Cotton Genomics and Genetics 2025, Vol.16, No.6, 278-289 http://cropscipublisher.com/index.php/cgg 280 effector proteins like VdCP1 will also be released, quietly interfering with the host's metabolism and immune response, leaving loopholes in the plant's defense system. This is followed by yellowing of the leaves, Browning and necrosis of the vascular bundles, which often indicate the disruption of water transport. What is even more troublesome is that the microsclerotia remaining in the soil can re-enter dormancy and wait for the arrival of the next crop season, which also explains why yellow wilt is always difficult to be completely eradicated. 2.2 Physiological and cellular responses The process of pathogen invasion is actually closely intertwined with the physiological changes of plants. The secretions from the roots of cotton first induce the germination of microsclerotia. The mycelium penetrates through the epidermis or pores, passes through the cortex, and eventually reaches the xylem vessels. All of this usually happens very quickly. In the vessels, the Trichoderma lanceolata continues to produce conidia, which move upward like an elevator along the transpiration flow, infecting the leaves and stems and causing systemic lesions. During this period, cell wall degrading enzymes (CWDEs) released by pathogens, such as gliase, cellulase and xylanase, gradually relax the tissue structure (Umer et al., 2023). Toxins and effector proteins follow closely, and VdCP1 is one of them. It can interfere with metabolic pathways and signal transduction, weakening the host's immunity. When water cannot be transported smoothly, cotton will show typical symptoms such as wilting and leaf necrosis. And those tough microsclerotia, once they enter dormancy, can survive in the soil for many years, which also makes the prevention and control of yellow wilt a "long-term battle" in agriculture. 2.3 Host defense strategies Cotton is not just waiting to die. It has both "innate" defenses and can be "temporarily mobilized". The former includes structural barriers such as thickening of the cell wall and secretion of antibacterial compounds; The latter, upon being stimulated by pathogen molecules (PAMPs) or effector proteins, initiates two layers of immune responses: mode-triggered immunity (PTI) and effector protein-triggered immunity (ETI). Behind these defense responses, the synergy of three signaling channels is indispensable: salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). The SA pathway is often associated with systemic acquired resistance (SAR) and allergic reactions (HR), while JA and ET are more active in response to necrotic pathogens or mechanical injuries (Xiong et al., 2021a). Through proteomics research, many key roles have been identified: disease-related proteins (PR), phenylalanine metabolic enzymes such as PAL and POD, and secondary metabolic enzymes involved in lignin and flavonoid synthesis (Tang et al., 2019). In addition, some transcription factors, such as WRKY, MYB and Bel1-like genes (GhBLH7-D06), are also regulating these defense networks. The MAPK cascade reaction and calcium signaling pathway are like command systems, coordinating the timing and intensity of various defense responses (Ma et al., 2020). Research generally holds that the metabolism of phenylpropyl and the synthesis of lignin are the key pathways for the differentiation of disease-resistant and susceptible varieties. Ultimately, the balance point of these complex defense systems determines the fate of a cotton plant: whether it survives infection or is invaded by the pathogen. The application of proteomics is gradually enabling us to uncover the underlying molecular logic of this resistance. 3 Proteomic Methodologies in Cotton Pathogen Research 3.1 Protein extraction and identification tools In the research on the interaction between cotton and the Trichoderma lucidum, the first challenge often encountered is not analysis but extraction. The cotton tissue is rich in polysaccharides, phenols and various secondary metabolites, which makes protein purification extremely difficult. Researchers usually have to repeatedly explore methods. TCA/ acetone precipitation method, phenol extraction method, and buffer solution extraction method are all employed to obtain soluble protein components that are of controllable quality and suitable for subsequent analysis as much as possible.
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