Molecular Microbiology Research, 2025, Vol.15, No.2, 69-81 http://microbescipublisher.com/index.php/mmr 71 lead to cotton bolls not cracking, seriously affecting the quality of cotton fiber (Abdelraheem et al., 2019). In addition, the pathogen can be spread through cotton seeds, which can easily cause large-scale sowing with the disease, and then cause large-scale death during the seedling stage. In India, Brazil and other countries, anthracnose has become an important limiting factor affecting seedling survival rate and boll number (Gaspar et al., 2014). Leaf spot is one of the common leaf diseases of cotton in the middle and late stages, caused by a variety of fungi such as Alternaria spp. (brown spot), Corynespora cassiicola (target spot), Stemphyliumspp. (black spot) and so on (Maryum et al., 2022). In the early stage of leaf spot disease, gray-brown, round or polygonal lesions appear on the leaf surface. In severe cases, the spots merge and cause the leaves to fall prematurely, affecting photosynthesis and later yield formation (Li et al., 2021). It is particularly susceptible to high temperature, high humidity and poor ventilation. In recent years, it has been aggravated in some cotton-growing areas in Brazil and southern China (Puia et al., 2021). Compared with wilt diseases, the control pressure of anthracnose and leaf spot is slightly lower, but due to their hidden onset, wide distribution of pathogens and rapid epidemic speed, they will still cause "hidden yield reduction" to cotton yield formation (Zhao et al., 2023). It is worth noting that these leaf diseases are often intertwined with improper cultivation and management factors such as fertilizer and water imbalance and resistance degradation. 3 Genetic Basis Related to Disease Resistance 3.1 Identification and positioning of major disease resistance genes The genetic basis of cotton resistance to fungal diseases is relatively complex, generally belonging to quantitative traits, and is jointly regulated by multiple genes (Aini et al., 2022). Through genetic positioning and map analysis, researchers have identified many QTLs (quantitative trait loci) and candidate genes related to disease resistance (Cui et al., 2021). For example, when linkage analysis and genome-wide association analysis (GWAS) were performed on materials resistant to Verticillium wilt, disease resistance QTLs were located on multiple chromosomes, especially on chromosome D05 (Zhao et al., 2023). Shi et al. (2016) found a total of 48 disease resistance QTLs in a backcross population constructed from sea island cotton and upland cotton, some of which were repeated in multiple populations, showing strong stability. In recent years, the application of BSA-Seq (body analysis sequencing) and high-density SNP chips has improved the positioning accuracy. For example, the GhDRP gene, a disease-related protein gene closely related to Verticillium wilt resistance, was finely located in an area of about 300 kb and had specific mutations in disease-resistant varieties (Guo et al., 2022). Functional verification showed that the expression of this gene was significantly induced under pathogen infection, and its knockout significantly reduced cotton's resistance to Verticilliumwilt. In addition, some classic disease resistance genes, such as Ve homologous genes and Rboh genes, have also been shown to be involved in the recognition of pathogen signals and activation of defense pathways in cotton (Li et al., 2021). In current breeding practice, the use of these stable QTLs for molecular marker-assisted selection (MAS) has become an important strategy, but its practical application still needs to be further optimized due to environmental interference and polygenic genetic characteristics. 3.2 Gene family and expression regulation mechanism 3.2.1 Functional roles of WRKYandNBS-LRRgenes WRKY transcription factors and NBS-LRR disease resistance proteins are the two most studied functional gene families. WRKY proteins regulate multiple immune responses including PR proteins, JA pathways, and SA signals by binding to the W-box of the target gene promoter (Billah et al., 2021). In cotton, GhWRKY70 and GhWRKY22 have been shown to enhance resistance to Verticillium dahliae, while GhWRKY55 is a typical negative regulator, whose knockout can promote lignin synthesis and defense gene expression (Ma et al., 2023).
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