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Changes in global DNA methylation under climatic stress in two related grasses suggest a possible role of epigenetics in the ecological success of polyploids

  • Kelly, A. E. & Goulden, M. L. Rapid shifts in plant distribution with recent climate change. Proc. Natl. Acad. Sci. U.S.A. 105, 11823–11826. https://doi.org/10.1073/pnas.0802891105 (2008).

    ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wiens, J. J. Climate-related local extinctions are already widespread among plant and animal species. PLoS Biol. 14, e2001104. https://doi.org/10.1371/journal.pbio.2001104 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Swinnen, J., Burkitbayeva, S., Schierhorn, F., Prishchepov, A. V. & Müller, D. Production potential in the “bread baskets” of Eastern Europe and Central Asia. Global Food Secur. 14, 38–53. https://doi.org/10.1016/j.gfs.2017.03.005 (2017).

    Article 

    Google Scholar 

  • Henry, R. J. Innovations in plant genetics adapting agriculture to climate change. Curr. Opin. Plant Biol. 56, 168–173. https://doi.org/10.1016/j.pbi.2019.11.004 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Stokes, C. & Howden, M. Adapting Agriculture to Climate Change: Preparing Australian Agriculture, Forestry and Fisheries for the Future (Csiro Publishing, 2010).

    Book 

    Google Scholar 

  • Bräutigam, K. et al. Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol. Evol. 3, 399–415. https://doi.org/10.1002/ece3.461 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yaish, M. W., Colasanti, J. & Rothstein, S. J. The role of epigenetic processes in controlling flowering time in plants exposed to stress. J. Exp. Bot. 62, 3727–3735. https://doi.org/10.1093/jxb/err177 (2011).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Yaish, M. W. DNA methylation-associated epigenetic changes in stress tolerance of plants. In Molecular Stress Physiology of Plants (eds Rout, G. R. & Das, A. B.) 427–440 (Springer India, 2013).

    Chapter 

    Google Scholar 

  • Suji, K. K. & Joel, A. J. An epigenetic change in rice cultivars underwater stress conditions. Electron. J. Plant Breed. 1, 1142–1143 (2010).

    Google Scholar 

  • Peng, H. & Zhang, J. Plant genomic DNA methylation in response to stresses: Potential applications and challenges in plant breeding. Prog. Nat. Sci. 19, 1037–1045. https://doi.org/10.1016/j.pnsc.2008.10.014 (2009).

    CAS 
    Article 

    Google Scholar 

  • Baduel, P. & Colot, V. The epiallelic potential of transposable elements and its evolutionary significance in plants. Philos. Trans. R. Soc. B 376, 20200123. https://doi.org/10.1098/rstb.2020.0123 (2021).

    CAS 
    Article 

    Google Scholar 

  • Labra, M. et al. Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol. 4, 694–699. https://doi.org/10.1055/s-2002-37398 (2002).

    CAS 
    Article 

    Google Scholar 

  • Wang, W.-S. et al. Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J. Exp. Bot. 62, 1951–1960. https://doi.org/10.1093/jxb/erq391 (2011).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Šmarda, P., Bureš, P., Horová, L., Foggi, B. & Rossi, G. Genome size and GC content evolution of Festuca: Ancestral expansion and subsequent reduction. Ann. Bot. 101, 421–433. https://doi.org/10.1093/aob/mcm307 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Tomczyk, P. P., Kiedrzyński, M., Jedrzejczyk, I., Rewers, M. & Wasowicz, P. The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: An example from fine-leaved Festuca species (Poaceae). PeerJ 8, e9227. https://doi.org/10.7717/peerj.9227 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Piękoś-Mirkowa, H. & Mirek, Z. Distribution patterns and habitats of endemic vascular plants in the Polish Carpathians. Acta Soc. Bot. Pol. 78, 321–326 (2009).

    Article 

    Google Scholar 

  • Kiedrzyński, M., Zielińska, K. M., Rewicz, A. & Kiedrzyńska, E. Habitat and spatial thinning improve the Maxent models performed with incomplete data. J. Geophys. Res. Biogeosci. 122(6), 1359–1370. https://doi.org/10.1002/2016JG003629 (2017).

    Article 

    Google Scholar 

  • Rewicz, A. et al. Morphometric traits in the fine-leaved fescues depend on ploidy level: The case of Festuca amethystina L. PeerJ 6, e5576. https://doi.org/10.7717/peerj.5576 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kiedrzyński, M. et al. Tetraploids expanded beyond the mountain niche of their diploid ancestors in the mixed-ploidy grass Festuca amethystina L. Sci. Rep. 11, 18735 (2021).

    ADS 
    Article 

    Google Scholar 

  • Mounger, J. et al. Epigenetics and the success of invasive plants. Philos. Trans. R. Soc. B 376, 20200117. https://doi.org/10.1098/rstb.2020.0117 (2021).

    CAS 
    Article 

    Google Scholar 

  • Bewick, A. J. & Schmitz, R. J. Epigenetics in the wild. Elife 4, e07808. https://doi.org/10.7554/eLife.07808 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sahu, P. P. et al. Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Rep. 32(8), 1151–1159. https://doi.org/10.1007/s00299-013-1462-x (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Alonso, C. et al. Interspecific variation across angiosperms in global DNA methylation: Phylogeny, ecology and plant features in tropical and Mediterranean communities. New Phytol. 224(2), 949–960. https://doi.org/10.1111/nph.16046 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Angers, B., Castonguay, E. & Massicotte, R. Environmentally induced phenotypes and DNA methylation: How to deal with unpredictable conditions until the next generation and after. Mol. Ecol. 19(7), 1283–1295. https://doi.org/10.1111/j.1365-294X.2010.04580.x (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Batog, J. & Wawro, A. Process of obtaining bioethanol from sorghum biomass using genome shuffling. Cellul. Chem. Technol. 53, 459–467 (2019).

    CAS 
    Article 

    Google Scholar 

  • Richards, C. L., Schrey, A. W. & Pigliucci, M. Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecol. Lett. 15, 1016–1025. https://doi.org/10.1111/j.1461-0248.2012.01824.x (2012).

    Article 
    PubMed 

    Google Scholar 

  • Li, N. et al. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. New Phytol. 223(2), 979–992. https://doi.org/10.1111/nph.15820 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Róis, A. S. et al. Epigenetic rather than genetic factors may explain phenotypic divergence between coastal populations of diploid and tetraploid Limonium spp. (Plumbaginaceae) in Portugal. BMC Plant Biol. 13(1), 205. https://doi.org/10.1186/1471-2229-13-205 (2013).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, A. et al. DNA methylation in genomes of several annual herbaceous and woody perennial plants of varying ploidy as detected by MSAP. Plant Mol. Biol. Rep. 29, 784–793. https://doi.org/10.1007/s11105-010-0280-3 (2011).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Sokolova, D. A., Vengzhen, G. S. & Kravets, A. P. An Analysis of the correlation between the changes in satellite DNA methylation patterns and plant cell responses to the stress. Cell Bio 2, 163–171. https://doi.org/10.4236/cellbio.2013.23018 (2013).

    CAS 
    Article 

    Google Scholar 

  • Johnson, L. I. & Tricker, P. J. Epigenomic plasticity within populations: Its evolutionary significance and potential. Heredity 105, 113–121. https://doi.org/10.1038/hdy.2010.25 (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zheng, X. et al. Transgenerational variations in DNA methylation induced by drought stress in two rice varieties with distinguished difference to drought resistance. PLoS One 8(11), e80253. https://doi.org/10.1371/journal.pone.0080253 (2013).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Karan, R., DeLeon, T., Biradar, H. & Subudhi, P. K. Salt Stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS One 7(6), e40203. https://doi.org/10.1371/journal.pone.0040203 (2012).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Richards, C. L. & Pigliucci, M. Epigenetic inheritance. A decade into the extended evolutionary synthesis. Paradigmi 38, 463–494. https://doi.org/10.30460/99624 (2020).

    Article 

    Google Scholar 

  • Chelaifa, H., Monnier, A. & Ainouche, M. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytol. 186(1), 161–174. https://doi.org/10.1111/j.1469-8137.2010.03179.x (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Al-Lawati, A., Al-Bahry, S., Victor, R., Al-Lawati, A. H. & Yaish, M. W. Salt stress alters DNA methylation levels in alfalfa (Medicago spp.). Genet. Mol. Res. 15, 15018299. https://doi.org/10.4238/gmr.15018299 (2016).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lewandowska-Gnatowska, E. et al. Is DNA methylation modulated by wounding-induced oxidative burst in maize?. Plant Physiol. Biochem. 82, 202–208. https://doi.org/10.1016/j.plaphy.2014.06.003 (2014).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Marfil, C. et al. Changes in grapevine DNA methylation and polyphenols content induced by solar ultraviolet-B radiation, water deficit and abscisic acid spray treatments. Plant Physiol. Biochem. 135, 287–294. https://doi.org/10.1016/j.plaphy.2018.12.021 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zedek, F. et al. Endopolyploidy is a common response to UV-B stress in natural plant populations, but its magnitude may be affected by chromosome type. Ann. Bot. 126(5), 883–889. https://doi.org/10.1093/aob/mcaa109 (2020).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pandey, N. & Pandey-Rai, S. Deciphering UV-B-induced variation in DNA methylation pattern and its influence on regulation of DBR2 expression in Artemisia annua L. Planta 242(4), 869–879. https://doi.org/10.1007/s00425-015-2323-3 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Molinier, J. Genome and epigenome surveillance processes underlying UV exposure in plants. Genes 8(11), 316. https://doi.org/10.3390/genes8110316 (2017).

    CAS 
    Article 
    PubMed Central 

    Google Scholar 

  • Niederhuth, C. E. et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 17, 194. https://doi.org/10.1186/s13059-016-1059-0 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lira-Medeiros, C. F. et al. Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One 5, e10326. https://doi.org/10.1371/journal.pone.0010326 (2010).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Richards, C. L., Verhoeven, K. J. F. & Bossdorf, O. Evolutionary significance of epigenetic variation. In Plant Genome Diversity Vol. 1 (eds Wendel, J. F. et al.) 257–274 (Springer Vienna, 2012).

    Chapter 

    Google Scholar 

  • Paun, O. et al. Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Mol. Biol. Evol. 27, 2465–2473. https://doi.org/10.1093/molbev/msq150 (2010).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xie, H. et al. Global DNA methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz). Front. Plant Sci. 8, 130398. https://doi.org/10.3389/fpls.2017.01860 (2017).

    Article 

    Google Scholar 

  • Herrera, C. M. & Bazaga, P. Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol. 187(3), 867–876. https://doi.org/10.1111/j.1469-8137.2010.03298.x (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Portis, E., Acquadro, A., Comino, C. & Lanteri, S. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci. 166, 169–178. https://doi.org/10.1016/j.plantsci.2003.09.004 (2004).

    CAS 
    Article 

    Google Scholar 

  • R Core Team. R: A language and environment for statistical computing. http://www.R-project.org (R Foundation for Statistical Computing, 2013).

  • Schloerke, B. et al. GGally: Extension to “ggplot2” R package version 2.1.0. https://CRAN.R-project.org/package=GGally (2021).

  • StatSoft, Inc. STATISTICA (Data Analysis Software System), Version 10. http://www.statsoft.com (2011).

  • Tomczyk, P. Phenotypic measurement of inbreeding depression in grasses—An overview of traits (Fenotypowe miary depresji wsobnej u traw—przegląd cech). Wiad. Bot. https://doi.org/10.5586/wb.2019.005 (2019).

    Article 

    Google Scholar 

  • Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37(12), 4302–4315. https://doi.org/10.1002/joc.5086 (2017).

    Article 

    Google Scholar 

  • Fox, J. & Weisberg, S. An {R} Companion to Applied Regression (Sage Publications, 2019).

    Google Scholar 


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