Cotton Genomics and Genetics 2025, Vol.16, No.3, 137-147 http://cropscipublisher.com/index.php/cgg 143 found that most cotton varieties planted in Xinjiang only have a certain degree of disease resistance, not real high resistance, which shows that we still need to develop more new disease-resistant materials (Liu et al., 2012). Figure 2 Different responses of JK1775 (R) and Z8 (S) to V592 at 15 dpi. (A) Disease symptoms of JK1775 and Z8 after inoculation with V592. (B) Observation of vascular bundle browning in longitudinal stem sections of JK1775 and Z8 plants cut lengthwise by hand. (C) Fungal recovery assay of the stems of JK1775 and Z8. (D) The disease indices of JK1775 and Z8. (E) Fungal biomass in the stems of JK1775 and Z8 plants was measured by qRT-PCR. Significance was determined using Duncan’s multiple range test, indicated by ** p ≤ 0.01 (Adopted from Zhang et al., 2024) 8.2 Transcriptomic profiling reveals key resistance-associated genes Transcriptome analysis of Xinjiang cotton varieties found that disease-resistant varieties had more genes undergoing significant expression changes after infection with Verticillium dahliae. In contrast, susceptible varieties had fewer changes. These differentially expressed genes are mainly concentrated in the MAPK signaling pathway and phenylpropanoid metabolism, especially those that regulate lignin and coumarin synthesis, which are related to cell wall thickening and disease resistance (Zhang et al., 2024). In terms of Fusarium disease, the GbC4H gene in Sea Island cotton can regulate the synthesis of flavonoids. If this gene is silenced, cotton resistance will weaken, indicating that the accumulation of flavonoids is important for disease resistance (Qu et al., 2023). This type of response is also regulated by the methyl jasmonic acid (MeJA) and salicylic acid (SA) signaling pathways. Through GWAS and transcriptome combined analysis, the researchers found several genes related to resistance, such as GhAMT2, Ghir_A01G006660 and Ghir_A02G008980. These genes are involved in lignin synthesis, ROS homeostasis maintenance, and immune signaling (Ayyaz et al., 2025). Further experiments, including gene silencing and overexpression, have demonstrated that these genes play an important role in disease resistance. 8.3 Outcomes for breeding programs and regional disease management These molecular information in Xinjiang cotton varieties provide a lot of useful genetic resources for breeding. The location of disease-resistant genes and related QTLs helps researchers better conduct marker-assisted breeding and allows them to breed more disease-resistant cotton varieties (Li et al., 2017a). In terms of breeding methods, transgenic methods have also played a positive role. For example, after the introduction of the GAFP
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