Spatiotemporal methylome remodeling during fiber differentiation in Gossypium hirsutum

Whole-genome methylome analysis reveals DNA methylation dynamics during upland cotton (Gossypium hirsutum) fiber development. DNA methylation levels initially increased and then decreased from -3 days post-anthesis (DPA) to 5 DPA, with a significant rise during the rapid elongation stage (5 DPA to 14 DPA), particularly in CHH methylation levels. Integrated transcriptome analysis links elevated DNA methylation to reduced demethylase gene expression (DME, ROS1, DML3). DNA methylation remodeling modulates fiber development through coordinated regulation of lipid metabolism, DNA replication, phosphatidylinositol signaling system and hormonal signaling pathways. Several key transcription factors, such as TCP14, HD1, HOX3, and MYB25-like, showed a strong correlation with DMRs, suggesting their regulation by DNA methylation. Furthermore, Multi-omics integration posits that DNA methylation may regulate genes related to fiber development, particularly those related to fatty acid biosynthesis and metabolism, ultimately influencing upland cotton fiber development. Analysis of genes highly correlated with changes in differentially methylated regions (DMRs) indicates DNA methylation can modulate the expression of KCS family genes, including KCS13, as well as KCRL1, thereby participating in the fatty acid elongation pathway.