Cotton Genomics and Genetics 2025, Vol.16, No.6, 278-289 http://cropscipublisher.com/index.php/cgg 283 CRI 12 exhibits a hierarchical defense model: it not only recognizes pathogens but also makes rapid adjustments at the metabolic level. This multi-level protein response enables it to maintain a relative physiological balance when infected, thereby slowing down the progression of the disease. 4.3 Implications and applications The research on CRI 12 not only revealed the response logic of resistant cotton, but also provided molecular clues that can be directly applied to breeding. Differential proteins such as PR protein, phenylalaninase and ROS regulatory factors may serve as markers for disease resistance screening, providing support for subsequent marker-assisted breeding. Through these molecular characteristics, researchers can more specifically screen disease-resistant materials and even achieve precise editing at the genetic level. In addition, some stress chaperone proteins and signal regulatory molecules discovered in the research are also regarded as potential genetic engineering targets. The stability of plant defense responses may be enhanced in the future through transgenic or CRISPR-mediated regulation (Li et al., 2019a). When proteomics is integrated with transcriptomic, metabolomic and other data, a more complete immune regulatory network gradually emerges. Such system-level analysis not only explains resistance but also provides tools for precise breeding and sustainable control. The case of CRI 12 clearly demonstrates that proteomics is no longer merely a means of observing molecular changes, but a path to understanding the panorama of plant-pathogen interactions. It has led resistance breeding from experience to mechanism, and also made the prevention and control ideas of Fusarium wilt more forward-looking. 5 Functional Categorization of Differentially Expressed Proteins 5.1 Defense and stress-related proteins Among the cotton (Gossypium hirsutum) infected with Verticillium dahliae, defense proteins are always the first group to be "alarmed". Proteomic analysis has repeatedly shown that these proteins almost determine whether cotton can withstand the first round of pathogen attack. The most obvious changes come from disease-related proteins (PR), among which the upregulation of PR-1, chitinase, β-1, 3-glucanase and sweet-like proteins is the most significant. Their functions are simple and direct, that is, to weaken the cell wall of fungi and at the same time strengthen the host's own defense barrier. But the reaction of cotton did not stop there. Infection is often accompanied by a sharp increase in reactive oxygen species (ROS), and thus the antioxidant system is fully activated. Superoxide dismutase (SOD), catalase (CAT), ascorbic acid peroxidase (APX), and peroxidase (POD) take turns to be used to eliminate ROS and stabilize the REDOX balance within cells (Wang et al., 2019). Without them, oxidative damage to lipids and proteins is sufficient to cause the collapse of cell structure. Meanwhile, the expression of heat shock proteins (HSP70, HSP90) and molecular chaperones also increased accordingly. They act like "emergency workers", helping damaged proteins refold and maintaining the stability of the entire proteome. Glutathione S-transferase (GSTs) and lipoxygenase (LOXs) are involved in detoxification and lipid signaling pathways, further strengthening the resistance network. It can be said that the combined effect of these proteins is like building a biochemical "firewall", enabling cotton to maintain cell integrity when pathogens invade and resist the chain reactions triggered by oxidative stress. 5.2 Metabolic reprogramming proteins Once an infection occurs, the metabolic activities of cotton are almost "re-planned". After the invasion of V. dahliae, proteins related to photosynthesis (such as the RuBisCO subunit, oxygen-releasing enhancer protein, and chlorophyllin binding protein) are generally downregulated, and plants seem to actively slow down their growth, shifting energy to defense.
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