Cotton Genomics and Genetics 2025, Vol.16, No.4, 184-191 http://cropscipublisher.com/index.php/cgg 187 infection, especially in disease-resistant varieties. It can also stimulate its own continuous expression, forming a positive feedback. This factor controls many important defense-related genes, such as those involved in phenylpropanoid metabolism, lignin synthesis, and flavonoid synthesis. These metabolites can strengthen the "body defense line" of cotton. In addition, a class of WRKY factors called IId also improves cotton's resistance to Fusarium oxysporumthrough the MAPK signaling pathway (Wang et al., 2022; Xiao et al., 2023). These findings all indicate that transcription factors play a critical role in disease resistance. 4.3 Annotation and validation of core genes in signaling pathways Through functional analysis and experiments, researchers have found some signaling pathways that are particularly important in the disease resistance process, such as salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). Many immune genes undergo different changes after pathogen invasion or hormone treatment. For example, a study found that 24 genes responded to both Verticillium dahliae and methyl jasmonate. This suggests that these genes are related to jasmonic acid and may be directly involved in the defense response. Subsequent experiments also verified their role in producing reactive oxygen species and transmitting hormone signals, which are important for improving disease resistance (Xu et al., 2014). 5 Integrated Models of Immune Pathways and Defense Mechanisms 5.1 Pattern recognition receptors (PRRs) and early signaling events The immune system of cotton starts with recognition. It first uses some "sensors" to identify the enemy. These sensors are called pattern recognition receptors, such as receptor-like kinases and extracellular proteins. They can recognize certain molecular signals of pathogens. For example, kinases like GbEIR5A/D will trigger the accumulation of reactive oxygen species (ROS) and cell death when they recognize fungi, thereby initiating two immune responses: one is PAMP-triggered (PTI) and the other is effector-triggered (ETI) (Sun et al., 2024). There are also some proteins, such as CRR1, which can protect defense enzymes from being destroyed by pathogen enzymes. Enzymes like chitinase 28, under the protection of CRR1, can better work outside the cell and block pathogens (Han et al., 2019). These reactions occur quickly and can start subsequent immune responses in time. 5.2 Hormonal signaling networks and immune coordination Once cotton recognizes pathogens, it will regulate defense through several hormones in the plant body. The most common are salicylic acid (SA), jasmonic acid (JA) and ethylene (ET). Like a command system, they mobilize various parts of the plant to resist diseases. For example, some beneficial bacteria (such as Bacillus subtilis NCD-2) will activate these hormone pathways in cotton, which can increase the expression of defense genes such as NPR1, ICS1, COI1 and LOX1 in cotton. If any of these pathways is "turned off", cotton's disease resistance will also decrease, indicating that these pathways are indispensable (Mo et al., 2025). In addition, some proteins, such as GhJAZ2, can bind to transcription factors to control JA signals, helping cotton find a balance between "growing" and "preventing diseases" (He et al., 2018). There is also a membrane protein such as GhSYP121, which can regulate SA signals, indicating that hormones and cell transport systems work together (Gao et al., 2024). 5.3 Systematic integration of resistance-induced pathways and regulatory networks The disease resistance mechanism of cotton is not just a single route, it integrates many signal pathways. Transcription factors such as WRKY will form a "positive feedback" circle. Once activated, they will continuously activate many defense genes, such as genes that control phenylpropanoid metabolism and lignin synthesis (Hu et al., 2021; Xiao et al., 2023). There is also a signal "amplifier" called MAPK in cotton, which can amplify early pathogen recognition signals and transmit them to downstream genes. For example, GhMPK9 and GhWRKY40a are such a link. They work together to help cotton deal with different types of pathogens at the same time (Wang et al., 2022; Mi et al., 2024). Some studies have also used proteomic and transcriptomic methods to find that these regulatory systems are very flexible and also involve reactive oxygen metabolism, secondary metabolite production and epigenetic control. These reactions are intertwined, allowing cotton to form a comprehensive and rapid immune system (Zhang et al., 2017; Liu et al., 2024).
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