Assessing Global DNA Methylation Changes Associated with Plasticity in Seven Highly Inbred Lines of Snapdragon Plants (Antirrhinum majus)

Abstract

Genetic and epigenetic variations are commonly known to underlie phenotypic plastic responses to environmental cues. However, the role of epigenetic variation in plastic responses harboring ecological significance in nature remains to be assessed. The shade avoidance response (SAR) of plants is one of the most prevalent examples of phenotypic plasticity. It is a phenotypic syndrome including stem elongation and multiple other traits. Its ecological significance is widely acknowledged, and it can be adaptive in the presence of competition for light. Underlying genes and pathways were identified, but evidence for its epigenetic basis remains scarce. We used a proven and accessible approach at the population level and compared global DNA methylation between plants exposed to regular light and three different magnitudes of shade in seven highly inbred lines of snapdragon plants (Antirrhinum majus) grown in a greenhouse. Our results brought evidence of a strong SAR syndrome for which magnitude did not vary between lines. They also brought evidence that its magnitude was not associated with the global DNA methylation percentage for five of the six traits under study. The magnitude of stem elongation was significantly associated with global DNA demethylation. We discuss the limits of this approach and why caution must be taken with such results. In-depth approaches at the DNA sequence level will be necessary to better understand the molecular basis of the SAR syndrome.

Epigenetic variation for agronomic improvement: an opportunity for vegetatively propagated crops

“…Epigenetic characterization of variants at the scale of populations, which is necessary for epibreeding, is also limiting. These population level approaches lack precision (Gourcilleau et al., ). Technological progress is fast, and these problems will soon be solved.…”

Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype

“…This addition is provided de novo and maintained by methyltransferase enzymes through three different sequence contexts in plants: CG, CHG and CHH (Meyer 2015). Over recent years, many studies have highlighted the role of DNA methylation in many biological and ecological mechanisms in plants, such as development (Guo et al 2018, responses to biotic and abiotic stressors (Tricker 2015, Crisp et al 2016, Lämke and Bäurle 2017, cellular-stress response memory and priming (Mauch-Mani et al 2017, Sow et al 2018, phenotypic plasticity (Gourcilleau et al 2010, Baulcombe and Dean 2014, Kooke et al 2015, Conde et al 2017, and possibly adaptation (Bräutigam et al 2013, Kawakatsu et al 2016, Rey et al 2016, Schmid et al 2018, Gourcilleau et al 2019. Kooke et al (2015) used 99 Epigenetic Recombinant Inbred Lines (epiRILs) of Arabidopsis thaliana, consisting of crosses between the parents Col-0 and the hypomethylated mutant lines ddm1 and ddm2, to compare the morphological responses of the plants exposed to saline conditions.…”

The Epigenetics Dilemma

“…In this issue, it is shown that phenotypic, and thus potentially gene expression changes, can precede epigenetic changes [3], or that they occur after the initial environmental stimulus [4,5]. It is also shown that epigenetic modifications can be associated with the magnitude of change in reaction norms of some but not all phenotypic traits [6]. In addition, even when considering the same bearer of epigenetic information (e.g., DNA methylation), different organisms show different types of DNA methylation (e.g., [1][2][3][4][5][6]) with potentially different types of phenotypic effects.…”

“…It is also shown that epigenetic modifications can be associated with the magnitude of change in reaction norms of some but not all phenotypic traits [6]. In addition, even when considering the same bearer of epigenetic information (e.g., DNA methylation), different organisms show different types of DNA methylation (e.g., [1][2][3][4][5][6]) with potentially different types of phenotypic effects. Nevertheless, epigenetic changes do not occur randomly along the genome.…”

“…First, it is the very definition of epigenetics (considered a "heritable but reversible changes in gene function"; paraphrased as e.g. "regulation of transcription" used in [2], "gene activation" by Gavery et al [4], and "gene expression" in [6]) that makes a clear and unambiguous claim of a link between epigenetics and gene function, i.e., the (molecular) phenotypes. Such a claim is absent from definitions of genetics ("Genetics is the study of heredity"; e.g., [9]) thus orphaning those changes in chromatin structure that do not lead to detectable changes in gene function.…”