Cotton Genomics and Genetics 2025, Vol.16, No.6, 278-289 http://cropscipublisher.com/index.php/cgg 279 including enzymes that alleviate oxidative stress, structural proteins that reinforce cell walls, and kinases involved in secondary metabolism and signal transduction (Huang et al., 2021). In cotton, many comparative proteomics and VIGS studies have pointed out that molecules such as gossypol, jasmonic acid, and brassinosterol are all involved in the process of resisting V. dahliae. Recent studies in phosphorylated proteomics have further demonstrated that signaling pathways such as the MAPK cascade, calcium-binding proteins, and hormone regulatory networks are rapidly activated upon pathogen invasion, coordinating defense responses. By integrating proteomic, transcriptomic and metabolomic data, scientists are gradually drawing a more complete "cotton immune regulation map", which provides a solid direction for molecular breeding and the development of disease-resistant varieties (Feng et al., 2023). This study focuses on the protein changes in cotton leaves after infection with Trichoderma boldii, aiming to identify the key proteins and pathways related to host defense. By comparing the protein profiles of healthy and infected plants, we aim to capture the molecular characteristics that reflect defense activation, metabolic recombination and stress adaptation. The research content includes differential expression analysis, functional classification, and exploration of their roles in pathogen recognition, signal transduction, and defense metabolism. Ultimately, we expect these results to further reveal the molecular response pattern of cotton in the face of the Variegata boldii and provide new ideas and targets for future disease-resistant molecular breeding. 2 Pathogenesis of Verticillium Wilt in Cotton 2.1 Infection mechanism The story of Fusarium wilt often begins deep in the soil. The long-dormant Verticillium dahliae hides in the root zone in the form of microsclerotia until the substances secreted by the cotton root system "awaken" it. After being stimulated, the microsclerotia germinate into hyphae. Some directly penetrate the root epidermis, while others take advantage of the natural pores to infiltrate the cortex and finally enter the vascular tissue all the way (Zhu et al., 2023). Once inside the vessels, the fungus begins to multiply in large numbers, producing conidia. These spores are carried to the above-ground parts along the transpiration flow, causing systemic infection (Figure 1). Figure 1 Infection cycle of V. dahliae in generic host plants (Adopted from Zhu et al., 2023) During the process of infection, pathogenic bacteria are not merely mechanical invaders. It secretes a series of cell wall degrading enzymes (CWDEs), such as pectinase, cellulase, xylanase, etc., gradually weakening the strength of the tissue and making the vascular bundles prone to blockage and collapse. At the same time, toxins and
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