Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability.
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MK was supported by Australian Awards, AusAID (Australian Agency for International Development); MW was partly supported by the Biotechnology and Biological Sciences Research Council (BBS/E/0012843C) and CR is currently partially supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Program number 2352987000.
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2020.553907/full#supplementary-material It is also available for download as the additional file listed at the end of this record.
Konate, Moumouni; Wilkinson, Michael J.; Taylor, Julian; Scott, Eileen S.; Berger, Bettina; and Rodriguez Lopez, Carlos M., "Greenhouse Spatial Effects Detected in the Barley (Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation" (2020). Horticulture Faculty Publications. 46.