Analysis of the Regulatory Network of Cotton Fiber Development Based on Transcriptomics and Epigenomics

Cotton fiber development represents a distinctive model of plant cell elongation and differentiation. In this study, we systematically analyzed the regulatory network underlying cotton fiber development by integrating transcriptomic and epigenomic data. Temporal expression profiling revealed stage-specific gene expression during fiber initiation, elongation, and maturation, with key transcription factors such as MYB, NAC, and bHLH playing pivotal roles. Non-coding RNAs including lncRNAs and miRNAs were also identified as important regulators of post-transcriptional gene silencing. Epigenomic analyses uncovered dynamic DNA methylation patterns and histone modifications correlating with fiber-specific gene activity, alongside changes in chromatin accessibility and 3D genome architecture during development. Through multi-omics integration, we constructed regulatory networks highlighting co-expression modules, signaling pathways, and environmental responses, and validated these networks using a case study on Gossypium hirsutum , focusing on the GhMYB25-like-centered cascade. Our results underscore the complexity of gene regulation in fiber development and suggest that advanced technologies such as single-cell omics and CRISPR-based validation will further refine our understanding and enable molecular breeding strategies to enhance cotton fiber quality and yield.