Cotton Genomics and Genetics 2025, Vol.16, No.6, 269-277 http://cropscipublisher.com/index.php/cgg 272 variation alters the binding patterns of TFS such as GhFLZ, GhABF3, and GhRVE8, resulting in differences in activation under drought or hormonal treatment. The more you look, the more you will find that similar stress response elements are enriched in the promoters of genes such as NAC, ERF, P5CS, CKX, and VLN. (Deep & Pandey, 2024; Hamid et al., 2024). Ultimately, when the structure of the promoter changes, the set point of TF also changes accordingly, and this kind of influence is hard to ignore. 4.2 Gene expression differences caused by promoter variants Not every promoter variation will bring about significant effects, but the M-650 insertion/deletion in GhHSP70-26 can be regarded as a "positive example" - whether in the field or in transgenic experiments, this variation almost always corresponds to higher expression and stronger drought resistance. The research team tested using the GUS fusion gene and other reporter systems and it was clear that the expression levels of specific promoter fragments would change after stress or hormone treatment, with some enhanced and some inhibited (Guo et al., 2023). Similar situations can also be observed in the large families of NAC, ERF, P5CS, and CKX. The expression differences under different tissues and pressures are often associated with those minor variations in the promoter. Some allelic promoter types can make genes "more easily awakened" and more likely to respond immediately (Sun et al., 2018; Zafar et al., 2022). Of course, not all variations can lead to good results; some may even disrupt the original rhythm of expression. 4.3 The relationship between promoter variants and stress response pathways If the promoter only adjusts one gene, it's not that troublesome. The problem is that it affects the whole situation. Transcription factors such as WRKY, TCP, and triple helix proteins often recognize motifs such as W-box, TCP elements, GT-box, or MYB sites, and subsequently regulate a whole set of defense mechanisms including ABA pathways, osmotic regulation, and antioxidation (Wang et al., 2019; 2023). When variations occur around these sites, it is often not just the expression of one gene that is driven, but rather affects the activation rhythm of the entire stress pathway. These changes can sometimes enhance the drought resistance, salt tolerance or cold tolerance of cotton, but they may also make the response slow or excessive. In other words, although the promoter seems to be just a sequence segment, it actually influences the entire regulatory network behind it. Combining transcriptome and functional studies to decode these variations can provide a clearer reference path for subsequent targeted breeding. 5 Molecular Mechanisms of Promoter Variants 5.1 The impact of sequence diversity in promoter regions on gene expression regulation The promoter region of cotton is actually not "quiet" at all. Especially in gene families such as P5CS, CNGC, and CKX, cis-regulatory elements (CAREs) are densely packed. Elements like MYB, ABRE, and Cat-box that respond to hormonal and abiotic stresses can be seen everywhere (Zhao et al., 2022). Their existence determines how transcription factors bind and what patterns gene expression ultimately exhibits. What truly sets cotton apart in adverse conditions is the diversity of the promoters themselves - variations such as SNPS, indels, and structural rearrangements can all alter these binding sites, thereby changing gene activity. For instance, some haplotypes or EQTls have been confirmed to be directly linked to salt resistance or cold resistance (Hamid et al., 2024; Fang et al., 2025). However, not every mutation works. Whether it can "make a sound" depends on where it lands. It is precisely these regional differences that support the functional differentiation among the members of the genetic family and also give cotton the confidence to adapt to various complex environments. 5.2 The role of DNA methylation and histone modifications in promoter variants Not all expression differences can be attributed to the sequence itself; epigenetic factors can also be quite "troublesome". Mechanisms such as DNA methylation and histone modification often act as "switches" in stress responses. Changes in the methylation level of the promoter region can alter the openness of chromatin, thereby affecting whether transcription factors can approach, sometimes inhibiting expression and sometimes activating. In cotton, heat stress can cause an increase in histone markers such as H3K4me2 and H4K5ac, corresponding to enhanced expression of a batch of heat shock factors and proteins (Zhang et al., 2020). In addition, regulatory molecules such as JmjC demethylases and histone acetyltransferases (HATs) also change in expression under
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