Phenotypic Response to Light Versus Shade Associated with DNA Methylation Changes in Snapdragon Plants (Antirrhinum majus)

Abstract

The phenotypic plasticity of plants in response to change in their light environment, and in particularly, to shade is a schoolbook example of ecologically relevant phenotypic plasticity with evolutionary adaptive implications. Epigenetic variation is known to potentially underlie plant phenotypic plasticity. Yet, little is known about its role in ecologically and evolutionary relevant mechanisms shaping the diversity of plant populations in nature. Here we used a reference-free reduced representation bisulfite sequencing method for non-model organisms (epiGBS) to investigate changes in DNA methylation patterns across the genome in snapdragon plants (Antirrhinum majus L.). We exposed plants to sunlight versus artificially induced shade in four highly inbred lines to exclude genetic confounding effects. Our results showed that phenotypic plasticity in response to light versus shade shaped vegetative traits. They also showed that DNA methylation patterns were modified under light versus shade, with a trend towards global effects over the genome but with large effects found on a restricted portion. We also detected the existence of a correlation between phenotypic and epigenetic variation that neither supported nor rejected its potential role in plasticity. While our findings imply epigenetic changes in response to light versus shade environments in snapdragon plants, whether these changes are directly involved in the phenotypic plastic response of plants remains to be investigated. Our approach contributed to this new finding but illustrates the limits in terms of sample size and statistical power of population epigenetic approaches in non-model organisms. Pushing this boundary will be necessary before the relationship between environmentally induced epigenetic changes and phenotypic plasticity is clarified for ecologically relevant mechanisms with evolutionary implications.

epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing

“…To date, published papers using epiGBS have been mainly limited to plant species (e.g. Alvarez et al, 2020; Moorsel et al, 2019; Mouginot et al, 2021; Mounger et al, 2021; Prudencio et al, 2018), but also include studies from vertebrates (Meröndun et al, 2019) and molluscs (Johnson & Kelly, 2020). By making the use of restriction enzymes more flexible (including double RE digest), epiGBS2 allows for easier implementation in many different organisms, including those where standard RRBS used to be the preferred method.…”

Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

“…It has been proved that DNA methylation is responsible of phenotypic variation in plants ( Martin et al, 2009 ; Mougninot et al, 2021 ; Zhao et al, 2021 ). Considering that different types of stress, such as abiotic stress, can trigger methylation, eventually leading to variation of gene expression, this field of research has become a useful tool for understanding how tree species deal with the environment variations.…”

Non‐reproducible signals of adaptation to elevation between open and understorey microhabitats in snapdragon plants

“…A unique seasonal peak of germination across years is documented in snapdragon cultivated plants (Bhargava et al, 2015 ; Kang & Choi, 2006 ). Furthermore, snapdragon plants exhibit a strong phenotypic plasticity in response to shade and its suite of covarying environmental factors, for example temperature, water availability (Gourcilleau et al, 2019 ; Mouginot et al, 2021 ; Mousset et al, 2021 ), including in their seed germination that is delayed up to several days or prevented by shade (Kang & Choi, 2006 ; Smith & Whitelam, 1997 ). Germination sensitiveness to light is common in small‐seeded species (Baskin & Baskin, 2014 ).…”