Anther development in flowering plants is highly sensitive to high-temperature (HT) stress. Understanding the potential epigenetic mechanism of anther infertility induced by HT stress in cotton (Gossypium hirsutum L.) is crucial for the effective use of genetic resources to guide plant breeding. Using the whole-genome bisulfite sequencing, we map cytosine methylation at single-base resolution across the whole genome of cotton anthers, and changes in the methylome of the cytoplasmic male sterility system associated with HT stress were analysed in two cotton lines with contrasting HT stress tolerance. The cotton anther genome was found to display approximately 31.6%, 68.7%, 61.8%, and 21.8% methylation across all sequenced C sites and in the CG, CHG, and CHH sequence contexts, respectively. In an integrated global methylome and transcriptome analysis, only promoter-unmethylated genes showed higher expression levels than promoter-methylated genes, whereas gene body methylation presented an obvious positive correlation with gene expression. The methylation proﬁles of transposable elements in cotton anthers were characterized, and more differentially methylated transposable elements were demethylated under HT stress. HT-induced promoter methylation changes led to the up-regulation of the mitochondrial respiratory chain enzyme-associated genes GhNDUS7, GhCOX6A, GhCX5B2, and GhATPBM, ultimately promoting a series of redox processes to form ATP for normal anther development under HT stress. In vitro application of the common DNA methylation inhibitor 5-azacytidine and accelerator methyl trifluoromethanesulfonate demonstrated that DNA demethylation promoted anther development, while increased methylation only partially inhibited anther development under HT stress.
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