Cotton Genomics and Genetics 2025, Vol.16, No.1, 39-47 http://cropscipublisher.com/index.php/cgg 45 Of course, these studies cannot be implemented by "omics" alone. What really promotes the emergence of "super cotton" varieties is the deep combination of comparative genomics and breeding technology. These new cottons show not only longer fibers or higher yields, but also better resistance to challenges such as drought, pests and diseases. As for the genetic basis behind it, pan-genome and large-scale genetic surveys provide many new clues. Some key gene markers and favorable alleles have begun to be identified, opening up a new situation for germplasm improvement. At a time when the cotton industry is facing climate pressure and sustainable development pressure, these technologies are not icing on the cake, but a rigid need. It can be said that this stage is a new starting point for cotton research and breeding in the true sense. Comparative genomics is not just a toolkit, but more like a central system that connects traditional breeding with modern technology. Next, what needs to be done is not "whether it is useful" but "how well it is used" - genome assembly must be more accurate, and the integration between multi-omics must also keep up. Breeding methods can no longer follow the old path, and we must dare to try new paths. And for these ideas to be truly implemented, no one can bypass the collaboration between scientific research teams, data sharing and communication mechanisms. Only in this way will these technologies not remain in papers, but actually land in cotton fields and support the future of cotton. Acknowledgments The author thanks the anonymous peer reviewers for their time and comments that helped improve the manuscript. 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 Ashraf J., Zuo D., Wang Q., Malik W., Zhang Y., Abid M., Cheng H., Yang Q., and Song G., 2018, Recent insights into cotton functional genomics: progress and future perspectives, Plant Biotechnology Journal, 16(3): 699-713. https://doi.org/10.1111/pbi.12856 Billings G., Jones M., Rustgi S., Bridges W., Holland J., Hulse-Kemp A., and Campbell B., 2022, Outlook for implementation of genomics-based selection in public cotton breeding programs, Plants, 11(11): 1446. https://doi.org/10.3390/plants11111446 Chang X., He X., Li J., Liu Z., Pi R., Luo X., Wang R., Hu X., Lu S., Zhang X., and Wang M., 2023, High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres, Plant Communications, 5(2): 100722. https://doi.org/10.1016/j.xplc.2023.100722 Chen Z., Sreedasyam A., Ando A., Song Q., De Santiago L., Hulse-Kemp A., Ding M., Ye W., Kirkbride R., Jenkins J., Plott C., Lovell J., Lin Y., Vaughn R., Liu B., Simpson S., Scheffler B., Wen L., Saski C., Grover C., Hu G., Conover J., Carlson J., Shu S., Boston L., Williams M., Peterson D., Mcgee K., Jones D., Wendel J., Stelly D., Grimwood J., and Schmutz J., 2020, Genomic diversifications of five Gossypiumallopolyploid species and their impact on cotton improvement, Nature Genetics, 52(5): 525-533. https://doi.org/10.1038/s41588-020-0614-5 Fang L., Wang Q., Hu Y., Jia Y., Chen J., Liu B., Zhang Z., Guan X., Chen S., Zhou B., Mei G., Sun J., Pan Z., He S., Xiao S., Shi W., Gong W., Liu J., Ma J., Cai C., Zhu X., Guo W., Du X., and Zhang T., 2017, Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits, Nature Genetics, 49(7): 1089-1098. https://doi.org/10.1038/ng.3887 He S., Sun G., Geng X., Gong W., Dai P., Jia Y., Shi W., Pan Z., Wang J., Wang L., Xiao S., Chen B., Cui S., You C., Xie Z., Wang F., Sun J., Fu G., Peng Z., Hu D., Wang L., Pang B., and Du X., 2021, The genomic basis of geographic differentiation and fiber improvement in cultivated cotton, Nature Genetics, 53(6): 916-924. https://doi.org/10.1038/s41588-021-00844-9 Hu Y., Chen J., Fang L., Zhang Z., Ma W., Niu Y., Ju L., Deng J., Zhao T., Lian J., Baruch K., Fang D., Liu X., Ruan Y., Rahman M., Han J., Wang K., Wang Q., Wu H., Mei G., Zang Y., Han Z., Xu C., Shen W., Yang D., Si Z., Dai, F., Zou L., Huang F., Bai Y., Zhang Y., Brodt A., Ben-Hamo H., Zhu X., Zhou B., Guan X., Zhu S., Chen X., and Zhang T., 2019, Gossypium barbadense and Gossypium hirsutumgenomes provide insights into the origin and evolution of allotetraploid cotton, Nature Genetics, 51(4): 739-748. https://doi.org/10.1038/s41588-019-0371-5 Ijaz B., Zhao N., Kong J., and Hua J., 2019, Fiber quality improvement in upland cotton (Gossypium hirsutumL.): quantitative trait loci mapping and marker assisted selection application, Frontiers in Plant Science, 10: 1585. https://doi.org/10.3389/fpls.2019.01585
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