Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 265 closely related to the differences in fiber development. To verify this, researchers introduced fragments of island cotton (G. barbadense) into the upland cotton (G. hirsutum) strain and conducted transcriptome analysis on them. The results showed that there were a number of differentially expressed genes in the A07 region, mainly involved in processes such as cell wall tissue formation, polysaccharide metabolism and hormone signal transduction (Lu et al., 2017; Song et al., 2020). These seemingly basic metabolic and regulatory activities actually directly affect the strength and elongation of fibers. It is worth noting that in this QTL cluster, GhRBB1_A07 has been confirmed as an important candidate gene for high-quality fibers. There is a significant association between its sequence variation and the change in expression level and the improvement of traits. In other words, the inversion of A07 is not merely a structural change, but also a molecular "clue" behind the difference in fiber quality. 6.3 Breeding implications and marker development The significance of the inverted position of A07 is not limited to revealing the mechanism; it also brings practical value. Researchers screened out a batch of SSR and SNP loci near the QTL peak of chromosome A07 and developed a marker system that can be used for molecular marker-assisted selection (MAS) based on this (Fang et al., 2020). This enables breeders to screen high-quality fiber materials more efficiently and precisely. What is more concerning is that qFS-c7-1 QTL shows stable performance and strong transferability in different populations and generations, and has become a core reference marker for multiple breeding projects. Meanwhile, functional markers like GhRBB1_A07 have also been gradually established, which can help researchers identify and aggregate favorable fragments to achieve a balanced improvement in quality and yield (Li et al., 2019). It can be said that these breeding strategies based on structural variations are bringing the improvement of upland cotton and Pima cotton into a new stage that is more precise and efficient. 7 Applications in Breeding and Genetic Improvement 7.1 SV-informed breeding strategies Cotton breeding does not solely rely on traditional genotype selection; the intervention of structural variations (SV) makes this process more targeted. Structure-level changes such as insertions, deletions, inversions, and presence/deletion variations (PAVs) often conceal clues that affect key traits. In recent years, with the establishment of high-quality reference genomes and the application of resequencing chips, genome-wide association studies (GWAS) have revealed hundreds of structural variations significantly associated with fiber quality, yield, and disease resistance (Liu et al., 2023). Interestingly, the SVS corresponding to different traits are not evenly distributed-for instance, those related to fibers are mostly in the D subgenome, while the signals for yield traits are concentrated in the A subgenome. Now, researchers are attempting to apply these SV markers or haplotype blocks (especially those derived from gene infiltration) to molecular breeding to guide the screening and combination of favorable alleles. In this way, not only can the genetic diversity of the population be maintained, but also the environmental adaptability of the breeding materials can be enhanced. Compared with the traditional selection method that only relies on SNPS, integrating SV data can help discover those complex but easily overlooked superior traits (Li et al., 2021). 7.2 Genome editing approaches targeting SV regions In the past, structural variations were almost all "natural products", and people were more likely to observe and record them rather than intervene. It was not until the emergence of CRISPR/Cas technology that this situation was completely broken. Nowadays, researchers can not only manipulate genes but also precisely edit those regions related to structural variations (SVS). The CRISPR/Cas9 and Cas12a systems have been successfully applied in cotton, enabling the creation of deletions, insertions, and simultaneous modification of multiple sites (Sheri et al., 2025). This enables people to directly verify for the first time exactly what role a certain structural variation has, and even artificially create new alleles. It is worth noting that with the continuous optimization of the guide RNA design and verification system, the complex genomic structure of polyploid cotton is no longer an obstacle, and the editing efficiency has been significantly improved (Hui et al., 2024). It is precisely for this reason that the results of gene modification in the laboratory are gradually being brought into breeding practice to improve the quality, yield and stress resistance of fibers(Wang and Zhang, 2024). CRISPR technology is not intended to replace traditional breeding, but it has indeed turned precise improvement from theory into reality.
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