Ecological plant epigenetics: Evidence from model and non‐model species, and the way forward

Abstract

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

Context-Dependent Developmental Effects of Parental Shade Versus Sun Are Mediated by DNA Methylation

“…Although other modes of epigenetic transmission may be involved as well (Bonduriansky and Day, 2009; Akkerman et al, 2016), DNA methylation is increasingly viewed as a likely transmission mechanism for transgenerational effects of parental conditions (Kappeler and Meaney, 2010; Herman et al, 2014; Colicchio et al, 2015). In plants, changes in DNA methylation states are known to mediate the effects of several types of environmental stress on progeny phenotypes, e.g., salinity (Boyko et al, 2010), nitrogen deficiency (Kou et al, 2011), drought (Alsdurf et al, 2015; Herman and Sultan, 2016), and herbivory (Akkerman et al, 2016) (additional examples in Bossdorf et al, 2008; Bonduriansky and Day, 2009; Verhoeven et al, 2010, 2016; Herman and Sultan, 2011; Holeski et al, 2012; Richards et al, 2017). …”

“…Resolving the entire causal pathway, from stress induction, to precise epigenetic changes and their transmission, to phenotypic effects and functional consequences, is a demanding task indeed. More broadly, understanding the mechanisms, dynamics, and adaptive importance of transgenerational effects in plant populations will require not only improved genomic tools for epigenetic studies in non-model species (Richards et al, 2017), but collaborative investigations that draw on molecular, developmental, and ecological expertise.…”

“…While changes to cytoplasmic factors are more difficult to test, methods for studying certain epigenetic modifications – in particular DNA methylation – are now well established (Bossdorf et al, 2008; Verhoeven et al, 2016; Richards et al, 2017). In both plants and animals, the addition or removal of methyl groups from cytosine nucleotides at specific loci may be induced by environmental conditions and the altered DNA subsequently transmitted to offspring (e.g., Verhoeven et al, 2010; Dowen et al, 2012; Pastor et al, 2013; Yu et al, 2013; Zheng et al, 2013; Skinner, 2014).…”

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

“…The high genetic diversity in P. australis makes it more difficult to detect the epigenetic changes during the invasion. The epigenetic variation in natural populations can originate from genetic factor (B1), spontaneous epimutations (B2), and environmentally induced epigenetic changes (B3) (Richards et al., 2017). In addition, epigenetic change can create novel genetic variation through regulating transposable elements activity (Richards et al., 2017).…”

“…The epigenetic variation in natural populations can originate from genetic factor (B1), spontaneous epimutations (B2), and environmentally induced epigenetic changes (B3) (Richards et al., 2017). In addition, epigenetic change can create novel genetic variation through regulating transposable elements activity (Richards et al., 2017). In our study, the similarity of genetic and epigenetic structure reflects the drivers B1 and B2.…”