Determination of DNA methylation associated with Acer rubrum (red maple) adaptation to metals: analysis of global DNA modifications and methylation‐sensitive amplified polymorphism

Abstract

Red maple (Acer rubum), a common deciduous tree species in Northern Ontario, has shown resistance to soil metal contamination. Previous reports have indicated that this plant does not accumulate metals in its tissue. However, low level of nickel and copper corresponding to the bioavailable levels in contaminated soils in Northern Ontario causes severe physiological damages. No differentiation between metal‐contaminated and uncontaminated populations has been reported based on genetic analyses. The main objective of this study was to assess whether DNA methylation is involved in A. rubrum adaptation to soil metal contamination. Global cytosine and methylation‐sensitive amplified polymorphism (MSAP) analyses were carried out in A. rubrum populations from metal‐contaminated and uncontaminated sites. The global modified cytosine ratios in genomic DNA revealed a significant decrease in cytosine methylation in genotypes from a metal‐contaminated site compared to uncontaminated populations. Other genotypes from a different metal‐contaminated site within the same region appear to be recalcitrant to metal‐induced DNA alterations even ≥30 years of tree life exposure to nickel and copper. MSAP analysis showed a high level of polymorphisms in both uncontaminated (77%) and metal‐contaminated (72%) populations. Overall, 205 CCGG loci were identified in which 127 were methylated in either outer or inner cytosine. No differentiation among populations was established based on several genetic parameters tested. The variations for nonmethylated and methylated loci were compared by analysis of molecular variance (AMOVA). For methylated loci, molecular variance among and within populations was 1.5% and 13.2%, respectively. These values were low (0.6% for among populations and 5.8% for within populations) for unmethylated loci. Metal contamination is seen to affect methylation of cytosine residues in CCGG motifs in the A. rubrum populations that were analyzed.

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

“…Consistent with previous studies of other species distributed across different habitats observing equal or higher epigenetic than genetic diversity (Foust et al, 2016;Herrera & Bazaga, 2010;Richards, Schrey, & Pigliucci, 2012;Schulz, Eckstein, & Durka, 2014), we found slightly higher levels of epigenetic than genetic diversity in V. negundo and epigenetic variation and habitat may show different patterns in varying species. When running simple and partial Mantel tests, we obtained the same pattern as for Borrichia frutescens (Foust et al, 2016), failing to detect any relationship between epigenetic and habitat environment using crude binary data to describe complex habitats, as we had a larger number and range of sampling plots than the previous studies (Foust et al, 2016;Kim et al, 2016;Robertson, Schrey, Shayter, Moss, & Richards, 2017;Schulz et al, 2014). Limited studies have been conducted of epigenetic differentiation in natural populations across heterogeneous habitat conditions, and there is an urgent need to develop or replace the binary method to comprehensively characterize the complex habitat conditions.…”

“…The epigenetic mechanism may be restricted when natural plant populations endure some discrete human‐caused disturbance, such as heavy metal pollution (Kim et al., ), experimental disturbance (Herrera & Bazaga, ), and oil spills (Robertson et al., ). According to our field investigations and planting experiments (Du et al., ), Chinese chastetree tends to distribute in open habitats with plentiful light.…”

“…The epigenetic mechanism may be restricted when natural plant populations endure some discrete human-caused disturbance, such as heavy metal pollution (Kim et al, 2016), experimental disturbance , and oil spills (Robertson et al, 2017).…”

“…Biologists have illuminated that the amount and pattern of DNA methylation in model plants is sensitive to various environmental stressors under laboratory conditions, and ecologists have focused on the variation in DNA methylation in wild populations to understand the role of DNA methylation in plant adaptation to real environmental stress in nature (Bossdorf, Richards, & Pigliucci, ; Kilvitis et al., ). The rapidly increasing number of publications has illustrated that variation in DNA methylation is correlated with herbivory in violets (Herrera & Bazaga, ), salinity in marsh perennials (Foust et al., ), artificial disturbance in Lavandula latifolia (Herrera & Bazaga, ), metals in red maple (Kim, Im, & Nkongolo, ), and climate in Quercus lobata (Gugger, Fitz‐Gibbon, PellEgrini, & Sork, ; Platt, Gugger, Pellegrini, & Sork, ).…”

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

“…When divergence occurred, the uHe index was preferred because of the limited number of individuals from each group (Nei, 1978). Consistent with most previous epigenetic studies of natural population differentiation (Choi, Roy, Park, & Kim, 2016; Foust et al., 2016; Kim, Im, & Nkongolo, 2016; Qiu et al., 2016; Schulz et al., 2014), more epigenetic variance existed within groups than genetic variance. One general explanation for this is that a population with limited genetic diversity, especially after genetic drift, can extend its ecological niche through epigenetic variation, which is potentially sensitive to environmental stimulation (Richards, 2006).…”