Cotton Genomics and Genetics 2025, Vol.16, No.4, 184-191 http://cropscipublisher.com/index.php/cgg 189 7 Concluding Remarks Recent studies have found that cotton’s natural immune system is actually quite complex. It has several layers of defense mechanisms. Some disease-resistant genes react very quickly, such as a transcription factor called WRKY41, which can regulate phenylpropanoid metabolism and drive subsequent defense steps to help cotton resist pathogens such as Verticillium dahliae. Studies have also found that cotton's immune sensors work with the immune response triggered by pathogens, and some special receptor kinases, such as GbEIR5A/D, can enhance this defense response. In addition, proteins such as SR45a can cause different splicing versions of the same gene, which can also affect cotton's immunity, with some varieties performing well and others not so well. Plant hormones (such as salicylic acid, jasmonic acid, and ethylene) also participate in regulating immunity, and cotton must find a balance between "growing fast" and "strong disease resistance." Despite these advances, there are still some challenges. We still don't understand the disease resistance mechanisms of some cotton varieties, and there are not many disease-resistant genes that can really be used for breeding. In addition, cotton is polyploid, and its genome itself is quite complex, with many variations and splicing methods, which makes research more difficult. To transfer the disease resistance of wild cotton to cultivated cotton, genetic barriers or unwanted traits are often encountered. In addition, many experiments are done under laboratory conditions, and they have to be tried repeatedly in real fields to see if the results are reliable. In the future, more large-scale genome association analysis can be done to find more disease-resistant genes. Wild cotton resources can also be used to find new useful traits. If high-throughput phenotypic analysis, gene editing technology (such as CRISPR/Cas9) and large-scale genetic research can be combined, varieties with strong disease resistance can be bred more quickly. At the same time, we must continue to study how gene expression is regulated, especially complex mechanisms such as alternative splicing. This will allow us to have a more comprehensive understanding of the cotton immune system and make it easier to breed good varieties that can adapt to different diseases and have more stable resistance. Acknowledgments I am grateful to Dr. Z. Xu for his assistance with the serious reading and helpful discussions during the course of this work. 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 Bihani D., Khuman A., and Chaudhary B., 2024, Comparative Transcriptomics reveals novel spatial gene expression profiles in cotton (Gossypium hirsutumL.) under herbivory and drought stress, Journal of Plant Growth Regulation, 43(11): 4018-4037. https://doi.org/10.1007/s00344-024-11362-3 Bjornson M., Pimprikar P., Nürnberger T., and Zipfel C., 2020, The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity, Nature Plants, 7(5): 579-586. https://doi.org/10.1038/s41477-021-00874-5 Bu B., Qiu D., Zeng H., Guo L., Yuan J., and Yang X., 2014, A fungal protein elicitor PevD1 induces Verticillium wilt resistance in cotton, Plant Cell Reports, 33(3): 461-470. https://doi.org/10.1007/s00299-013-1546-7 Chang B., Zhao L., Feng Z., Wei F., Zhang Y., Zhang Y., Huo P., Cheng Y., Zhou J., and Feng H., 2023, Galactosyltransferase GhRFS6 interacting with GhOPR9 involved in defense against Verticillium wilt in cotton, Plant Science, 328: 111582. https://doi.org/10.1016/j.plantsci.2022.111582 De Jong E., and Bosco A., 2021, Unlocking immune-mediated disease mechanisms with transcriptomics, Biochemical Society Transactions, 49(2): 705-714. https://doi.org/10.1042/BST20200652 Gao L., Pei Y., Wang P., Cen Y., Yan X., and Hou Y., 2024, Cotton SNARE complex component GhSYP121 regulates salicylic acid signaling during defense against Verticillium dahliae, Journal of Cellular Physiology, 239(11): e31329. https://doi.org/10.1002/jcp.31329 Han L., Li Y., Wang F., Wang W., Liu J., Wu J., Zhong N., Wu S., Jiao G., Wang H., and Xia G., 2019, The cotton apoplastic protein CRR1 stabilizes chitinase 28 to facilitate defense against the fungal pathogen Verticillium dahliae, The Plant Cell, 31(2): 520-536. https://doi.org/10.1105/tpc.18.00390
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