Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress

Abstract

DNA methylation has been referred as an important player in plant genomic responses to environmental stresses but correlations between the methylome plasticity and specific traits of interest are still far from being understood. In this study, we inspected global DNA methylation levels in salt tolerant and sensitive rice varieties upon salt stress imposition. Global DNA methylation was quantified using the 5-methylcytosine (5mC) antibody and an ELISA-based technique, which is an affordable and quite pioneer assay in plants, and in situ imaging of methylation sites in interphase nuclei of tissue sections. Variations of global DNA methylation levels in response to salt stress were tissue- and genotype-dependent. We show a connection between a higher ability of DNA methylation adjustment levels and salt stress tolerance. The salt-tolerant rice variety Pokkali was remarkable in its ability to quickly relax DNA methylation in response to salt stress. In spite of the same tendency for reduction of global methylation under salinity, in the salt-sensitive rice variety IR29 such reduction was not statistically supported. In ‘Pokkali’, the salt stress-induced demethylation may be linked to active demethylation due to increased expression of DNA demethylases under salt stress. In ‘IR29’, the induction of both DNA demethylases and methyltransferases may explain the lower plasticity of DNA methylation. We further show that mutations for epigenetic regulators affected specific phenotypic parameters related to salinity tolerance, such as the root length and biomass. This work emphasizes the role of differential methylome flexibility between salt tolerant and salt sensitive rice varieties as an important player in salt stress tolerance, reinforcing the need to better understand the connection between epigenetic networks and plant responses to environmental stresses.

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

“…Certainly, it has been widely reported that salinity imposes extensive, genome-wide modification of DNA methylation patterns, with more methylation changes being reported in leaves when compared with roots [25][26][27]33,[57][58][59][60], a trend that is clearly in accordance with our findings. Taken at face value, the greater abundance of salt-induced methylation changes in leaves than in roots appears counterintuitive, since roots are in direct contact with salt stress.…”

Salt stress alters DNA methylation levels in alfalfa (Medicago spp)

“…This result is in agreement with the widely accepted view that closely related species may possess some methylome flexibility, and consequently gene expression diversity (Postnikova et al, 2013). For example, rice cultivars with different salinity-tolerance capacities exhibit different DNA methylation patterns in response to salinity stress (Ferreira et al, 2015;Garg et al, 2015;Wang et al, 2015b). Overall, the mean number of methylated MSAP loci increased while the number of hemi and non-methylated loci decreased (Figure 4).…”

“…This may partly explain the increase in DNA methylation levels detected by the MSAP and ELISA methods. DNA methyltransferase and demethylase gene expression in response to salt stress is genotype-dependent in rice (Oryza sativa L.) (Ferreira et al, 2015). A salt-tolerant rice variety only exhibited an increase in DNA demethylase gene expression, whereas a saltsusceptible variety exhibited an increase in the expression levels of both DNA demethylase and methyltransferase genes (Ferreira et al, 2015).…”

Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings

“…Researchers also aspired to disclose the associations between DNA methylation and stress-tolerance via artificial generation of DNA methylation differences between two genotypes of contrasting tolerances (Wang et al, 2011; Gayacharan and Joel, 2013; Gao et al, 2014; Ferreira et al, 2015; Garg et al, 2015; Wang W. et al, 2016). However, DNA methylation is genotype-specific (Karan et al, 2012).…”