Cotton Genomics and Genetics 2025, Vol.16, No.6, 269-277 http://cropscipublisher.com/index.php/cgg 270 This study will systematically explore the regulatory role of promoter variations in cotton stress-responsive genes and review the current understanding of promoter structures and their impact on gene regulation under stress conditions. Identify the key promoter variations related to enhancing the stress resistance of cotton; Evaluate the potential of these variations to improve cotton through molecular breeding and genetic engineering. By clarifying the mechanism by which promoter variations regulate the expression of stress response genes, this study aims to provide a theoretical basis for breeding cotton varieties with stronger stress resistance, thereby supporting sustainable cotton production and economic stability while addressing environmental challenges. 2 Structure and Function of Promoters 2.1 Definition and basic structure of promoters The promoter is not a strange new concept. It is a fragment on DNA close to the starting point of a gene, like a switch, used to regulate whether the gene is "turned on". Whether RNA polymerase and various transcription factors can "find the door" lies in this region. However, this structure is not simply a single board; it is often composed of several areas: In the core area in the middle, "classic elements" such as the TATA box and the CAAT box can often be seen. There are also proximal and distal control areas embedded with various CRE components, which are responsible for dealing with different TFs. No matter which section it is, if any one is missing, the transcription starting point may not be accurately identified, let alone smoothly transferred. 2.2 The role of promoters in gene transcription regulation Many people know that transcription initiation relies on RNA polymerase, but to "invite" it to the right position, the promoter is the key. This place is not only its stopover point, but also a venue for the collection of various transcription factors (Khan et al., 2023). The CRE element in the promoter is like an "interface" prepared for different signals. Who binds it, how it binds it, and for how long, these determine whether the gene is activated throughout the day or in phases (Cai et al., 2020). The expression pattern sometimes comes from organizational specificity, sometimes it only becomes active when triggered by the external environment, and even can be artificially designed to be activated whenever one wants. Also, don't underestimate the sequence structure of the promoter. Details such as GC content and motif arrangement often affect transcriptional efficiency and accuracy (Bansal et al., 2014). In crops like cotton that often have to cope with environmental changes, the regulatory power of promoters is the most important link. 2.3 Types and sources of promoter variants The promoter sequence is not static; it undergoes various variations. These variations sometimes result from the accumulation of natural selection, sometimes are induced mutations by humans, or may be "assemblies" designed in the laboratory (Bao et al., 2020). For instance, some promoters are inherently "all-weather", like the CaMV35S, which can be expressed by any organization. However, there are also some that are more "selective", only lighting up at the leaves, roots or a certain developmental stage. There is another category that only speaks up when there is something to do. Once stimulated by the environment or hormones, they will be activated (Kummari et al., 2020). Synthetic promoters are more like "customized products", allowing researchers to combine various components as needed to achieve more precise control. There are also many forms of variation, ranging from simple SNPS, insertions/deletions to large fragment rearrangements, and even artificial assembly of new components. These changes may not only affect the binding ability of TF, but also alter the "character" of the entire promoter, thereby making the gene expression stronger, weaker or responding faster. There have been many examples of this in crops such as cotton. 3 Characteristics and Function of Cotton Stress-Responsive Genes 3.1 Classification of cotton stress-responsive genes Over the years, with more research, it has been found that the types of genes mobilized by cotton in response to stress are indeed quite numerous. In addition to the well-known transcription factors, such as DREB, MYB, NAC, bZIP, WRKY and GARP families (Wang et al., 2024), there are also some "familiar faces" involved in regulating metabolism, synthesis or defense. Such as SAMS, LEA, CDKs, PLA1, RF2 and P5CS, etc. (Figure 1) (Gu et al., 2023; Fang et al., 2025). The specific functions of these genes are also quite scattered. Some are responsible for
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