roots to shoots. We have discussed the mechanisms via which drought stress adaptations and resistance are acquired at the whole-plant level, and have proposed the importance of quantitative phenotyping for measuring plant growth under drought conditions.

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.

Harnessing the power of multi-omics data for predicting climate change response

Predicting how species will respond to future climate change is of central importance in the midst of the global biodiversity crisis, and recent work has demonstrated the utility of population genomics for improving these predictions. Here, we suggest a broadening of the approach to include other types of genomic variants that play an important role in adaptation, like structural (e.g. copy number variants) and epigenetic variants (e.g. DNA methylation). These data could provide additional power for forecasting response, especially in weakly structured or panmictic species. Incorporating structural and epigenetic variation into estimates of climate change vulnerability, or maladaptation, may not only improve prediction power but also provide insight into the molecular mechanisms underpinning species' response to climate change.

Robotic Assay for Drought (RoAD): an automated phenotyping system for brassinosteroid and drought responses

Brassinosteroids (BRs) are a group of plant steroid hormones involved in regulating growth, development, and stress responses. Many components of the BR pathway have previously been identified and characterized. However, BR phenotyping experiments are typically performed in a low-throughput manner, such as on Petri plates. Additionally, the BR pathway affects drought responses, but drought experiments are time consuming and difficult to control. To mitigate these issues and increase throughput, we developed the Robotic Assay for Drought (RoAD) system to perform BR and drought response experiments in soil-grown Arabidopsis plants. RoAD is equipped with a robotic arm, a rover, a bench scale, a precisely controlled watering system, an RGB camera, and a laser profilometer. It performs daily weighing, watering, and imaging tasks and is capable of administering BR response assays by watering plants with Propiconazole (PCZ), a BR biosynthesis inhibitor. We developed image processing algorithms for both plant segmentation and phenotypic trait extraction to accurately measure traits including plant area, plant volume, leaf length, and leaf width. We then applied machine learning algorithms that utilize the extracted phenotypic parameters to identify image-derived traits that can distinguish control, drought-treated, and PCZ-treated plants. We carried out PCZ and drought experiments on a set of BR mutants and Arabidopsis accessions with altered BR responses. Finally, we extended the RoAD assays to perform BR response assays using PCZ in Zea mays (maize) plants. This study establishes an automated and non-invasive robotic imaging system as a tool to accurately measure morphological and growth-related traits of Arabidopsis and maize plants in 3D, providing insights into the BR-mediated control of plant growth and stress responses.

Epigenetics for Crop Improvement in Times of Global Change

Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles

In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.

Distinct cellular strategies determine sensitivity to mild drought of Arabidopsis natural accessions

The worldwide distribution of Arabidopsis (Arabidopsis thaliana) accessions imposes different types of evolutionary pressures, which contributes to various responses of these accessions to environmental stresses. Responses to drought stress have mostly been studied in the Columbia accession, which is predominantly used in plant research. However, the reactions to drought stress are complex and our understanding of the responses that contribute to maintaining plant growth during mild drought (MD) is very limited. Here, we studied the mechanisms with which natural accessions react to MD at a physiological and molecular level during early leaf development. We documented variations in MD responses among natural accessions and used transcriptome sequencing of a drought-sensitive accession, ICE163, and a drought-insensitive accession, Yeg-1, to gain insights into the mechanisms underlying this discrepancy. This revealed that ICE163 preferentially induces jasmonate- and anthocyanin-related pathways, which are beneficial in biotic stress defense, whereas Yeg-1 has a more pronounced activation of abscisic acid signaling, the classical abiotic stress response. Related physiological traits, including the content of proline, anthocyanins, and reactive oxygen species, stomatal closure, and cellular leaf parameters, were investigated and linked to the transcriptional responses. We can conclude that most of these processes constitute general drought response mechanisms that are regulated similarly in drought-insensitive and -sensitive accessions. However, the capacity to close stomata and maintain cell expansion under MD appeared to be major factors that allow to better sustain leaf growth under MD.

Seed 'primeomics': plants memorize their germination under stress

Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl₂ and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

Background

DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperature-sensitive genic male sterile (P/TGMS) lines play an important role in hybrid seed production of wheat. However, only a few studies have reported on the effect of DMT genes on temperature-sensitive male sterility of wheat. Although DMT genes have been investigated in some plant species, the identification and analysis of DMT genes in wheat (Triticum aestivum L.) based on genome-wide levels have not been reported.

Results

In this study, a detailed overview of phylogeny of 52 wheat DMT (TaDMT) genes was presented. Homoeolog retention for TaDMT genes was significantly above the average retention rate for whole-wheat genes, indicating the functional importance of many DMT homoeologs. We found that the strikingly high number of TaDMT genes resulted mainly from the significant expansion of the TaDRM subfamily. Intriguingly, all 5 paralogs belonged to the wheat DRM subfamily, and we speculated that tandem duplications might play a crucial role in the TaDRM subfamily expansion. Through the transcriptional analysis of TaDMT genes in a TGMS line BS366 and its hybrids with the other six fertile lines under sterile and fertile conditions, we concluded that TaCMT-D2, TaMET1-B1, and TaDRM-U6 might be involved in male sterility in BS366. Furthermore, a correlation analysis showed that TaMET1-B1 might negatively regulate the expression of TaRAFTIN1A, an important gene for pollen development, so we speculated regarding an epigenetic regulatory mechanism underlying the male sterility of BS366 via the interaction between TaMET1-B1 and TaRAFTIN1A.

Conclusions

Our findings presented a detailed phylogenic overview of the DMT genes and could provide novel insights into the effects of DMT genes on TGMS wheat.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07600-7.

The epiallelic potential of transposable elements and its evolutionary significance in plants

DNA provides the fundamental framework for heritability, yet heritable trait variation need not be completely ‘hard-wired’ into the DNA sequence. In plants, the epigenetic machinery that controls transposable element (TE) activity, and which includes DNA methylation, underpins most known cases of inherited trait variants that are independent of DNA sequence changes. Here, we review our current knowledge of the extent, mechanisms and potential adaptive contribution of epiallelic variation at TE-containing alleles in this group of species. For the purpose of this review, we focus mainly on DNA methylation, as it provides an easily quantifiable readout of such variation. The picture that emerges is complex. On the one hand, pronounced differences in DNA methylation at TE sequences can either occur spontaneously or be induced experimentally en masse across the genome through genetic means. Many of these epivariants are stably inherited over multiple sexual generations, thus leading to transgenerational epigenetic inheritance. Functional consequences can be significant, yet they are typically of limited magnitude and although the same epivariants can be found in nature, the factors involved in their generation in this setting remain to be determined. On the other hand, moderate DNA methylation variation at TE-containing alleles can be reproducibly induced by the environment, again usually with mild effects, and most of this variation tends to be lost across generations. Based on these considerations, we argue that TE-containing alleles, rather than their inherited epiallelic variants, are the main targets of natural selection. Thus, we propose that the adaptive contribution of TE-associated epivariation, whether stable or not, lies predominantly in its capacity to modulate TE mobilization in response to the environment, hence providing hard-wired opportunities for the flexible exploration of the phenotypic space.

This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

Ecological, (epi)genetic and physiological aspects of bet-hedging in angiosperms

KEY MESSAGE

Bet-hedging is a complex evolutionary strategy involving morphological, eco-physiological, (epi)genetic and population dynamics aspects. We review these aspects in flowering plants and propose further research needed for this topic. Bet-hedging is an evolutionary strategy that reduces the temporal variance in fitness at the expense of a lowered arithmetic mean fitness. It has evolved in organisms subjected to variable cues from the external environment, be they abiotic or biotic stresses such as irregular rainfall or predation. In flowering plants, bet-hedging is exhibited by hundreds of species and is mainly exerted by reproductive organs, in particular seeds but also embryos and fruits. The main example of bet-hedging in angiosperms is diaspore heteromorphism in which the same individual produces different seed/fruit morphs in terms of morphology, dormancy, eco-physiology and/or tolerance to biotic and abiotic stresses in order to 'hedge its bets' in unpredictable environments. The objective of this review is to provide a comprehensive overview of the ecological, genetic, epigenetic and physiological aspects involved in shaping bet-hedging strategies, and how these can affect population dynamics. We identify several open research questions about bet-hedging strategies in plants: 1) understanding ecological trade-offs among different traits; 2) producing more comprehensive phylogenetic analyses to understand the diffusion and evolutionary implications of this strategy; 3) clarifying epigenetic mechanisms related to bet-hedging and plant responses to environmental cues; and 4) applying multi-omics approaches to study bet-hedging at different levels of detail. Clarifying those aspects of bet-hedging will deepen our understanding of this fascinating evolutionary strategy.

Small DNA Methylation, Big Player in Plant Abiotic Stress Responses and Memory

DNA methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability and regulating gene expression. As sessile organisms, plants have evolved sophisticated regulatory systems to endure or respond to diverse adverse abiotic environmental challenges, i.e., abiotic stresses, such as extreme temperatures (cold and heat), drought and salinity. Plant stress responses are often accompanied by changes in chromatin modifications at diverse responsive loci, such as 5-methylcytosine (5mC) and N 6-methyladenine (6mA) DNA methylation. Some abiotic stress responses are memorized for several hours or days through mitotic cell divisions and quickly reset to baseline levels after normal conditions are restored, which is referred to as somatic memory. In some cases, stress-induced chromatin marks are meiotically heritable and can impart the memory of stress exposure from parent plants to at least the next stress-free offspring generation through the mechanisms of transgenerational epigenetic inheritance, which may offer the descendants the potential to be adaptive for better fitness. In this review, we briefly summarize recent achievements regarding the establishment, maintenance and reset of DNA methylation, and highlight the diverse roles of DNA methylation in plant responses to abiotic stresses. Further, we discuss the potential role of DNA methylation in abiotic stress-induced somatic memory and transgenerational inheritance. Future research directions are proposed to develop stress-tolerant engineered crops to reduce the negative effects of abiotic stresses.

Leaf Soluble Sugars and Free Amino Acids as Important Components of Abscisic Acid-Mediated Drought Response in Tomato

Water deficit has a global impact on plant growth and crop yield. Climate changes are going to increase the intensity, duration and frequency of severe droughts, particularly in southern and south-eastern Europe, elevating the water scarcity issues. We aimed to assess the contribution of endogenous abscisic acid (ABA) in the protective mechanisms against water deficit, including stomatal conductance, relative water potential and the accumulation of osmoprotectants, as well as on growth parameters. To achieve that, we used a suitable model system, ABA-deficient tomato mutant, flacca and its parental line. Flacca mutant exhibited constitutively higher levels of soluble sugars (e.g., galactose, arabinose, sorbitol) and free amino acids (AAs) compared with the wild type (WT). Water deficit provoked the strong accumulation of proline in both genotypes, and total soluble sugars only in flacca. Upon re-watering, these osmolytes returned to the initial levels in both genotypes. Our results indicate that flacca compensated higher stomatal conductance with a higher constitutive level of free sugars and AAs. Additionally, we suggest that the accumulation of AAs, particularly proline and its precursors and specific branched-chain AAs in both, glucose and sucrose in flacca, and sorbitol in WT, could contribute to maintaining growth rate during water deficit and recovery in both tomato genotypes.

Genotypic variation in the persistence of transgenerational responses to seasonal cues

Phenotypes respond to environments experienced directly by an individual, via phenotypic plasticity, or to the environment experienced by ancestors, via transgenerational environmental effects. The adaptive value of environmental effects depends not only on the strength and direction of the induced response but also on how long the response persists within and across generations, and how stably it is expressed across environments that are encountered subsequently. Little is known about the genetic basis of those distinct components, or even whether they exhibit genetic variation. We tested for genetic differences in the inducibility, temporal persistence, and environmental stability of transgenerational environmental effects in Arabidopsis thaliana. Genetic variation existed in the inducibility of transgenerational effects on traits expressed across the life cycle. Surprisingly, the persistence of transgenerational effects into the third generation was uncorrelated with their induction in the second generation. Although environmental effects for some traits in some genotypes weakened over successive generations, others were stronger or even in the opposite direction in more distant generations. Therefore, transgenerational effects in more distant generations are not merely caused by the retention or dissipation of those expressed in prior generations, but they may be genetically independent traits with the potential to evolve independently.