Cotton DNA Methylation and Its Analysis Under the Salt- and Draught-Stress

DNA methylation, an important component of epigenetics induced usually by adversity, plays a vital role in the response to various stresses including drought and salt. A methylation-sensitive amplification polymorphism method based on capillary electrophoresis was used to explore the epigenetic mechanisms of salt tolerance and heterosis in Upland cotton (Gossypium hirsutum L.), and the results indicated that hypermethylation and demethylation could be an important mechanism to resist the stresses. And the demethylation could be the mechanism to explain heterosis in cotton hybrid. The results of whole genome methylation sequencing showed high DNA methylation density usually occurs in promoter regions and transposons areas. Methylated cytosines in different sequence contexts (CG, CHG and CHH) have different functions and methylation levels. And the results also showed methylated cytosines in asymmetric CHH sequence context are dynamic, being mostly related to stresses. Combined with transcriptome data, we found long non-coding RNAs (lncRNAs) may involve in the regulation of DNA methylation in response to drought stress. All these results could provide theoretical reference value for the mechanism research of tolerance in cotton.