Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 261 presence/deletion variations (PAVs). When the dose of genes increases, their expression may also increase accordingly, especially for those genes involved in basal metabolism. However, there are exceptions-some dose-insensitive genes are often concentrated in stress responses or signaling pathways instead. These seemingly subtle dose differences are precisely one of the important driving forces behind the phenotypic differentiation between upland cotton and Pima cotton. 3.2 Disruption of regulatory elements by SVs Not all variations occur within the genes themselves; more often than not, they appear in the "controlled regions" of the genes. Regulatory elements-such as promoters, enhancers or topologically associated domain (TAD) boundaries-can easily disrupt the balance of gene regulation once they are affected by structural variations (SVS). In the study of cotton, thousands of structural variations have been discovered in these regions, many of which are related to significant expression differences between upland cotton (G. hirsutum) and sea island cotton (G. barbadense) (You et al., 2022). For instance, a small 16 bp fragment was added to the promoter of the RLP6 gene in sea island cotton (which was not present in upland cotton). As a result, the expression of RLP6 was enhanced, and the resistance to yellow wilt was also improved accordingly (Figure 1) (Zhang et al., 2025). What is more complex is that SV can also reshape TAD boundaries, change the three-dimensional structure of the genome, and recombine originally adjacent or cooperative gene regulatory networks (Long et al., 2021). In addition, the replacement of transcription factor binding sites (TFBS) also occurred, further promoting the formation of new expression patterns, especially in fiber-related genes, which was most evident. Figure 1 Functional analysis ofRLP6gene via gene silencing and overexpression assays(Adopted from Zhang et al., 2025)
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