Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across different salt stress in Maize (Zea mays L.)

DNA methylation is a vital epigenetic modification for the regulation of plant response to environmental stresses. In order to investigate changes in DNA methylation under salt stress, the levels of cytosine methylation in maize leaves at the seedling stage were estimated using the Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) method. The profiling of the DNA methylation results showed that a total of 163.27 million raw reads were obtained, with an average 33.06% of which were uniquely mapped to a specific region in the maize genome. Cytosine methylation mainly occurred in CG, CHG, and CHH (H = A, T, or G) sites, and the CG contexts were lower than CHG and CHH contexts. The distribution of highly methylated regions (HMRs) mainly focused on the upstream 2k, intron, and downstream 2k, and the HMR distribution in these elements of YH 200 was higher than control (YH 0) and other samples. In addition, a total of 4402 differential methylated region (DMR)-associated genes were observed between stress samples and control, in which more hypomethylation-related genes were present than hypermethylation-related ones under 100 and 200 mmol L−1 NaCl stress. Meanwhile, these DMR-associated genes were found to be involved in many biological functions by gene ontology (GO) analysis, such as cellular processes, metabolic processes, and signal transduction. Real-time qRT-PCR results showed that the expression of some methylated genes was consistent with the results of MeDIP-seq, while others showed an opposite trend, indicating that DNA-methylated regions did not uniformly affect the transcription of the corresponding genes. These experimental results are expected to improve our understanding of salt tolerance in maize.