Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

Abstract

BackgroundEpigenetic modifications, such as cytosine methylation, are inherited in plant species and may occur in response to biotic or abiotic stress, affecting gene expression without changing genome sequence. Laguncularia racemosa, a mangrove species, occurs in naturally contrasting habitats where it is subjected daily to salinity and nutrient variations leading to morphological differences. This work aims at unraveling how CpG-methylation variation is distributed among individuals from two nearby habitats, at a riverside (RS) or near a salt marsh (SM), with different environmental pressures and how this variation is correlated with the observed morphological variation.Principal FindingsSignificant differences were observed in morphological traits such as tree height, tree diameter, leaf width and leaf area between plants from RS and SM locations, resulting in smaller plants and smaller leaf size in SM plants. Methyl-Sensitive Amplified Polymorphism (MSAP) was used to assess genetic and epigenetic (CpG-methylation) variation in L. racemosa genomes from these populations. SM plants were hypomethylated (14.6% of loci had methylated samples) in comparison to RS (32.1% of loci had methylated samples). Within-population diversity was significantly greater for epigenetic than genetic data in both locations, but SM also had less epigenetic diversity than RS. Frequency-based (GST) and multivariate (βST) methods that estimate population structure showed significantly greater differentiation among locations for epigenetic than genetic data. Co-Inertia analysis, exploring jointly the genetic and epigenetic data, showed that individuals with similar genetic profiles presented divergent epigenetic profiles that were characteristic of the population in a particular environment, suggesting that CpG-methylation changes may be associated with environmental heterogeneity.ConclusionsIn spite of significant morphological dissimilarities, individuals of L. racemosa from salt marsh and riverside presented little genetic but abundant DNA methylation differentiation, suggesting that epigenetic variation in natural plant populations has an important role in helping individuals to cope with different environments.

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

“…While the structure of B1 and B2 can only be shaped through natural selection, B3 could be direct changed by the environment. The epigenetic differentiation was observed in contrast habitats without variation differentiation (Foust et al., 2016; Gugger et al., 2016; Lira‐Medeiros et al., 2010; Schulz et al., 2014), but it remained unexplored how stable and inheritable the B3 variation is in these studies. Common garden filtered the plastic B3 variation in our study, and epigenetic divergence between populations in the introduced region and in its original region was weakened.…”

“…Epigenetic diversity can generate massive heritable variation of ecologically relevant plant traits such as root allocation, drought tolerance and nutrient plasticity (Zhang, Fischer, Colot, & Bossdorf, 2013), and it appears to increase the productivity and stability of plant populations in Arabidopsis thaliana under artificial conditions (Latzel et al., 2013). An increasing number of studies have also demonstrated the common existence and significant role of epigenetic variation in plant populations of herbs (Foust et al., 2016; Herrera, Medrano, & Bazaga, 2014; Medrano et al., 2014; Preite et al., 2015; Schulz, Eckstein, & Durka, 2014), shrubs (Avramidou, Ganopoulos, Doulis, Tsaftaris, & Aravanopoulos, 2015; Herrera & Bazaga, 2013, 2016), and trees (Guarino, Cicatelli, Brundu, Heinze, & Castiglione, 2015; Gugger, Fitz‐Gibbon, PellEgrini, & Sork, 2016; Lira‐Medeiros et al., 2010; Platt, Gugger, Pellegrini, & Sork, 2015; Sáez‐Laguna et al., 2014) under natural conditions. Therefore, epigenetic variation can be a very important mechanism for invasive plant success in a broad range of environments (Douhovnikoff & Dodd, 2014; Richards, Schrey, & Pigliucci, 2012).…”

Epigenetic Variation, Inheritance, and Selection in Plant Populations

“…However, because such unique epialleles that cause phenotypic changes can only be distinguished from genetic variants by in-depth molecular analyses, epigenetic alterations independent of observable phenotypes are now being analyzed at the genomewide level. Several studies in nonmodel organisms have shown by methylation-sensitive amplified polymorphism (MSAP) analyses that natural populations vary more in DNA methylation than in DNA sequence, that is, their epigenetic diversity is higher than their genetic diversity (Cervera et al 2002;Keyte et al 2006;Salmon et al 2008;Herrera and Bazaga 2010;Lira-Medeiros et al 2010). In addition, DNA methylation patterns were analyzed in Arabidopsis using high-throughput sequencing of bisulfite-treated genomic DNA (BS-Seq).…”

“…Broadening the search for naturally occurring epialleles revealed variation in DNA methylation patterns in several nonmodel species living in diverse natural settings (Salmon et al 2008;Marfil et al 2009;Herrera and Bazaga 2010;Lira-Medeiros et al 2010;Paun et al 2010). In these reports, cytosine methylation polymorphisms were detected using MSAP analyses that enables the sampling of information about the methylation status across the genome without prior knowledge of the genome sequence.…”

“…In these reports, cytosine methylation polymorphisms were detected using MSAP analyses that enables the sampling of information about the methylation status across the genome without prior knowledge of the genome sequence. A recent study explored the correlation between environmental factors and epigenetic variation in Laguncularia racemosa, a mangrove tree (Lira-Medeiros et al 2010). Laguncularia occurs in two contrasting but nearby habitats, that is, riverside and salt marsh settings.…”