Cotton Genomics and Genetics 2025, Vol.16, No.4, 163-172 http://cropscipublisher.com/index.php/cgg 168 Figure 2 The role of the interaction between GhMCesA35 and GhCesA7 in plant response to stress and cellulose synthesis (Adapted from Zhao et al., 2022) 7 Implications for Cotton Breeding and Biotechnology 7.1 Molecular breeding applications In the past, cotton seed selection relied on experience, but today's breeding is no longer based on intuition. Technologies such as DNA markers, QTL mapping, and genome-wide association analysis have become the "essentials" of molecular breeding (Zhang et al., 2020; Kushanov et al., 2021). Marker-assisted selection (MAS) is particularly widely used because it allows breeders to directly identify cotton plants with high potential at the DNA level, eliminating the need to wait until cotton fluffs form to assess their performance (Shahzad et al., 2022). This naturally saves considerable time. The current trend is to combine high-throughput genotyping technologies with trait analysis, leveraging identified candidate genes and QTL loci to directly identify varieties with outstanding yield, fiber quality, or resistance (Yang et al., 2022; Joshi et al., 2023). 7.2 Genetic engineering and CRISPR-based approaches Not every trait can be slowly selected through traditional breeding, especially in a complex crop like cotton. Sometimes, when faced with insufficient insect resistance, suboptimal fiber quality, or poor drought and salt tolerance, traditional methods prove insufficient. In these cases, genetic engineering becomes a shortcut. Gene-editing tools like CRISPR have seen extensive use in cotton in recent years (Wang et al., 2023a; Ahmed et al., 2024). Both CRISPR/Cas9 and Cas12 can not only target specific DNA segments but also create mutant libraries, effectively allowing researchers to test all suspected genes that may influence traits (Thangaraj et al., 2024; Wang et al., 2024). Of course, some goals are to enhance expression, while others aim to "delete" negative regulatory factors. Want to prevent a gene from doing all the harm it can? Simply delete it. A further step is to develop “edited” varieties without foreign DNA, thus circumventing the regulatory barriers that govern genetically modified crops (Khan et al., 2023; Kumar et al., 2024). In other words, this would make “modification” more covert and more efficient. 7.3 Conservation and utilization of gene diversity Take a casual stroll through a cotton field these days and you'll find that most cotton plants look similar, as if they were all grown from the same "best" variety. But this is precisely where the problem lies: in the pursuit of high yield or quality, we repeatedly select for certain superior varieties, gradually losing less obvious but valuable genes. In fact, many old local varieties or wild cotton relatives (referring to wild cotton related to cultivated cotton; Baran et al., 2023; Abbas et al., 2024) may not look impressive or have high yields, but they may harbor genes
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