Cotton Genomics and Genetics 2025, Vol.16, No.3, 126-136 http://cropscipublisher.com/index.php/cgg 133 Of course, proteomics data alone is not enough. Looking at it alone is always like seeing only half of a picture. So later everyone began to try to piece it together with the transcriptome. What was the result? Some key regulatory nodes and signal pathways have gradually surfaced. These clues have indeed played a guiding role in subsequent variety improvement. Not to mention that some new technologies have emerged, such as proteomic analysis at the single-cell level, and more sophisticated quantitative methods, which allow us to "see smaller" and "see more accurately". Although these methods are still under development, the trend is already clear - in the future, cotton stress-resistant breeding may rely more on these molecular-level "micro-operations". Integrating proteomics and other omics methods, coupled with functional verification of key proteins, is the key to turning experimental results into practical applications. In the future, continued research in this area will accelerate the pace of breeding stress-resistant cotton, and will also help cotton maintain stable yields and sustainable development in the face of increasingly severe natural environments. Acknowledgments I would like to express my heartfelt gratitude to Ms. Xuan for reviewing the draft of this paper and providing suggestions for improvement, which made the structure and content of the paper clearer and more rigorous. I would also like to thank the two anonymous peer reviewers for their professional reviews and insightful comments, which have helped me further enhance the quality and academic rigor of this paper. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Ahmad A., Sajjad M., Sadau S., Elasad M., Sun L., Quan Y., Wu A., Lian B., Wei F., Wu H., Chen P., Fu X., Ma L., Wang H., Wei H., and Yu S., 2024, GhJUB1_3-At positively regulate drought and salt stress tolerance under control of GhHB7, GhRAP2-3 and GhRAV1 in cotton, Physiologia Plantarum, 176(5): e14497. https://doi.org/10.1111/ppl.14497 Alaiya A., Alharbi B., Shinwari Z., Rashid M., Albinhassan T., Bouchama A., Alwesmi M., Mohammad S., and Malik S., 2024, Proteomics analysis of proteotoxic stress response in in-vitro human neuronal models, International Journal of Molecular Sciences, 25(12): 6787. https://doi.org/10.3390/ijms25126787 Athar H., Zulfiqar F., Moosa A., Ashraf M., Zafar Z., Zhang L., Ahmed N., Kalaji H., Nafees M., Hossain M., Islam M., Sabagh E., and Siddique K., 2022, Salt stress proteins in plants: an overview, Frontiers in Plant Science, 13: 999058. https://doi.org/10.3389/fpls.2022.999058 Bano N., Fakhrah S., Mohanty C., and Bag S., 2022, Transcriptome meta-analysis associated targeting hub genes and pathways of drought and salt stress responses in cotton (Gossypium hirsutum): a network biology approach, Frontiers in Plant Science, 13: 818472. https://doi.org/10.3389/fpls.2022.818472 Bawa G., Liu Z., Zhou Y., Fan S., Ma Q., Tissue D., and Sun X., 2022, Cotton proteomics: dissecting the stress response mechanisms in cotton, Frontiers in Plant Science, 13: 1035801. https://doi.org/10.3389/fpls.2022.1035801 Chen L., Sun H., Kong J., Xu H., and Yang X., 2020, Integrated transcriptome and proteome analysis reveals complex regulatory mechanism of cotton in response to salt stress, Journal of Cotton Research, 4(1): 11. https://doi.org/10.1186/s42397-021-00085-5 Choudhary R., Ahmad F., Kaya C., Upadhyay S., Muneer S., Kumar V., Meena M., Liu H., Upadhyay H., and Seth C., 2025, Decrypting proteomics, transcriptomics, genomics, and integrated omics for augmenting the abiotic, biotic, and climate change stress resilience in plants, Journal of Plant Physiology, 305: 154430. https://doi.org/10.1016/j.jplph.2025.154430 Deeba F., Pandey A., Ranjan S., Mishra A., Singh R., Sharma Y., Shirke P., and Pandey V., 2012, Physiological and proteomic responses of cotton (Gossypium herbaceum L.) to drought stress, Plant Physiology and Biochemistry, 53: 6-18. https://doi.org/10.1016/j.plaphy.2012.01.002 Ding R., Li J., Wang J., Li Y., Ye W., Yan G., and Yin Z., 2024, Molecular traits of MAPK kinases and the regulatory mechanism of GhMAPKK5 alleviating drought/salt stress in cotton, Plant Physiology, 196(3): 2030-2047. https://doi.org/10.1093/plphys/kiae415 Du C., Li H., Liu C., and Fan H., 2020, Understanding of the postgerminative development response to salinity and drought stresses in cucumber seeds by integrated proteomics and transcriptomics analysis, Journal of Proteomics, 232: 104062. https://doi.org/10.1016/j.jprot.2020.104062
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