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. 2010 Apr 26;5(4):e10326.
doi: 10.1371/journal.pone.0010326.

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

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Free PMC article

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

Catarina Fonseca Lira-Medeiros et al. PLoS One. .
Free PMC article

Abstract

Background: Epigenetic 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 findings: Significant 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 (G(ST)) and multivariate (beta(ST)) 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.

Conclusions: In 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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Map of the mangrove forest and pictures of Laguncularia racemosa illustrating the morphological differences between natural populations.
(A) Map of Rio de Janeiro State, where the city of Rio de Janeiro is painted in red. There is an aerial view of the conserved Sepetiba Bay's mangrove forest. The salt marsh formation is visible in gray (no vegetation) above the study area delimited by a green line. (B) Individual of L. racemosa from the riverside (RS) location, almost 10 meters tall. (C) Typical L. racemosa individual from the area near a salt marsh (SM) with abnormal development, reaching only 1.5 meters in height.
Figure 2
Figure 2. PCA analyses of Laguncularia racemosa natural populations using both genetic and epigenetic data separately.
Multivariate analysis of the genetic (EcoRI/MspI) and epigenetic (EcoRI/HpaII) components of L. racemosa plants found at riverside (RS represented as number 1) and the salt marsh (SM represented as number 2) locations of Sepetiba's Bay mangrove forest. (A) PCA on covariance matrix for genetic profiles obtained using EcoRI/MspI data. (B) PCA on covariance matrix for epigenetic profiles obtained using EcoRI/HpaII data. F1 and F2 values show the contribution of the two principal components summarizing the total variance of each dataset. βST was calculated using Between-group EigenAnalysis (BPCA) for both genetic and epigenetic profiles and tested with 9999 permutations.
Figure 3
Figure 3. Co-Inertia analysis of Laguncularia racemosa natural populations using genetic and epigenetic data.
The Co-Inertia analysis maximized the covariance of PCAs shown in Figure 2. The significance test of this association was done with 9999 permutations. RS samples are numbered as 1 while SM samples are numbered as 2. Circles (○) correspond to the projection of genetic profiles (EcoRI/MspI) and arrowheads (▸) the projection of epigenetic profiles (EcoRI/HpaII). Black-filled arrows indicate three RS samples that had similar genetic profiles with three SM samples, but divergent epigenetic profiles. F1 and F2 values show the contribution of the two principal components summarizing the total variance of each dataset.

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