Cotton Genomics and Genetics 2025, Vol.16, No.1, 29-38 http://cropscipublisher.com/index.php/cgg 29 Review and Progress Open Access Genomic Research on Key Loci for Cotton Disease and Insect Resistance Jiayi Wu, Xiaoyan Chen Modern Agriculture Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: xiaoyan.chen@cuixi.org Cotton Genomics and Genetics, 2025, Vol.16, No.1 doi: 10.5376/cgg.2025.16.0004 Received: 11 Jan., 2025 Accepted: 17 Feb., 2025 Published: 25 Feb., 2025 Copyright © 2025 Wu and Chen, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wu J.Y., and Chen X.Y., 2025, Genomic research on key loci for cotton disease and insect resistance, Cotton Genomics and Genetics, 16(1): 29-38 (doi: 10.5376/cgg.2025.16.0004) Abstract Cotton production is often threatened by various pests and diseases, resulting in significant yield losses and quality degradation. With the advent of advanced genomic technologies, resistance breeding has entered a new era of precision and efficiency. This study comprehensively analyzed the major cotton pathogens and pests and evaluated their combined effects on crop yield. We further detailed the genomic tools used to identify resistance loci, including genome-wide association studies (GWAS), transcriptomics, and pan-genomic approaches. Special emphasis was placed on key loci such as NB-LRR genes, Bt transgenic loci, and other metabolism- and signaling-related genes that contribute to resistance enhancement. This study also discussed functional validation strategies such as gene silencing, CRISPR/Cas-based editing, and marker-assisted selection in conjunction with practical applications. Through a case study on the field application of resistance loci, the successes and challenges of translating genomic discoveries into commercial cotton varieties were highlighted. Despite progress, the continued evolution of pests and pathogens, coupled with regulatory and technical challenges, necessitates continued innovation. This study highlights the importance of integrated genomics-driven strategies in ensuring sustainable cotton production and lays the foundation for future resistance breeding research. Keywords Cotton resistance breeding; Genomic loci; Disease and insect pests; CRISPR/Cas; Marker-assisted selection 1 Introduction Cotton is a very important crop in the global textile industry, but its yield is always affected by many pests and diseases, such as Verticillium wilt, Fusarium wilt, root-knot nematodes, whiteflies, aphids, and cotton bollworms (Li et al., 2016; Abdelraheem et al., 2019; Huo et al., 2023). These problems often reduce cotton yields and deteriorate fiber quality, posing great challenges to the sustainable cultivation of cotton. Common methods used in the past, such as spraying pesticides, are not very effective. Pesticides may not only be bad for the environment, but also easily cause pests to develop resistance. Therefore, people are now increasingly hoping to breed some cotton varieties that are resistant at the genetic level (Chen et al., 2021; Sun et al., 2023). Now, the development of genomics has greatly changed the way we identify key genes and functions related to cotton disease and pest resistance. High-throughput technologies such as genome-wide association studies (GWAS), transcriptome analysis, and CRISPR/Cas9 gene editing can help us discover quantitative trait loci (QTLs), potential resistance genes, and regulatory networks that control these resistance traits (Li et al., 2017; Zaidi et al., 2019; Zhang et al., 2023b; Wang et al., 2024). These methods can use resistance-related loci in breeding, which not only facilitates us to select resistance with markers, but also provides new ideas for us to develop broader-spectrum and more durable cotton resistance. This study not only summarizes some theories, but also wants to string together the new genomic technologies, key genes and practical methods currently used in cotton disease and insect resistance breeding. In fact, there have been many studies on how QTL is located and what molecular mechanisms are related to resistance. But what's interesting is that tools such as GWAS, transcriptome, and gene editing have shown quite different effects in different experiments, and specific problems need to be analyzed specifically. We will focus on picking out a few key sites to talk about their functions, and also talk about how these results are implemented in actual breeding. Although the focus is on cotton resistance, it is not limited to disease and insect prevention. Some new technologies and discoveries that have emerged in recent years have just opened up ideas for us to explore sustainable cotton cultivation-this is also a part we particularly want to emphasize.
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