Cotton Genomics and Genetics 2025, Vol.16, No.3, 137-147 http://cropscipublisher.com/index.php/cgg 140 expression of defense-related genes and physiological changes in plants (Xu et al., 2014). The interaction between these hormones determines the strength and specific mode of the immune response. When pathogens invade, both SA and JA signaling pathways are usually activated. Overall, cotton's innate immune system coordinates PRR-mediated PTI, NLR-triggered ETI, and various hormone signals to form a complete defense system to help cotton resist Verticillium wilt and Fusarium wilt, which also provides a basis for the breeding of disease-resistant varieties in the future. 4 Transcriptomic and Proteomic Responses to Infection 4.1 Gene expression changes during early and late stages of infection Studies have found that after cotton is infected with Verticillium dahliae or Fusarium oxysporum, its gene expression changes significantly. Transcriptomic analysis shows that many genes related to disease resistance change significantly in the early stage of infection (generally within 24 to 48 hours). These genes are mainly involved in the synthesis of flavonoids, hormone signaling, and the interaction between plants and pathogens (Zhang et al., 2020; Li et al., 2024). Thousands of differentially expressed genes (DEGs) can be seen in both resistant and susceptible varieties. However, the response of susceptible varieties is often more obvious (Zhang et al., 2021a). As the infection continues, some genes involved in lignin synthesis, cell wall changes, and immune signaling remain active. This shows that cotton continues to adjust its defense and adaptation mechanisms. 4.2 Differential protein expression and post-translational modifications Proteomics studies have shown that the expression levels of many proteins in infected cotton have changed. Most of these proteins are related to stimulus response, secondary metabolism and plant hormone signaling pathways (Gao et al., 2013). In disease-resistant cotton, key proteins such as peroxidase, polyphenol oxidase and cottonpol biosynthesis enzymes increase, which can help cotton improve resistance (Li et al., 2019). In addition, many proteins have undergone post-translational modifications, such as those related to phenylpropanoid pathways and hormone regulation, which can also enhance or change their functions (Gao et al., 2013). Some important proteins, such as GbCAD1, which is involved in cottonpol synthesis, will reduce cotton resistance if they are inhibited, which also shows that these proteins play a key role in defense. 4.3 Functional enrichment of defense-related pathways Many functional enrichment analysis results show that cotton activates a series of defense pathways when infected with pathogens. For example, in reactive oxygen species (ROS) metabolism, some genes and proteins involved in ROS production and removal are upregulated, which helps plants send out rapid response signals. Lignin synthesis and phenylpropanoid metabolic pathways are also enhanced, making cell walls stronger and limiting the spread of pathogens (Sun et al., 2013). In addition, glutathione metabolism is also important. Studies have found that the detoxification role of glutathione S-transferase in the disease resistance process cannot be ignored (Xing et al., 2024). For example, in terms of hormone signal transduction, related pathways such as salicylic acid, jasmonic acid, ethylene and brassinosteroids are also activated. These signals can cooperate with each other to jointly regulate immune responses (Zhang et al., 2013). These "omics" studies at different levels have given us a more comprehensive understanding of the molecular mechanisms of cotton's resistance to Verticillium wilt and Fusarium wilt, and have also helped us find many disease-resistant genes and key pathways worthy of attention, providing important clues for breeding. 5 Key Molecular Players in Resistance 5.1 Resistance (R) genes and their functional classification The reason why cotton can resist Verticillium wilt and Fusarium wilt is closely related to whether it has disease resistance genes and whether these genes are active. In particular, those genes encoding NBS-LRR proteins (which have nucleotide binding sites and leucine repeat structures) (Abdelraheem et al., 2019). Through genome-wide association analysis (GWAS) and QTL mapping, researchers have found many NBS-LRR genes on multiple chromosomes. Some of these genes can also resist two diseases at the same time (Li et al., 2017b). For example, a candidate gene called CG02, which contains a TIR-NBS-LRR domain, is more highly expressed in disease-resistant cotton. If it is silenced, cotton will be less resistant to Verticillium dahliae. Some R genes are also
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