Abstract
Epigenetic mechanisms such as DNA methylation are considered as an important pathway responsible for phenotypic responses and rapid acclimation of plants to different environments. To search for empirical evidence that DNA methylation is implicated in stress-responses of non-model species, we exposed genetically uniform, experimental populations of the wetland clonal plant Hydrocotyle vulgaris to two manipulated flood regimes, i.e., semi-submergence vs. submergence, measured phenotypic traits, and quantified different types of DNA methylation using MSAP (methylation-sensitive amplified polymorphism). We found different epi-phenotypes and significant epigenetic differentiation between semi-submerged and submerged populations. Compared to subepiloci (denoting DNA methylation conditions) for the CG-methylated state, unmethylation and CHG-hemimethylation subepiloci types contribute more prominently to the epigenetic structure of experimental populations. Moreover, we detected some epimarker outliers potentially facilitate population divergence between two flood regimes. Some phenotypic variation was associated with flood-induced DNA methylation variation through different types of subepiloci. Our study provides the indication that DNA methylation might be involved in plant responses to environmental variation without altering DNA sequences.
Highlights
Plants exposed to environmental changes often exhibit plastic phenotypes (Putnam et al, 2016; Colicchio et al, 2018)
We examined the direct effects of methylation variation and the environmental factor on phenotypic variation, and indirect effects of flood regimes on phenotypic traits through methylation variation
Principal coordinate analyses showed a clear epigenetic differentiation between the semi-submergence and the submergence experimental populations of H. vulgaris, indicating that environmental conditions could shape DNA methylation patterns of plant populations (Note that if DNA methylation changes largely arise from random epimutation, the presence/absence of private bands would be observed in many loci and such epiloci could be neutral so that the treatment-induced epigenetic differentiation would not occur) (Boyko and Kovalchuk, 2010; Schulz et al, 2014; Zhang et al, 2016)
Summary
Plants exposed to environmental changes often exhibit plastic phenotypes (Putnam et al, 2016; Colicchio et al, 2018). Epigenetic regulation (e.g., DNA methylation, histone modifications, chromatin remodeling, and expression of non-coding RNAs) without changing DNA sequence has been widely considered as another candidate mechanism accounting for plant phenotypic variation (Bossdorf et al, 2008; Marfil et al, 2009). DNA methylation patterns are sensitive to changing environments and commonly possess a much higher variation rate (Schulz et al, 2014; Jueterbock et al, 2020). Such variation can be reversibly transient within one generation or stably heritable to several generations (Angers et al, 2010; Paun et al, 2010; Colicchio et al, 2018). Environment-induced epigenetic regulation could offer a rapid pathway for phenotypic plasticity, and underlie plant adaptive evolution when across-generational plasticity confers fitness benefits in predictable environments (Putnam et al, 2016; Huang et al, 2017; Groot et al, 2018; Colicchio and Herman, 2020)
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