Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 264 6 Case Study: SVs in a Key Locus Influencing Fiber Quality 6.1 Identification of a major inversion on chromosome A07 Research on the quality of cotton fibers has always focused on chromosome A07. Researchers have discovered a significant structural variation on this chromosome-a major inversion, which is closely related to multiple fibrous traits. Using high-throughput resequencing technology, Inv(A07) p1.09-p2.23 inlocation was detected in dark brown fiber cotton. This structural change not only causes microdeletions near the breakpoints but also leads to the destruction or abnormal expression of some genes. It is worth noting that this inversion only occurs in dark brown fiber cotton and is significantly correlated with properties such as fiber color, length and strength (Figure 2) (Wen et al., 2020). The nucleotide diversity in the affected areas has declined, recombination has been suppressed, and linkage disequilibrium has intensified, suggesting that it may have special significance in evolution and breeding. In addition, there is a 1.4Mb inversion on chromosome A07 that is connected to the GhTT2_A07 gene. This variation activates the biosynthesis of flavonoids, thereby affecting fiber color and potential quality traits. Multiple QTL mapping and association analyses also repeatedly identified stable QTL clusters in the same region, suggesting that this might be a concentrated area of beneficial alleles. Figure 2 Inversion structure of Inv(A07)p1.09p2.23 andgene disruptionofGhir_A07G000980. (a) Inversion structure in the dark-brown fibre mutant. “+” and “-” indicate the sense and antisense strands in the reference genome, respectively. The stars indicate the truncated fragments. The green colour indicates the inverted fragment. The numbers means the physical position in genome. The arrows indicate the direction of alignment with the reference genome. (b) Structure ofGhir_A07G000980disrupted by breakpoints and micro-deletion. (c) Transcript ofGhir_A07G000980derived fromRNAof HD208,ys, and Pima90-53.Gh_ub7was used as the control (Adopted from Wen et al., 2020) 6.2 Functional analysis and expression profiling The inversion in the A07 region is not merely a "static decoration" in the genome; it does indeed alter the expression pattern of genes. Functional analysis revealed that some key genes were abnormally expressed in the context of inversion, such as Ghir_A07G000980. Both its functional disorder and expression imbalance were
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