Cotton Genomics and Genetics 2025, Vol.16, No.3, 126-136 http://cropscipublisher.com/index.php/cgg 132 hormone signals, and some specialize in membrane transport. These are considered to be more reliable candidate targets, especially when doing genetic engineering and molecular marker-assisted breeding (Sun et al., 2023). Of course, it is not just the protein itself that can "rise to the top". Some key genes that can regulate the removal of reactive oxygen species and maintain ion balance have also been functionally verified in subsequent studies. These genes have one thing in common - they are very stable in improving cotton's ability to resist stress, both in the laboratory and in the field. Having said that, using the results of proteomics in actual breeding is still a little way from "direct transformation". But these basic studies have slowly built bridges - allowing molecular-level information to truly serve cotton variety improvement. Especially in places where climate change is frequent and water and salt pressure is high, these results may bring some real changes. 8 Future Directions and Research Gaps 8.1 Integration with multi-omics approaches Proteomics can provide a lot of clues, but it is unrealistic to say that "it can help us understand how cotton resists stress". After all, information from one dimension is never enough. Now more and more studies tend to integrate "omics puzzle" - genome, transcriptome, metabolome, and even phenotypic data must be pulled together. Not every study can be well integrated at the beginning, especially in the early days of proteomics, most of which were single-line analysis. But now it is different, especially the development of single-cell proteomics technology, which gives us a "magnifying glass" to observe the responses of different cells under adversity, which is much more detailed and specific (Bawa et al., 2022). These different omics are put together not just for show. It does give us the opportunity to see how more key molecules work together, especially when cotton copes with drought or salt stress. Some studies have also begun to use these integrated ideas to screen varieties with stronger stress resistance. Although it is still in progress, the direction is clear (Ijaz et al., 2024; Choudhary et al., 2025). 8.2 Functional characterization of key proteins Although many stress-related proteins have been found, many of them are still unclear about how they work. We still need more genetic and biochemical experiments to further verify the true functions of these proteins (Xiao et al., 2020). Methods such as gene editing, overexpression or gene silencing, if combined with phenotypic analysis and physiological tests, can more clearly show whether these proteins can help cotton resist drought or salt (Li et al., 2015). In addition, functional studies are also very important to understand how proteins interact with each other and how post-translational modifications are regulated (Hu et al., 2015; Liu et al., 2019). 8.3 Translational potential in stress-resilient cotton The ultimate goal of proteomics research is to apply these molecular-level discoveries to actual cotton improvement. Now some stress-related proteins and pathways have been found, which can be used as molecular markers for breeding and as targets for transgenics (Perveen et al., 2025). But the problem is that the results in the laboratory must be verified in different environments and different cotton varieties before they can be truly transformed into the field (Zhou et al., 2014). Therefore, in the future, we must continue to integrate proteomic, transcriptomic and functional genomic data and combine them with modern breeding technology, so that we can select good varieties that are truly drought-resistant and salt-resistant and adapt to future climates. 9 Concluding Remarks Proteomics studies have given us a clearer understanding of how cotton responds to drought and salt stress. These studies have found that in stress-resistant cotton varieties, many proteins involved in photosynthesis, antioxidants, defense, metabolic regulation, and stress signaling are expressed more. In varieties that are more susceptible to stress, protein expression in these pathways tends to decrease. Whether it is drought or salt stress, energy metabolism, ion transport, hormone signaling, and detoxification mechanisms in plants will change. Although some reactions are common, each stress also has its own unique proteins and reaction pathways. It is not objective to say that proteomics has not brought us anything new in recent years. It has indeed helped us find a number of key proteins and candidate genes related to stress resistance. This information is a valuable resource for breeding or genetic engineering, especially in issues such as "who to choose and who not to choose", the targets are much clearer.
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