Cotton Genomics and Genetics 2025, Vol.16, No.3, 126-136 http://cropscipublisher.com/index.php/cgg 128 genes, cotton does behave differently-the germination rate is higher, the roots are longer, and the oxidative damage is less (Zhang et al., 2023). In addition to genes, proteins such as LEA are also present. They can stabilize the internal state of cells in a high-salt environment and can be regarded as the "balancer" of cotton. 2.3 Combined stress scenarios The fields are not so simple. Drought is coming, and salinity may not be far behind. These two stresses often come together, doubling the pressure and causing more trouble to cotton. But cotton is not completely helpless. Studies have found that signaling pathways such as MAPK cascades (such as GhMAP4K13, GhMAPKK5, and GhMAPK3) are activated simultaneously under two stresses (Jian et al., 2024). This shows that they may follow the same "procedure" when responding to different stresses. Transcription factors GhABF3 and GbTCP4, as well as stress proteins such as LEA3, are actively expressed in both stress environments. They help cotton retain water and resist oxidation, and can also regulate many stress-related genes (Wang et al., 2022). Combining proteomic and transcriptomic data, scientists have found many key points that allow cotton to "shoot from both sides" (Bano et al., 2022; Ahmad et al., 2024). These achievements have also laid a lot of foundations for future breeding and genetic engineering. 3 Proteomics Approaches in Stress Response Studies 3.1 Techniques in proteomic analysis There are two common methods for studying protein changes in plants under stress: gel-based and non-gel-based methods. Two-dimensional electrophoresis (2-DE) and two-dimensional difference gel electrophoresis (2D-DIGE) are commonly used in gel-based methods, which separate proteins based on their isoelectric point and molecular weight. There are more non-gel-based methods, such as isotope-coded affinity tags (ICAT), isotope tag quantification (iTRAQ), and various mass spectrometry platforms, such as liquid chromatography-mass spectrometry (LC-MS) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). These techniques can quickly analyze many proteins with high sensitivity and quantification (Jan et al., 2022). These techniques help us more easily find proteins whose expression changes under drought or salt stress, and can also more accurately analyze their quantity (Choudhary et al., 2025). 3.2 Protein identification and bioinformatics After protein separation and detection, researchers generally use mass spectrometry to determine the type of protein. After that, bioinformatics tools are used to analyze the data. Through functional network and pathway analysis, differently expressed proteins can be classified into categories, and their roles in plant adaptation to adversity can be clarified, such as participating in photosynthesis, sugar metabolism, signal transduction, and defense processes (Alaiya et al., 2024). Bioinformatics tools can also integrate proteomic data with other omics data, so that we can better understand the overall response of plants to stress (Guo et al., 2021). 3.3 Challenges and limitations Although proteomics has achieved a lot of results in plant stress research, there are still many challenges. First of all, the protein database of many crops is still incomplete, and there are many genetic differences between varieties, and the types of proteins are also very complex, which makes it difficult to fully identify and analyze proteins (Nesatyy and Suter, 2007). In addition, some technical problems are also common, such as insufficient efficiency of protein extraction, large differences in protein content, and unstable experimental results, which will affect the reliability of research results (Hossain et al., 2013). Another important issue is that in order to accurately explain the changes in proteins under stress, very rigorous experiments need to be designed and subsequent verification needs to be done (Kosováet al., 2011). In order to truly apply the results of proteomics to crop improvement, these problems must be solved step by step. 4 Key Proteomic Findings in Drought Stress Response 4.1 Stress perception and signal transduction When drought strikes, cotton does not "give up" all at once. It will first sense changes in the environment and then slowly respond. However, this "perception" process is not simple at all. Some proteins, such as signal receptors distributed on the cell membrane and some proteins called molecular chaperones, will be the first to "perceive" the
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