Cotton Genomics and Genetics 2025, Vol.16, No.1, 29-38 http://cropscipublisher.com/index.php/cgg 33 5.3 Marker-assisted and genomic selection Marker-assisted selection (MAS) and genomic selection (GS) are two breeding methods that combine molecular markers and genomic information to speed up the selection of resistant varieties. Through the gene editing and functional verification mentioned above, we can find some reliable resistance sites and then turn these sites into MAS markers. The GS method uses genome-wide marker data to predict which varieties are more valuable for breeding, thereby selecting good genotypes. If these methods are used in conjunction with gene editing, multiple disease-resistant genes can be combined to breed stronger and more pest-resistant cotton varieties. 6 Case Study: Field Implementation of Resistance Loci 6.1 Deployment of resistance loci in commercial cultivars Scientists have now introduced resistance genes into commercial cotton varieties through traditional breeding and modern biotechnology, and have achieved some results. Technologies such as recombinases can precisely add multiple disease resistance genes to target cotton lines. Some lines have now integrated Verticillium wilt resistance genes and are used as basic materials for further breeding (Li et al., 2022b). In addition, since the 1990s, favorable alleles such as Lsnp1, Lsnp4, Lsnp5, Lsnp8 and Lsnp9 have been increasingly used, and their promotion has also helped improve the resistance of Chinese cotton to Verticillium wilt. Marker-assisted selection (MAS) and dedicated PCR markers such as KASP have also made it easier to use disease resistance QTLs (such as those for leaf curl virus and Verticillium wilt) in breeding. 6.2 Resistance performance in variable environments Sometimes, resistance genes that perform well in the laboratory are not suitable for the field. But this is not always the case. Many studies have tested key resistance loci in the field and in the greenhouse, and the results are quite consistent. In particular, the QTL related to Verticillium wilt has similar resistance effects regardless of the year and the location. What's more interesting is that some QTLs not only prevent Verticillium wilt, but also Fusarium wilt, killing two birds with one stone. However, it does not mean that a single QTL can solve all problems. Sometimes, putting multiple resistance loci together can have a better effect. This "combination punch" approach can make cotton more stable and last longer in various environments (Abdelraheem et al., 2019). In addition, using multi-parent materials for experiments and combining them with meta-analysis can screen out QTL hotspots that are reliable under different genetic backgrounds and climatic conditions. This step is actually quite critical (Abdelraheem et al., 2017). 6.3 Institutional and private-sector collaborations In order for these resistance genes to be truly used in the field, cooperation between research institutions, breeding units and enterprises is very important. The development and verification of molecular markers, as well as the sharing of genetic information through platforms such as CottonGen, have greatly simplified the breeding process and accelerated the promotion of resistant varieties (Figure 2) (Schoonmaker et al., 2023). This kind of cooperation allows genetic research in the laboratory to be truly implemented and turned into practical variety improvement results, which can ultimately effectively improve cotton's resistance to diseases and pests and help farmers better manage diseases and pests (Zhao et al., 2021). 7 Challenges and Future Perspectives 7.1 Evolution of pathogens and pests Resistance is not a one-time thing. Even if the early performance is good, it may be "cracked" by pests and diseases after a few years. Black root rot is an example. It was not so common before, but it is becoming more and more frequent now. Some new pests that were not taken seriously before have also begun to appear and cause losses. Sometimes, these new threats will directly bypass the original effective resistance genes and even make Bt technology ineffective (Egan and Stiller, 2022). For example, some pests have adapted to Bt toxins and are not as responsive to Bt cotton as before (Khalid and Amjad, 2023). Therefore, it is definitely not enough to rely on existing methods alone. We must keep an eye on the changes in the fields, continue to monitor, and constantly look for new resistance resources, superimpose gene combinations, and try to extend the validity period.
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