Cotton Genomics and Genetics 2025, Vol.16, No.4, 184-191 http://cropscipublisher.com/index.php/cgg 186 other. In this case, cotton will increase the expression of genes involved in hormone transmission, MAPK signaling, and secondary metabolite synthesis. This "multi-pathway" approach can enable cotton to respond more effectively to different threats and enhance its overall stress resistance (He et al., 2018; Bihani et al., 2024). Figure 1 GhJAZ2 reduces methyl jasmonate (MeJA)-induced anthocyanin accumulation and the expression of jasmonate (JA)-responsive defence marker genes in cotton. (A) The cotyledon petioles of wild-type and GhJAZ2 transgenic cotton seedlings were treated with or without (MOCK) MeJA for 3 days. (B) Anthocyanin content of the cotyledon petioles in (A). The data are the mean ± standard error (SE) of three independent biological replications, and different letters indicate significant differences at P<0.05 (Duncan's multiple range test). (C) Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis of GhJAZ2, GhPDF1.2 and GhVSP in roots of wild-type and GhJAZ2 transgenic cotton lines treated with or without MeJA. Total RNAs were extracted from roots of seedlings at the indicated time points after treatment. The GhUBQ7 gene was used as the endogenous reference gene. The data represent the mean ± standard deviation (SD) of three technical replicates. WT, wild-type; J9 and J92, GhJAZ2-overexpressing cotton lines; JR3 and JR13, GhJAZ2-RNAi (RNA interference) cotton lines (Adopted from He et al., 2018) 4 Identification and Functional Annotation of Key Immune Genes 4.1 Expression patterns of resistance gene families Part of cotton's disease resistance comes from some specific gene families, such as NBS-LRR resistance genes. These genes are activated when pathogens invade, especially in varieties with strong disease resistance, such as Gossypium hirsutumL. and Gossypium barbadense L. When cotton is infected with Verticillium dahliae, receptor kinase genes such as BAK1 and CERK1 are activated, and their splicing patterns change. One of the key proteins is called GauSR45a, which can regulate the splicing of these immune genes, making cotton's defense response more flexible and effective. Interestingly, these genes in disease-resistant varieties have more changes in splicing, while those in disease-prone varieties have fewer changes. This suggests that there may be a great relationship between the diversity of gene splicing and cotton's disease resistance (Liu et al., 2024). 4.2 Regulatory roles of transcription factors Transcription factors are a class of regulatory proteins that can "switch" many genes, and the WRKY family is particularly important in this regard. For example, the factor GhWRKY41 can be quickly activated after pathogen
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