Cotton Genomics and Genetics 2025, Vol.16, No.3, 107-116 http://cropscipublisher.com/index.php/cgg 107 Research Insight Open Access Analysis of the Regulatory Network of Cotton Fiber Development Based on Transcriptomics and Epigenomics ZhenLi Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: zhen.li@hibio.org Cotton Genomics and Genetics, 2025, Vol.16, No.3 doi: 10.5376/cgg.2025.16.0011 Received: 01 Mar., 2025 Accepted: 10 Apr., 2025 Published: 01 May, 2025 Copyright © 2025 Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li Z., 2025, Analysis of the regulatory network of cotton fiber development based on transcriptomics and epigenomics, Cotton Genomics and Genetics, 16(3): 107-116 (doi: 10.5376/cgg.2025.16.0011) Abstract 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. Keywords Cotton fiber development; Transcriptomics; Epigenomics; Gene regulatory network; Multi-omics integration 1 Introduction The development of cotton fiber is a typical example of the elongation of a single plant cell, which provides a good research object for us to understand how cells grow, how they differentiate, and how cell walls are formed. The whole process can be divided into several different stages, such as how fiber cells start, how they elongate rapidly, and how secondary cell walls are formed later. These stages are affected by many genetic and epigenetic factors, which affect the quality and yield of cotton fiber (Li et al., 2020; Prasad et al., 2022; Bao et al., 2023). The process of controlling fiber development is a very complex regulatory system, which includes various transcription factors, gene modules, and signal transduction pathways. They work together to regulate the expression of thousands of genes and metabolites, which will affect traits such as fiber length and strength. Recent studies have shown that coordination between subgenomes and some special regulatory regions play a major role in fiber initiation and elongation, while non-coding RNA and epigenetic modifications also affect gene expression (You et al., 2023; Liu et al., 2024; Wang et al., 2024; Yang et al., 2024). In the past, we did not have a detailed understanding of gene expression and chromatin changes during cotton fiber development. Now the situation is different. High-throughput transcriptome and epigenomic technologies have opened up this field. Whether it is RNA sequencing, eQTL positioning, or DNA methylation and chromatin accessibility analysis, once these tools are used together, we can see a lot more. For example, some previously unnoticed regulatory factors, transcription factors, and epigenetic markers related to fiber traits can now be identified. Interestingly, genetic variation and epigenetic variation do not work alone. They may play their own roles, or they may restrain or cooperate with each other at certain stages, and finally show the diversity of fiber phenotypes. For breeding, this is a rare breakthrough (Xiong et al., 2024; Zhao et al., 2024). Our research is not to discover any new mechanism from scratch, but to string together the existing fragmented knowledge. The focus is on integration, not just telling a "omics" story, but combing the research results related to
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