Molecular Microbiology Research, 2025, Vol.15, No.2, 69-81 http://microbescipublisher.com/index.php/mmr 72 NBS-LRR proteins are directly involved in pathogen recognition and are the "sentinels" of plant immunity. They have NBS domains and LRR repeat structures in their structures, which can recognize pathogen effector proteins and trigger downstream defense responses (Li et al., 2021). In cotton, NBS-LRR genes such as GbCNL130 and GbaNA1 have been shown to play a key role in resistance to Verticillium wilt (Cui et al., 2021). Among them, GbCNL130 increases the plant's sensitivity to pathogen recognition by activating the SA pathway, while its silencing significantly reduces plant resistance (Guo et al., 2022). Since NBS-LRR genes are mostly distributed in clusters and are prone to recombination and mutation, their conservative expression in varieties is particularly important (Billah et al., 2021). 3.2.2 Epigenetic modification and gene expression response In addition to traditional coding genes, epigenetic mechanisms also play a role in cotton disease resistance. Studies have shown that DNA methylation and histone acetylation regulate the expression of multiple immune genes and participate in the rapid response of plants to pathogen infection (Zhi and Chang, 2021). In disease-resistant cotton plants, the methylation level of some key disease resistance gene promoters decreased significantly, thereby activating defense expression. Negative regulatory genes are highly methylated and inhibited under pathogen stress (Ding and Wang, 2015). In addition, non-coding small RNAs also play a role in regulating disease resistance-related pathways, such as miR164, miR482, etc., which can regulate the translation level of NAC transcription factors and NBS-LRR genes (Wei et al., 2020). For example, ghr-miR164 regulates the immune response in the middle and late stages by downregulating the expression of GhNAC100. Its overexpression or silencing will significantly change the disease resistance of cotton. With the development of epigenomics, it is expected that precise regulation and genetic enhancement of disease resistance traits can be achieved through targeted regulation of methylation modification or the use of RNA interference (Zhi and Chang, 2021). 4 Molecular Breeding Methods for Improved Disease Resistance 4.1 Molecular marker-assisted selection (MAS) 4.1 Marker-assisted selection (MAS) In traditional cotton disease resistance breeding, field inoculation screening is time-consuming and labor-intensive, and is significantly affected by environmental interference. The rise of marker-assisted selection (MAS) technology provides a new means for early and efficient identification of disease resistance traits. This method is based on the selection of molecular markers closely linked to the target disease resistance gene or quantitative trait locus (QTL), which can predict the resistance potential of the plant at an early stage, thereby significantly shortening the breeding cycle and improving the accuracy of selection. In the study of Verticilliumwilt resistance, QTL positioning has become a key basis for the development of MAS. At present, multiple QTLs related to resistance to Verticillium dahliae have been reported, distributed on multiple chromosomes of the A and D subgenomes. The study by Lahlali et al. (2022) systematically summarized the distribution of these QTLs. For example, qVW-D11-1 is located on chromosome D11 and is a disease resistance QTL with a high recurrence rate in multiple studies; qVW-A07-2 is located on chromosome A07 and is often used for resistance introduction in the sea island cotton background. Related research has developed a variety of markers including SSR, SNP, and KASP for auxiliary detection of these QTLs (Figure 1). In specific applications, the KASP marker developed by Zhang et al. (2020) based on high-throughput sequencing has been successfully used to identify SNP loci associated with resistance to Fusariumwilt, with an accuracy rate of more than 85%. With the support of the MAS platform, researchers have achieved the transfer of resistance QTLs in sea island cotton to upland cotton, and constructed multiple high-generation materials resistant to Verticillium wilt. In Xinjiang, China and Pakistan, MAS is also widely used for disease-resistant population construction and early screening, improving the efficiency of parent selection (Abdelraheem et al., 2019).
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