Cotton Genomics and Genetics 2025, Vol.16, No.3, 137-147 http://cropscipublisher.com/index.php/cgg 137 Review Article Open Access Molecular Response Mechanism of Cotton to Verticillium Wilt and Fusarium Wilt Xiaojing Yang, Tianze Zhang Modern Agriculture Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: tianze.zhang@cuixi.org Cotton Genomics and Genetics, 2025, Vol.16, No.3 doi: 10.5376/cgg.2025.16.0014 Received: 01 Apr., 2025 Accepted: 11 May, 2025 Published: 01 Jun., 2025 Copyright © 2025 Yang and Zhang, 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: Yang X.J., and Zhang T.Z., Molecular response mechanism of cotton to verticillium wilt and fusarium wilt, Cotton Genomics and Genetics, 16(3): 137-147 (doi: 10.5376/cgg.2025.16.0014) Abstract Cotton is an important fiber crop worldwide and is threatened by soil-borne fungal pathogens such as Verticillium dahliae and Fusarium oxysporum, which cause Verticillium wilt and Fusarium wilt, respectively. This study systematically explored the molecular responses of cotton to these two devastating diseases, aiming to lay the foundation for improved disease resistance strategies. We first outlined the biological characteristics, infection mechanisms, and global distribution of the pathogens, and then discussed in detail the innate immune response of cotton, including pattern recognition receptors, phytohormone-mediated pathways, and effector-triggered immune responses. We further emphasized the changes in the transcriptome and proteome during infection, as well as the functional roles of resistance genes, transcription factors, and secondary metabolites. We also discussed the recent progress in functional genomics and gene editing tools such as CRISPR/Cas in the discovery and validation of resistance genes, as well as the overlapping molecular responses triggered by the two pathogens. Using disease-resistant Xinjiang cotton varieties as an example, this study will provide a practical reference for regional breeding programs. This comprehensive study highlights the complexity of cotton-pathogen interactions and anticipates that integrating multi-omics data will be key to cultivating durable resistance through molecular breeding and precision agriculture. Keywords Cotton; Verticillium wilt; Fusarium wilt; Molecular resistance mechanism; Functional genomics 1 Introduction Cotton (Gossypium spp.) is the most basic raw material in the global textile industry. It is also an important cash crop in many countries, especially developing countries. Cotton plays a major role in the production of natural fibers and oilseeds (Shaban et al., 2018). However, cotton cultivation often encounters serious disease problems, especially Verticillium wilt caused by Verticillium dahliae and Fusarium wilt caused by Fusarium oxysporum. These two soil-borne fungal diseases are among the most serious biological factors that harm cotton worldwide (Man et al., 2022). These diseases not only reduce yields, but also affect fiber quality, putting considerable pressure on the sustainable development of cotton (Wang and Zhang, 2024). At present, breeding experts generally believe that breeding disease-resistant cotton varieties is the most effective, economical and environmentally friendly way to control Verticillium wilt and Fusarium wilt (Billah et al., 2021). But the problem is that there are relatively few disease-resistant genes available in cotton varieties, which makes breeding work very difficult (Liu et al., 2023). In order to promote the breeding of disease-resistant varieties and reduce dependence on fungicides, we need to have a deeper understanding of cotton's own disease resistance mechanisms, such as which genes are activated, which signaling pathways are involved, and which antifungal substances cotton produces (Liu et al., 2017). Only by mastering these molecular-level response mechanisms can we better apply genetic engineering technology and marker-assisted breeding methods to ultimately breed cotton varieties that can resist a wide range of diseases and have long-lasting resistance (Abdelraheem et al., 2019). This study will focus on the molecular response mechanisms of cotton to Verticillium wilt and Fusarium wilt. We will talk about which key disease resistance genes, signaling pathways, and physiological responses have been discovered and studied. This study will also analyze the challenges and possible breakthroughs encountered in
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