DNA methylation: The hidden mechanism enabling plants to adapt … – EurekAlert

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Experimental setup and phenotypic responses under common garden-conditions in Fragaria vesca plants after propagation at different temperatures for up to three asexual generations.

Credit: Horticulture Research

As global warming continues to redefine ecosystems, plants are increasingly tasked with swift adaptation to ensure their survival. One primary mechanism facilitating such rapid adaptation is epigenetic memory, specifically DNA methylation. DNA methylation, a form of epigenetic modification, involves the addition of a methyl group to the cytosine bases of the DNA, altering its accessibility in chromatin and modulating gene expression. In the context of a warming climate, changes in DNA methylation can be triggered by environmental factors like increased temperature. Such epigenetic adaptations play an instrumental role in allowing plants to synchronize their growth with evolving environmental cues. However, a comprehensive understanding of how these DNA methylation changes affect plant phenotypes, especially in response to warmer temperatures, remains unclear.

In July 2023, Horticulture Researchpublished a research paper entitled by Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vescaecotypes.

To examine the influence of temperature on phenotypic and epigenetic variations, an experiment was conducted across three asexual generations on four European F. vescaecotypes (ES12, ICE2, NOR2, IT4), exposing them to 18 and 28. At the phenotypic level, the ES12ecotype had an increased stolon production at 28 during the first asexual generation (AS1) but not by the third (AS3). Conversely, the IT4ecotype displayed decreased stolon production at 28 in both AS1and AS3. The ICE2and NOR2ecotypes showed significant delays in flowering time at 28 by AS3, with statistical significance at 0.05 > p > 0.001. For petiole length, plants from the ES12, ICE2, and NOR2ecotypes had longer lengths when grown at 28 during AS1. By AS3, the increased petiole length remained only for the NOR2ecotype.The results showed a statistically significant difference between theall phenotypic traits investigated and growth temperature in the experiment, which can be preserved during asexual reproduction. Further in-depth studies at the molecular level, bisulfite-sequencing of the genomic DNA samples from the ecotypes revealed discernible differences in DNA methylation patterns between the two temperature conditions, especially in the CHG and CHH contexts. NOR2exhibited the most pronounced difference in methylation levels between the temperature conditions. Principal Component Analysis (PCA) of methylation profiles showed clear differences between ecotypes grown at 18 and 28. Significant changes in both hypo- and hypermethylation occurred across all ecotypes with the largest temperature-specific methylation increases observed for the CHH context.Notably, methylation changes were identified to be correlated with genomic features such as transcription start sites (TSS) and transcription termination sites (TTS). Regions with differential CHG and CHH methylation typically exhibited hypermethylation.At the same time, transcriptome changes related to temperature increase were observed in approximately 3,500 to 5,000 differentially expressed genes (DEGs) in different ecotypes. In addition, this study also explored the ecotype specific methylation and expression patterns of genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. It was found that among three or fewer ecotypes, the absolute multiple change of 1,318 related differentially expressed and differentially methylated genes (DEDMGs) was>1.5.

In summary, the research indicates that temperature variations during asexual propagation induce considerable hereditary epigenetic and phenotypic modifications, underscoring the existence of a temperature-related epigenetic memory effect in F. vescaecotypes. This groundbreaking study not only deepens our understanding of plant adaptation but also opens the door for leveraging epigenetic memory to develop crops better suited to the warming world.

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References

Authors

YuPeng Zhang()1,2, Guangxun Fan3, Tuomas Toivainen3, Torstein Tengs2, Igor Yakovlev2, Paal Krokene2, Timo Hytnen3, Carl Gunnar Fossdal2,*, Paul E. Grini1,*

Affiliations

1. EVOGENE, Department of Biosciences, University of Oslo, 0313 Oslo, Norway

2. Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 s, Norway

3. Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland

AboutCarl Gunnar Fossdal & Paul E. Grini

Carl Gunnar Fossdal: He is currently head of Department Dept. Forest Health, Division for Biotechnology and Plant Health, NIBIO, Norway. His research areas are epigenetics, genomics, plant-pathogen interactions, phytobiome, forest health, wood decay, and fungal enzymes.

Paul E. Grini: He is a professor at the Department of Biological Sciences, University of Oslo. His research focuses on the biology of plant reproductive development.

Horticulture Research

Experimental study

Not applicable

Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes

31-Jul-2023

The authors declare that they have no competing interests.

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