Analysis of the DNA methylation of maize (Zea mays L.) in response to cold stress based on methylation-sensitive amplified polymorphisms

DNA methylation plays a vital role in tuning gene expression in response to environmental stimuli. Here, methylation-sensitive amplified polymorphisms (MSAP) were used to assess the effect of cold stress on the extent and patterns of DNA methylation in maize seedlings. Overall, cold-induced genome-wide DNA methylation polymorphisms accounted for 32.6 to 34.8% of the total bands at the different treatment time-points. It was demonstrated that the extent and pattern of DNA methylation was induced by cold stress through the cold treatment process and that the demethylation of fully methylated fragments was the main contributor of the DNA methylation alterations. The sequences of 28 differentially amplified fragments relevant to stress were successfully obtained. Under the cold stress, demethylation was detected in most fragments. BLAST results indicate that the homologues of these fragments are involved in many processes, including hormone regulation, cold response, photosynthesis, and transposon activation. The expression analysis demonstrated an increase in the transcription of five demethylated genes. Despite the fact that DNA methylation changes and cold acclimation are not directly associated, our results may indicate that the specific demethylation of genes is an active and rapid epigenetic response to cold in maize during the seedling stage, further elucidating the mechanism of maize adaptation to cold stress.