Cotton Genomics and Genetics 2025, Vol.16, No.3, 137-147 http://cropscipublisher.com/index.php/cgg 141 critical, such as GhAMT2, a high-affinity ammonium transporter that can link immune signals with cell wall reinforcement and systemic defense. In addition, through GWAS and transcriptome studies, genes such as Ghir_A01G006660 and Ghir_A02G008980 were also found to be related to disease resistance (Ayyaz et al., 2025). 5.2 Transcription factors (WRKY, MYB, NAC) involved in defense signaling Transcription factors are the core "switches" that regulate the plant defense system. When cotton is infected with pathogens, transcription factors from the WRKY, MYB and NAC families are rapidly activated. They can regulate many downstream defense genes and signal pathways. For example, they control the expression of pathogenesis-related proteins, hormone signaling elements, and some secondary metabolism-related genes. These regulations can enhance cotton's ability to respond to pathogens (Zhang et al., 2025). These transcription factors work together to help cotton achieve a balance between growth and defense. A typical example is GhSTR1, which plays an important role in regulating this balance (Cheng et al., 2025). 5.3 Secondary metabolites and antimicrobial peptides In addition to genes and transcription factors, some secondary metabolites and antimicrobial peptides are also important. They can directly inhibit the growth of pathogens and make cotton cell walls stronger. Proteins like PGIP (also called polygalacturonase inhibitory protein), such as GhPGIP1, can specifically inhibit the enzymes used by pathogens to break down plant cell walls. If this protein is expressed more in cotton, it can improve cotton's resistance to Verticillium wilt and Fusarium wilt (Liu et al., 2017). There are also germ-like proteins (GLPs), such as GhGLP2, which have the function of superoxide dismutase and can inhibit spore germination. It can also promote callose deposition and lignification, making the defense of the infected site stronger and improving antioxidant capacity (Pei et al., 2020). Lipid metabolism also plays a role, such as the GhSSI2 isoform, which can regulate oleic acid levels, activate defense pathways related to or unrelated to salicylic acid, and participate in nitric oxide signaling (Mo et al., 2021). In addition, proteins such as the ABCG transporter GhSTR1 and some proteins involved in ROS metabolism and cell wall modification are also very key molecules in cotton disease resistance. 6 Functional Genomics and Gene Editing Approaches 6.1 RNAi and CRISPR/Cas-mediated studies identifying key resistance genes Researchers often use RNA interference (RNAi) and virus-induced gene silencing (VIGS) to study the function of disease resistance genes in cotton. By silencing some key genes, such as GhAMT2, GhNDR1, GhMKK2, GhIQD1, GhEB1C, GbCRK18 and GbCNL130, cotton's resistance to Verticillium wilt will decrease, indicating that these genes are important in the defense process (Gao et al., 2011; Li et al., 2018). These experimental results show that "turning off" the function of specific genes can help us determine their role in disease resistance, and also lay the foundation for future gene editing using CRISPR/Cas technology. 6.2 Overexpression and knockdown studies validating gene function In addition to gene silencing, expressing genes more (also called "overexpression") is also a common method. For example, overexpression of GhAMT2 in Arabidopsis, or overexpression of GhIQD1 and GhEB1C in tobacco, can enhance plant resistance to Verticillium dahliae. If these genes are knocked down in cotton (that is, their expression is reduced), cotton will become more susceptible to pathogens (Xu et al., 2024b). In addition, studies have found that overexpression of GbCNL130 in Arabidopsis can enhance disease resistance, but if its expression is reduced in cotton, resistance will decrease (Li et al., 2021). These results show that functional verification is effective whether through overexpression or knockdown. Such resistance genes usually affect key defense processes such as hormone signaling, regulation of reactive oxygen species (ROS), and enhancement of cell walls (Xu et al., 2024a). 6.3 Use of genome-wide association studies (GWAS) and QTL mapping Genome-wide association analysis (GWAS) and quantitative trait loci (QTL) mapping techniques are also often used to identify key genes and regions related to resistance to Verticillium wilt (Zhu and Luo, 2024). For example, GWAS found a major QTL on chromosome A01, which contains the important gene GhAMT2. Another major
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