Molecular Microbiology Research, 2025, Vol.15, No.2, 69-81 http://microbescipublisher.com/index.php/mmr 69 Feature Review Open Access A Comprehensive Review of Genetic Basis and Breeding Strategies for Enhancing Cotton Resistance to Fungal Diseases Jin Zhou, Jiong Fu Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding author: jiong.fu@hibio.org Molecular Microbiology Research, 2025, Vol.15, No.2 doi: 10.5376/mmr.2025.15.0008 Received: 10 Feb., 2025 Accepted: 15 Mar., 2025 Published: 20 Apr., 2025 Copyright © 2025 Zhou and Fu, 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: Zhou J., and Fu J., 2025, A comprehensive review of genetic basis and breeding strategies for enhancing cotton resistance to fungal diseases, Molecular Microbiology Research, 15(2): 69-81 (doi: 10.5376/mmr.2025.15.0008). Abstract A variety of fungal diseases are widespread in cotton production, seriously threatening yield and quality. This paper reviews the global distribution and damage of major fungal diseases of cotton (such as Verticilliumwilt, Fusariumwilt, anthracnose and leaf spot), and analyzes the challenges faced by current disease-resistant breeding, such as the lack of genetic resources and pathogen variation. On this basis, the genetic basis related to cotton disease resistance is explained, including the identification and localization of key disease resistance genes, functional gene families such as WRKY transcription factors and NBS-LRR disease resistance proteins, and the mechanism of epigenetic regulation in disease resistance response. We focus on the strategies and progress of improving cotton disease resistance using molecular breeding methods such as molecular marker-assisted selection (MAS) and gene editing and transgenics. Through a case study of the breeding of a new cotton variety resistant to Verticillium wilt, the methods and results of material selection, field identification, resistance gene verification and functional analysis are detailed, and its breeding results and promotion potential are evaluated. In addition, the synergistic effect of comprehensive prevention and control measures combining disease-resistant varieties with chemical agents, biological control and agronomic measures is discussed. Finally, the integration of cotton multi-disease resistance breeding strategies and the emerging potential of genomics and artificial intelligence-assisted seed selection are prospected in the future. This study provides a reference for improving cotton's resistance to fungal diseases. Keywords Cotton; Fungal diseases; Disease resistance breeding; Genetic basis; Molecular breeding; Integrated prevention and control 1 Introduction Cotton is an important economic crop in the world and is widely planted in Xinjiang, the Yellow River Basin and the Yangtze River Basin in my country. However, cotton is often threatened by a variety of fungal diseases during its growth, which seriously affects its yield and quality. Among them, Verticilliumwilt and Fusariumwilt are the two most serious and widely distributed soil-borne diseases, known as "cotton cancer", and have been prevalent in many cotton-growing areas in my country for many years. Pathogens can survive in the soil for a long time and invade the vascular system of the plant through the roots, causing wilting, yellowing, leaf fall and even plant death (Man et al., 2022). According to surveys, the area of Verticillium wilt in China continues to expand, and the proportion of diseased fields in some cotton areas is as high as 50%-70%, which has become one of the main factors restricting high and stable yields (Palanga et al., 2021; Zhao et al., 2023). Fusariumwilt is more likely to break out under conditions of continuous cropping or poor management. The susceptibility rate is high in the seedling stage and the death rate is rapid. The harm cannot be ignored (Hu et al., 2024). In addition to wilt diseases, anthracnose and various leaf spot diseases are also common in different major cotton producing areas, showing a seasonal outbreak trend. Although the damage of this type of disease is relatively mild, it may still have a significant impact on yield and quality when it breaks out in a high temperature and high humidity environment together with the main disease. Therefore, building a systematic and effective disease prevention and control system is a common challenge facing cotton production at present (Abbas et al., 2022).
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