Cotton Genomics and Genetics 2025, Vol.16, No.6, 269-277 http://cropscipublisher.com/index.php/cgg 273 stress conditions, and their own promoters are also rich in stress response elements. These modifications can change at any time. They are not only flexible but also reversible, providing cotton with an operational space to quickly respond to sudden environmental changes. 5.3 Interaction between transcription factors and promoter variants A minor variation on the promoter can sometimes precisely trigger an entire regulatory chain, especially at the binding sites of transcription factors. TFS such as MYB, bZIP, NAC, and WRKY are the "main force" in the cotton stress response. Whether they can successfully bind to the promoter region often depends on whether these sequences have mutations (Naresh et al., 2024). Studies have found that specific promoter haplotypes do indeed alter the efficiency of TF binding and further affect the expression patterns of related genes, such as directly influencing the salt tolerance of cotton (Lin and Zhu, 2024). Looking deeper, the methylation state of DNA is also involved. Some TFS are highly sensitive to methylation, and some are even directly excluded (Heberle & Bardet, 2019). Therefore, promoter variations, TF binding, and methylation modifications are constantly interacting and in real-time dynamic state. This coordination enables the gene expression of cotton to remain "online" in complex environments. 6 Case Study: Promoter Variants in Specific Cotton Stress-Responsive Genes 6.1 Variants in the AtDREB1A promoter and salt tolerance The DREB family has long made an appearance in various studies on responses to coercion, and GhDREB1A is no exception. Its expression pattern under salt stress has been confirmed to be related to salt tolerance. In fact, not only cotton, but also in many crops, once the expression level of DREB genes is increased, the related downstream stress response genes will also become active, thereby making the plants more tolerant of salt. However, the promoter of DREB itself is not simple either - it usually contains multiple cis-regulatory elements related to stress and hormones, becoming one of the key nodes in the regulatory network. A few years ago, there were studies suggesting that CRISPR/Cas9 could be used to directly target these promoters for targeted modification, with the aim of achieving more precise expression (Mahmood et al., 2019). Meanwhile, GWAS and transcriptome data have increasingly linked DREB genes to the salt tolerance of cotton, especially in those salt-tolerant varieties, where the expression levels are more pronounced (Wang et al., 2023; Li et al., 2025). 6.2 Variants in the GhHSP70 promoter and heat tolerance In terms of heat resistance, the GhHSP70-26 promoter also performs quite "representative". For instance, some studies have found that there is a 22 bp deletion (M-1590-Del22, Hap2) at the -1590 bp site upstream of its promoter region. This variation leads to upregulation of gene expression under heat stress, resulting in stronger heat tolerance. Even better, this kind of variation is not only manifested in cotton - when applied to Arabidopsis thaliana, plants with the Hap2 promoter also showed higher activity after heat induction and ABA treatment, indicating that the function of this site is indeed solid (Guo et al., 2023). Interestingly, this natural variation can also serve as a molecular marker for breeding screening, and its practicality is not low. In addition, an insert-deletion variation (M-650-In360) also occurred in another region of the gene promoter (-650 bp). This structural difference is also associated with the improvement of drought resistance, which once again indicates from the side that the promoter variation is not an "embellishment", but a part of regulation. 6.3 Variants in the GhERF1 promoter and drought tolerance When it comes to drought response, genes like GhERF1 in the ERF family cannot be avoided. Its promoter structure is already quite rich, with a dense array of stress response elements inside, and the expression regulation is also rather complex. In arid environments, the expression of such genes will be controlled layer by layer. According to the results of transcriptome and co-expression network analysis, ERF genes are often upregulated in drought-tolerant cotton strains. The higher the expression, the more "resilient" the plants are in water-deficient environments (Figure 2) (Mahmood et al., 2019; Wang et al., 2023). Given this, it is no wonder that there are now studies attempting to enhance the expression of GhERF1 by modifying the promoter structure - after all, this approach seems more stable and easier to apply to actual breeding.
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