Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

Genome Biology and Evolution, Год журнала: 2024, Номер 16(2)

Опубликована: Фев. 1, 2024

Abstract There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that alter gene regulation and subsequently impact phenotypes. We first discuss origins variation nature, which may arise from genetic variation, spontaneous epimutations, drift, or capacitors. then review synthesize literature addressing three facets the aforementioned model: (i) causal effects on at level, (ii) divergence patterns natural populations distributed gradients, (iii) relationship between environmentally induced expression molecular level. focus DNA methylation, most extensively studied modification. find support for associated structure selection stable variants, inhibition enzymes frequently bears plasticity. However, there are pervasive confounding issues literature. Effects chromatin-modifying phenotype be independent marks, alternatively resulting functions protein interactions extrinsic epigenetics. Associations methylation strong plants mammals but notably absent invertebrates nonmammalian vertebrates. Given these challenges, we describe emerging approaches better investigate how affect regulation, plasticity, among populations.

Язык: Английский

---

DNA methylation dynamics during stress response in woodland strawberry (Fragaria vesca)

Horticulture Research, Год журнала: 2022, Номер 9

Опубликована: Янв. 1, 2022

Summary Environmental stresses can result in a wide range of physiological and molecular responses plants. These also impact epigenetic information genomes, especially at the level DNA methylation (5-methylcytosine). is hallmark heritable modification plays key role silencing transposable elements (TEs). Although an essential mechanism, fundamental aspects its contribution to stress adaptation remain obscure. We investigated epigenome dynamics wild strawberry (Fragaria vesca) response variable ecologically relevant environmental conditions level. F. vesca methylome responded with great plasticity abiotic hormonal stresses. Thermal resulted substantial genome-wide loss methylation. Notably, all tested marked hot spots differential near centromeric or pericentromeric regions, particularly non-symmetrical context. Additionally, we identified differentially methylated regions (DMRs) within promoter transcription factor (TF) superfamilies involved plant stress-response assessed effects these changes on gene expression. findings improve our understanding by highlighting correlation between methylation, TEs expression regulation plants subjected broad

Язык: Английский

---

Epigenomics in stress tolerance of plants under the climate change

Molecular Biology Reports, Год журнала: 2023, Номер 50(7), С. 6201 - 6216

Опубликована: Июнь 9, 2023

Язык: Английский

---

Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca)

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Май 16, 2024

Abstract Background In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted assess the heritability of heat stress-induced and transcriptomic changes following woodland strawberry ( Fragaria vesca ) reproduction. Strawberry is an ideal model study inheritance because it presents two modes reproduction: sexual (self-pollinated plants) asexual (clonally propagated plants named daughter plants). Taking advantage this model, investigated whether DNA methylation can transmitted via Results Our genome-wide provides evidence for acquisition maintenance in F. . We that specific marks or epimutations are stably over at least three generations. Some were associated with transcriptional after stress. Conclusion findings show methylome transcriptome respond a high level flexibility Notably, independent acquired same those inherited by their progenies. Overall, progenies retain some information genome past stresses encountered progenitors. This molecular memory, also documented level, might involved functional plasticity adaptation. Finally, these may contribute novel breeding approaches climate-ready plants.

Язык: Английский

---

Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions

Frontiers in Cell and Developmental Biology, Год журнала: 2022, Номер 10

Опубликована: Окт. 18, 2022

Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity natural populations. Studies show that environmental changes induce switches either independently or complementation with the genetic variation. Although most induced gets reset between generations and is short-lived, some variation becomes transgenerational results heritable traits. The short-term responses provide first tier transient required for local adaptations while stress memory help plants respond better recurring long-term stresses. These variations translate into an additional diversity which stable epialleles. In recent years, studies have been conducted on populations related various biological processes, ecological factors, communities, habitats. With advent advanced NGS-based technologies, targeting diverse environments manifold enhance stimuli facilitating fitness. Taking all points together a frame, present review compilation present-day knowledge role its fitness benefits systems

Язык: Английский

---

Study of the distribution of Glycyrrhiza uralensis production areas as well as the factors affecting yield and quality

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Март 29, 2023

Abstract Wild licorice in China is mainly distributed northern China, such as Gansu, Ningxia, and Inner Mongolia Provinces. The origin of wild has varied among historical periods. cultivated planted the same 59.26% licorice. distribution was shifted to northwest relative that yield quality vary greatly from different origins, showing a certain pattern variation west east. batch seedlings at 8 sites overlapping main production areas China. Baicheng experimental plot were low. Jingtai Altay plots high, but poor. Chifeng Yuzhong Principal component analysis environmental soil factors generated five characteristic roots with cumulative contribution rate 80%, three which related referred charge factor, water nutrient load coefficients factor largest. Soil conditions, especially nutrients, might have substantial effect on observed changes area. Generally, regulation nutrients merits special attention when selecting for cultivation This study can provide reference selection research high-quality techniques.

Язык: Английский

---

DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca)

New Phytologist, Год журнала: 2023, Номер 241(4), С. 1621 - 1635

Опубликована: Дек. 7, 2023

Due to the accelerating climate change, it is crucial understand how plants adapt rapid environmental changes. Such adaptation may be mediated by epigenetic mechanisms like DNA methylation, which could heritably alter phenotypes without changing sequence, especially across clonal generations. However, we are still missing robust evidence of adaptive potential methylation in wild populations. Here, studied genetic, and transcriptomic variation Fragaria vesca, a predominantly clonally reproducing herb. We examined samples from 21 natural populations three climatically distinct geographic regions, as well clones same individuals grown common garden. found that was partly associated with origin, particularly non-CG contexts. Importantly, large proportion this heritable Additionally, subset these changes affected expression genes mainly involved plant growth responses pathogen abiotic stress. These findings highlight influence on phenotypic traits. Our indicate can environmentally inducible heritable, enable adjust their conditions even absence genetic adaptation.

Язык: Английский

---

Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes

Horticulture Research, Год журнала: 2023, Номер 11(1)

Опубликована: Ноя. 27, 2023

Abstract The genetic and epigenetic mechanisms underlying the coexistence coordination of four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free genome for strawberry, which allowed us to uncover sequence, structure, divergences among subgenomes. diploid progenitors apart from subgenome A vesca), been subject public controversy. Phylogenomic analyses revealed close relationship between species Fragaria iinumae B, C, D. Subgenome A, closely related F. vesca, retains highest number genes, exhibits lowest content transposable elements (TEs), experiences strongest purifying selection, shows DNA methylation levels, displays expression level compared other three Transcriptome methylome that A-biased genes were enriched fruit development biological processes. contrast, although D contain equivalent amounts repetitive sequences, they exhibit particularly TEs located near genes. Taken together, our findings provide valuable insights into evolutionary patterns divergence dynamics strawberries, could be utilized strawberry genetics breeding research.

Язык: Английский

---

High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(4)

Опубликована: Март 22, 2023

Abstract Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, link between and DNAme has been scarcely examined natural populations, despite its potential shed light on evolutionary forces acting state. Here, we analyzed reduced-representation bisulfite sequencing whole-genome pool-seq data from marine freshwater stickleback populations examine relationship variation (between- within-population) nucleotide context adaptation. We find that sites differentially methylated have higher underlying standing variation, with among gained than those lost it. Strikingly, although generally lower population expected a bottleneck, this not case for methylation, which instead elevated compared marine. Subsequently, show ancestrally variable also positively correlates sensitivity environmentally induced change. The results suggest selection control state becomes relaxed, so too does against mutations at themselves. Increased epigenetic variance therefore likely precede diversification.

Язык: Английский

---

Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms—An Insightful Perspective on Ecoepigenetics

Epigenomes, Год журнала: 2022, Номер 7(1), С. 1 - 1

Опубликована: Дек. 26, 2022

Organisms adapt to different environments by selection of the most suitable phenotypes from standing genetic variation or phenotypic plasticity, ability single genotypes produce in environments. Because near identity, asexually reproducing populations are particularly for investigation potential and molecular underpinning latter alternative depth. Recent analyses on whole-genome scale differently adapted clonal animals plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications non-coding RNAs among pathways supporting plasticity is used stably Case studies revealed habitat-specific fingerprints were maintained over subsequent years pointing at existence ecotypes. Environmentally induced epimutations corresponding gene expression changes provide an ideal means fast directional adaptation changing new conditions, because they can synchronously alter many population members. microorganisms inclusive human pathogens also exploit epigenetically mediated environmental adaptation, this phenomenon considered a universal biological principle. The production same sequence response cues provides mechanistic explanation “general-purpose genotype hypothesis” “genetic paradox invasions”.

Язык: Английский

---