DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress

Wang, Wensheng; Zhao, Xiuqin; Pan, Ya-Jiao; Zhu, Linghua; Fu, Binying; Li, Zhikang

doi:10.1016/j.jgg.2011.07.006

Cited by 78 publications

(64 citation statements)

References 21 publications

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“…However, we also noted that the proportion of de novo methylation and demethylation events varied in the same manner in both roots and leaves, with a prevalence of hypomethylated events in both organs, albeit at different frequencies. It is possible that divergence between our findings and those of previous studies [7,[25][26][27]33,47] may simply be a feature of barley. However, it is also possible that the trend towards hypomethylation is a more general one and that our findings diverge because of methodological differences in the present work such as (1) the high-throughput sequencing used to generate methylation profiles; (2) the level of stringency in selecting DMMs (FDR < 0.01); and 3) the diversity of barley varieties used in this study to account for genotype-dependent DNA methylation [25][26][27].…”

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

confidence: 93%

“…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: 92%

“…Our results agree with many previous studies that have reported that the overall level and direction of methylation flux in response to salinity varies according to organ type, with a tendency towards hypomethylation in roots and hypermethylation in leaves [7,[25][26][27]33,47]. However, we also noted that the proportion of de novo methylation and demethylation events varied in the same manner in both roots and leaves, with a prevalence of hypomethylated events in both organs, albeit at different frequencies.…”

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

confidence: 92%

“…The primary challenge, particularly for crops with large genomes, resides in assembling a genome-wide picture of the role of methylation in orchestrating the molecular response to the stressor. As with the study of other stresses, works on methylation-based responses to salt stress have, therefore, largely relied on low throughput-targeted approaches, low genome coverage or anonymous markers applied to a low number of genotypes [7,[25][26][27]33,47]. However, our use here of methylation sensitive Genotyping-By-Sequencing (ms-GBS) to study salt-induced changes in DNA methylation in m CCGG contexts has allowed us to survey methylome flux across a reasonably representative portion of the genome (Figure 2).…”

Section: Discussionmentioning

confidence: 99%

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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 Leacontrasting

confidence: 93%

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

confidence: 92%

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

confidence: 92%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

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

et al. 2018

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“…Of the various approaches to study global methylation, the methylation-sensitive amplification polymorphism (MSAP) technique has demonstrated the consistency and reproducibility that are required to detect global cytosine methylation patterns and levels in several plant species, such as Arabidopsis thaliana (Cervera et al, 2002), Sorghum bicolor L. , Hordeum brevisubulatum (Li et al, 2008), Codonopsis lanceolata (Guo et al, 2007), and maize . Moreover, it has been used in various studies, all of which obtained useful results in areas such as biotic and abiotic stresses (Wang et al, 2011), development , and tissue culture (Kou et al, 2011;Wang et al, 2013). In addition, hybrid vigor has been studied at the DNA methylation level using this technique.…”

Section: Introductionmentioning

confidence: 99%

Analysis of DNA methylation patterns and levels in maize hybrids and their parents

et al. 2014

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ABSTRACT. Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 8459 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (4): 8458-8468 (2014) DNA methylation variations in maize hybrids and parents fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.

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Epigenetics and Epigenomics of Plants

Yadav

Pandey

Muthamilarasan

et al. 2018

Plant Genetics and Molecular Biology

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The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement. Graphical Abstract.

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DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress

Cited by 78 publications

References 21 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)

Analysis of DNA methylation patterns and levels in maize hybrids and their parents

Epigenetics and Epigenomics of Plants

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