Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens

Three-year study of DNA cytosine methylation dynamics in transplanted Malbec grapevines

DNA cytosine methylation, an epigenetic mechanism involved in gene regulation and genome stability, remains poorly understood in terms of its role under changing environmental conditions. Previous research using methylation-sensitive amplified polymorphism (MSAP) markers in a Vitis vinifera L. cv. Malbec clone showed vineyard-specific DNA methylation polymorphism, but no change in overall methylation levels. To complement these findings, the present study investigates the intra-seasonal epigenetic dynamics between genetically identical plants grown in different vineyards through a transplanting experiment. Cuttings of the same clone, showing differential methylation patterns imposed by the vineyard of origin (Agrelo and Gualtallary), were cultivated in a common vineyard (Lunlunta). Using high-performance liquid chromatography-ultraviolet detection, the quantification of global DNA 5-methylcytosine (5-mC) levels revealed relatively low overall 5-mC percentages in grapevines, with higher levels in Agrelo (5.8%) compared to Gualtallary plants (3.7%). The transplanted plants maintained the 5-mC levels differences between vineyards (9.8% vs 6.2%), which equalized in subsequent seasons (7.5% vs 7%). Additionally, the study examined 5-mC polymorphism using MSAP markers in Lunlunta transplanted plants over three seasons. The observed differences between vineyards in MSAP patterns during the initial growing season gradually diminished, suggesting a reprogramming of the hemimethylated pattern following implantation in the common vineyard. In contrast, the non-methylated pattern exhibited greater stability, indicating a potential memory effect. Overall, this study provides valuable insights into the dynamic nature of DNA methylation in grapevines under changing environmental conditions, with potential implications for crop management and breeding strategies.

Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study

Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.

Transgenerational effects of intertidal environment on physiological phenotypes and DNA methylation in Pacific oysters

Climate change and intensifying human activity are posing serious threats to marine organisms. The fluctuating intertidal zone forms a miniature ecosystem of a rapidly changing environment for studying biological adaptation. Transgenerational plasticity (TGP), an evolutionary phenomenon in which parental experience influences offspring phenotypes, provides an avenue for adaptation, but the molecular mechanism was poorly understood in marine molluscs. In this study, wild Pacific oysters (Crassostrea gigas), which were collected from intertidal zones, were used to conduct two-generation breeding in a subtidal area combined with a heat shock experiment in the laboratory to investigate the intertidal environment-induced TGP under temperate subtidal condition and thermally exposed condition, respectively. We showed that TGP could influence the physiological phenotypes related to the status of oxidation and energy in non-stress-exposed subtidal offspring for at least two generations. Genomic DNA methylation exhibited heritable divergence between intertidal and subtidal oysters, and 1655 (or 42.83 %) differentially methylated genes (DMGs) in F₀ were continuously reserved to F₂, which may mediate physiological TGP by participating in biological processes including macromolecule metabolism, cellular responses to stress, and the positive regulation of molecular function, especially fatty acid metabolism. The intertidal experience also influenced the thermal plasticity of physiological phenotypes within and across generations. Totally, 320 (or 14.74 %) specific thermal response DMGs in the intertidal F₀ generation were identified in F₁ and F₂, participating in pathways including carbohydrate, lipid, and energy metabolism, signal transduction, and the organismal immune system, which suggested transgenerational intertidal effect mediated by these genes could positively contribute to stress adaptation and had potential applications for aquaculture. This study demonstrates an epigenetic mechanism for TGP in stress adaptation in marine molluscs, and provides new avenues to improve the stress adaptation for marine resource conservation and aquaculture.

Activating stress memory: eustressors as potential tools for plant breeding

Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.

Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus)

DNA methylation is an epigenetic modification involved in phenotypic diversity, plant development, and environmental responses. However, the mechanisms of DNA methylation underpinning the adaption of lotus (Nelumbo nucifera) ecotypes to high and low latitudes remain unsolved, especially adaptive evolution of their storage organs. Tropical and temperate lotus ecotypes have thin and enlarged rhizomes which are adapted to low and high latitudes, respectively. Here, we investigated the DNA methylomes and transcriptomes of rhizomes of the temperate and tropical lotus to address this issue. Compared with that of the tropical lotus, the DNA of the temperate lotus was significantly more hypermethylated, indicating an increase in global DNA methylation in the lotus, with rhizome enlargement. Meanwhile, genes associated with differentially methylated regions in their promoters tended to be differentially expressed between the two ecotypes. Interestingly, the genes with their expression negatively correlated with methylation levels in their promoters and genomic regions displayed significantly higher transposon coverage, while the genes showing a significant positive correlation between expression and methylation showed lesser transposon coverage. Further, we identified that DNA methylation, especially in the promoter region, was significantly correlated with the expression of many starch-biosynthetic, gibberellin-, and brassinosteroid-signalling genes associated with rhizome differentiation. Overall, our study unveiled that distinct global and local methylation patterns between the two lotus ecotypes contribute to their expression differences and adaptive phenotypic divergence of their storage organs, highlighting the role of DNA methylation in shaping the ecotypic differentiation of lotus.

Vineyard environments influence Malbec grapevine phenotypic traits and DNA methylation patterns in a clone-dependent way

By studying three cv. Malbec clones cultivated in two vineyards with contrasting environmental conditions, we demonstrated that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent. Clonal selection and vegetative propagation determine low genetic variability in grapevine cultivars, although it is common to observe diverse phenotypes. Environmental signals may induce epigenetic changes altering gene expression and phenotype. The range of phenotypes that a genotype expresses in different environments is known as phenotypic plasticity. DNA methylation is the most studied epigenetic mechanism, but only few works evaluated this novel source of variability in grapevines. In the present study, we analyzed the effects on phenotypic traits and epigenome of three Vitis vinifera cv. Malbec clones cultivated in two contrasting vineyards of Mendoza, Argentina. Anonymous genome regions were analyzed using methylation-sensitive amplified polymorphism (MSAP) markers. Clone-dependent phenotypic and epigenetic variability between vineyards were found. The clone that presented the clearer MSAP differentiation between vineyards was selected and analyzed through reduced representation bisulfite sequencing. Twenty-nine differentially methylated regions between vineyards were identified and associated to genes and/or promoters. We discuss about a group of genes related to hormones homeostasis and sensing that could provide a hint of the epigenetic role in the determination of the different phenotypes observed between vineyards and conclude that DNA methylation has an important role in the phenotypic plasticity and that epigenetic modulation is clone-dependent.