Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

Wang, Wensheng; Huang, Fei; Qiao, Qin; Zhao, Xiuqin; Li, Zhikang; Fu, Binying

doi:10.1016/j.bbrc.2015.08.089

Cited by 62 publications

(49 citation statements)

References 35 publications

(45 reference statements)

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“…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.…”

Section: Salt Induces Different Changes To the Dna Methylation Of Leasupporting

confidence: 83%

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

et al. 2018

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Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are organ specific. Differentially Methylated Markers (DMMs) were mostly located in close proximity to repeat elements, but also in 1094 genes, of which many possessed gene ontology (GO) terms associated with plant responses to stress. Identified markers have potential value as sentinels of salt stress and provide a starting point to allow understanding of the functional role of DNA methylation in facilitating barley's response to this stressor.

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Section: Salt Induces Different Changes To the Dna Methylation Of Leasupporting

confidence: 83%

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

et al. 2018

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“…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).…”

Section: Discussionsupporting

confidence: 89%

“…This variation can be detected by developing suitable molecular genetic and epigenetic markers associated with salinity tolerance (Wang et al, 2015b). The construction of genetic maps using DNA markers and the localization of quantitative trait loci are routine practices in breeding programs.…”

Section: Introductionmentioning

confidence: 99%

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

Al-Bahry¹,

Victor²,

Al-Lawati³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Modification of DNA methylation status is one of the mechanisms used by plants to adjust gene expression at both the transcriptional and posttranscriptional levels when plants are exposed to suboptimal conditions. Under abiotic stress, different cultivars often show heritable phenotypic variation accompanied by epigenetic polymorphisms at the DNA methylation level. This variation may provide the raw materials for plant breeding programs that aim to enhance abiotic stress tolerance, including salt tolerance. In this study, methylation-sensitive amplified polymorphism (MSAP) analysis was used to assess cytosine methylation levels in alfalfa (Medicago spp) roots exposed to increasing NaCl concentrations (0.0, 8.0, 12.0, and 20.0 dS/m). Eleven indigenous landraces were analyzed, in addition to a salt-tolerant cultivar that was used as a control. There was a slight increase in DNA methylation upon exposure to high levels of soil salinity. Phylogenetic analysis using MSAP showed epigenetic variation within and between the alfalfa landraces when exposed to saline conditions. Based on MSAP and enzyme-linked immunosorbent assay results, we found that salinity increased global DNA methylation status, particularly in plants exposed to the highest level of salinity (20 dS/m). Quantitative reverse transcription-polymerase chain reaction indicated that this might be mediated by the overexpression of methyltransferase homolog genes after exposure to saline conditions. DNA demethylation using 5-azacytidine reduced seedling lengths and dry and fresh weights, indicating a possible decrease in salinity tolerance. These results suggest that salinity affects DNA methylation flexibility.

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“…Genome-wide DNA methylation under various abiotic and biotic stresses have been recorded for various plant species (Kou et al, 2011; Wang et al, 2011, 2015; Karan et al, 2012; Colaneri and Jones, 2013; Fan et al, 2013; Shan et al, 2013; Gao et al, 2014). 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).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios. We furthermore investigated the DNA methylation status in normal, osmotic-stressed, and re-watering treatments via the methylation-sensitive amplification polymorphism (MSAP). The averaged similarity between two rice accessions from tolerant and susceptible groups was approximately 50%, similar with that between two accessions within the tolerant/susceptible group. However, the proportion of overall tolerance-associated epiloci was only 5.2% of total epiloci. The drought-tolerant accessions revealed lower DNA methylation levels in the stressed condition and more de-methylation events when they encountered osmotic stress, compared to the susceptible group. During the recovery process, the drought-tolerant accessions possessed more re-methylation events. Fourteen differentially methylated epiloci (DME) were, respectively, generated in normal, osmotic-stressed, and re-watering treatments. Approximately, 35.7% DME were determined as tolerance-associated epiloci. Additionally, rice accessions with lower methylation degrees on DME in the stressed conditions had a higher survival ratio compared to these with higher methylation degrees. This result is consistent with the lower DNA methylation levels of tolerant accessions observed in the stressed treatment. Methylation degrees on a differentially methylated epilocus may further influence gene regulation in the rice seedling in response to the osmotic stress. All these results indicate that DME generated from a number of genotypes could have higher probabilityies for association with stress-tolerance, rather than DME generated from two genotypes of contrasting tolerance. The DME found in this study are suspected to be good epigenetic markers for the application in drought-tolerant rice breeding. They could also be a valuable tool to study the epigenetic differentiation in the drought-tolerance between upland and lowland rice ecotypes.

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Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

Cited by 62 publications

References 35 publications

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

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

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

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

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