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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Published in Epigenomes, v. 2, issue 2, 12, p. 1-27.

© 2018 by the authors. Licensee MDPI, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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M.K. was financially supported by an Australian Awards Scholarship, offered by AusAID (Australian Agency for International Development). M.J.W. was partly supported by the Biotechnology and Biological Sciences Research Council (BBS/E/0012843C).

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The following are available online at https://www.mdpi.com/2075-4655/2/2/12/s1. Supplemental Data Set S1. List of stable salt-induced differentially methylated markers in leaves and roots. Supplemental Data Set S2. List of salt-induced differentially methylated genes. Supplemental Data Set S3. Annotation of salt-induced differentially methylated genes in barley leaves and roots. Supplemental Data Set S4. List and annotation of salt induced DE genes and differentially methylated DE genes in roots of Clipper and LR Sahara. Supplemental Data Set S5. Sample information includes: Sequencing sample IDs, variety tissue, salt treatment (NaCl mM), sequencing barcode and sequencing plate.

epigenomes-02-00012-s001.zip (1564 kB)
Supplementary Materials