Cotton Genomics and Genetics 2025, Vol.16, No.3, 107-116 http://cropscipublisher.com/index.php/cgg 108 transcriptomics and epigenomics together. What we want to understand more is which molecular mechanisms are at work during the fiber initiation and elongation process, which genes are the key control points, and which pathways are worth paying attention to. Of course, we are not just at the level of understanding. Later we also talked about whether these mechanisms can be used in practice, for example, by regulating certain specific genes or epigenetic sites, is it possible to make cotton fibers longer, stronger, and have a higher yield. 2 Transcriptomic Insights into Fiber Development 2.1 Temporal expression profiling of key genes during fiber initiation, elongation, and maturation The development of cotton fiber is a complicated process from initiation to maturity. Now that the technical conditions are good, especially the development of spatial transcriptome and single-cell transcriptome, researchers can finally "separate and look", and analyze the gene expression in the development process in more detail by time period and cell. Not all genes are the same. Some "emerge" in the early stage, such as SVB, SVBL, DOX2, KCS19.4, and BEE3, which are closely related to the formation of cell walls (Figure 1) (Tuttle et al., 2015; Sun et al., 2025). But when the fiber transitions from the elongation stage to the synthesis of the secondary cell wall, the overall pattern of gene expression changes again. In other words, if the sampling time is not accurate, many important regulatory details will not be seen. Figure 1 a Spatiotemporal expression pattern of DOX2, SBT4.14, GH3.6.2, and SWEET15, the marker genes of integument cells based on spatial transcriptomics. The color intensity indicates the relative transcript level of each marker gene. b Nitro-blue tetrazolium-stained RNA ISH shows the spatiotemporal expression patterns of DOX2, SBT4.14, GH3.6.2, and SWEET15. No probe was used as a blank control. The positive cells are stained bluish-violet. The data shown are representative images of three independent experiments with similar results. OI, outer integument; II, inner integument; N, nucellus. Red arrows indicate fiber cells. Scale bars, 50 μm in - 1 DPA and 0 DPA; 100 μm in 3 DPA (Adopted from Sun et al., 2025) 2.2 Identification of transcription factors (e.g., MYB, NAC, bHLH) regulating fiber traits When it comes to the "commanders" who control fiber traits, transcription factors are definitely the highlight. MYB, NAC, and bHLH are often seen in research. Among them, GhMML3_A12 is a representative, which has been shown to be directly related to cotton fiber formation (Zhang et al., 2022). But we can't just focus on this one. Some other transcription factors are also closely related to specific gene modules at certain developmental stages, which in turn affect the quality and yield of the fiber. How do they work? Basically, they regulate cell elongation,
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