Molecular Microbiology Research, 2025, Vol.15, No.2, 69-81 http://microbescipublisher.com/index.php/mmr 70 Breeding disease-resistant varieties is considered to be the most economical, green and sustainable means of preventing and controlling fungal diseases, but cotton disease-resistant breeding still faces multiple challenges at this stage (Aini et al., 2022). On the one hand, cultivated upland cotton (Gossypium hirsutum) generally lacks strong resistance genes, and most of the existing high-yield varieties are susceptible materials, which can only provide a limited resistance basis (Cui et al., 2021). Although sea island cotton (G. barbadense) has a certain resistance, its yield traits and fiber quality are not suitable for the main planting needs, and hybrid utilization is progressing slowly (Man et al., 2022). On the other hand, pathogenic fungi have fast mutations and complex pathotypes. For example, Verticillium wilt has multiple physiological subspecies, which can break through existing resistance through mutation (Palanga et al., 2021). Long-term continuous planting of disease-resistant varieties will also form selection pressure, inducing the emergence of new pathogenic variants. In addition, in the practice of disease-resistant breeding, it is also necessary to take into account multiple agronomic indicators such as yield, fiber quality, and adaptability. Some disease-resistant genes have problems of poor linkage with high-yield genes or excessive expression metabolic costs, which affect the actual application value (Zhi and Chang, 2021). How to effectively aggregate multiple resistances while ensuring yield and quality is an important problem facing current disease-resistant breeding. This study focuses on the prevention and control of cotton fungal diseases and resistance improvement, comprehensively analyzes the main disease types and damage characteristics, explores the disease resistance gene basis and molecular breeding methods, and combines a case study of the development of Verticilliumwilt-resistant varieties for research and explanation, aiming to provide ideas and reference for subsequent cotton disease resistance breeding. 2 Overview of Common Fungal Diseases of Cotton 2.1 Verticilliumwilt andFusariumwilt Verticilliumwilt and Fusariumwilt are the two major wilt diseases that endanger cotton production and are widely occurring in cotton areas around the world (Palanga et al., 2021). Verticillium wilt is caused by Verticillium dahliae, which can invade the vascular system through the roots, causing yellowing of leaves, wilting of plants, and eventually death (Zhao et al., 2023). Its typical symptoms include irregular yellow spots on the leaves, which expand outward along the veins to form a "V"-shaped yellowing area. In severe cases, the leaves fall off early and the whole plant dies (Man et al., 2022). Fusariumwilt is caused by Fusarium oxysporumf. sp. vasinfectum. Its symptoms are similar to those of Verticilliumwilt, but it is usually more likely to occur under high temperature conditions, and the pathogen can survive in the soil for a long time (Hu et al., 2024). Both diseases are soil-borne diseases and can be spread through infected cotton seeds, irrigation water, agricultural tools, etc., making prevention and control difficult, and the area of the disease is expanding year by year (Ranga et al., 2020). In the main production areas of Xinjiang, Shandong, and Hebei in China, the area of Verticillium wilt continues to increase, becoming one of the bottlenecks restricting high-yield cultivation (Cui et al., 2021). According to field surveys, Verticillium wilt can reduce cotton yield by more than 30% in fields with suitable climatic conditions, and even cause total crop failure in severely affected areas (Aini et al., 2022). Fusariumwilt often breaks out in cotton fields with continuous cropping, dense planting, and poor soil drainage, and has a particularly significant impact on cotton plants in the seedling and boll stages (Abbas et al., 2022). At present, in actual cultivation, most upland cotton varieties are only moderately resistant or susceptible to the disease, and are difficult to resist pathogens with high infection intensity, resulting in a severe prevention and control situation (Guo et al., 2022). Therefore, the cultivation of disease-resistant varieties is still one of the key technical means for the prevention and control of Verticilliumwilt andFusariumwilt (Gao et al., 2017). 2.2 Anthracnose and leaf spot Anthracnose is mainly caused by Colletotrichum gossypii. It is a common stem, leaf, and boll disease on cotton, especially in the high-humidity areas of the south (Puia et al., 2021). Its typical symptoms are sudden wilting of cotton seedlings, sunken lesions on the stems, and damage to fruit branches during the boll stage, which can easily
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