Cotton Genomics and Genetics 2025, Vol.16, No.1, 29-38 http://cropscipublisher.com/index.php/cgg 35 public acceptance is also a hurdle. Many people still have concerns about genetic modification, coupled with concerns about biosafety, and there is a lot of resistance to the implementation of new varieties (Khan et al., 2023a). To break the deadlock, technology alone is not enough, but also needs to be accompanied by clear and transparent policies. Concepts such as "genetically modified cleanliness" are worth promoting (Khan et al., 2023b). In addition, cooperation among scientists, companies, and policymakers is also necessary. Only through real collaboration can these cutting-edge research be turned into disease-resistant and insect-resistant cotton varieties that can be grown in the fields and that farmers are willing to use. 8 Concluding Remarks The study of the genetic basis of cotton resistance to pests and diseases is not new, but progress has indeed been faster in recent years. The well-known gene cluster NB-LRR is still the focus of research, but there are also some new discoveries, such as the double TIR structural protein, which is very "intense" in triggering immune responses. Of course, not all data can show these differences at the beginning. It is necessary to combine phenotypic and genomic information to slowly piece together the outline of the resistance-related spectrum. Analysis methods such as GWAS, TWAS, and meta-QTL have their own focuses and are also useful. However, data alone is not enough. Some look like candidate genes, but they are not verified in the end. Scientists have done a lot of experiments through gene silencing and overexpression, and fortunately, a group of key genes that play a role in cotton defense have been confirmed. In addition, wild cotton and some old local varieties are not so easy to appear in the mainstream research field of vision, but their genetic resources have helped a lot and broadened the available resistance gene pool. These "non-mainstream" materials can sometimes bring unexpected breakthroughs. At present, the discovery and verification of these resistance sites have begun to play a role in breeding. Through molecular marker-assisted selection (MAS) and genomic selection (GS) methods, researchers are using these resistance sites to breed more disease-resistant cotton varieties, such as varieties that are resistant to Verticillium wilt, Fusarium wilt and cotton leaf curl virus. In actual breeding projects, the use of high-quality alleles and multiple QTL clusters has indeed made cotton perform better in the field and maintain resistance longer. These technologies provide breeders with more accurate tools to help breed adaptable cotton varieties more quickly. In order to truly turn these genomic studies into useful results, joint efforts are needed from all sides. There must be continuous cooperation between academic research, breeding work and enterprises to turn laboratory discoveries into results in the field. In the face of the ever-changing problems of pathogens and pests, it is also necessary to deal with the balance between genetic traits, and also solve some policy and management problems. Combining advanced genomic technologies, functional verification methods and actual field breeding is the key to promoting sustainable cotton production, so as to ensure that crops have long-term resistance. Acknowledgments We thank the anonymous reviewers for their careful review of the draft and their specific feedback helped us improve the quality of the manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Abdelraheem A., Elassbli H., Zhu Y., Kuraparthy V., Hinze L., Stelly D., Wedegaertner T., and Zhang J., 2019, A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton, Theoretical and Applied Genetics, 133(2): 563-577. https://doi.org/10.1007/s00122-019-03487-x Abdelraheem A., Liu F., Song M., and Zhang J., 2017, A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton, Molecular Genetics and Genomics, 292(6): 1221-1235. https://doi.org/10.1007/s00438-017-1342-0 Arora R., Kataria S., and Singh P., 2017, Breeding for insect resistance in cotton: advances and future perspectives, In: Arora R., and Sandhu S., (eds), Breeding Insect Resistant Crops for Sustainable Agriculture, Springer, Singapore, pp.265-288. https://doi.org/10.1007/978-981-10-6056-4_9
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