Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 262 3.3 SV-mediated creation of novel gene fusions or isoforms The arrangement of genes is not always regular. Occasionally, structural variations (SVS) can disrupt the original sequence, resplicing the boundaries between exons and introns, and even generating new splicing sites in unexpected places. The originally intact genes are thus "rewritten", with new fusion genes or alternative splicing isomers emerging. In cotton, this situation is actually not rare and is often related to the movement of the rotating seat component. Their insertion disrupts the splicing rhythm, enabling the same gene to produce multiple mRNA isomers and thereby generate different versions of proteins. The results of the comparative transcriptome also confirmed this point-many direct homologous genes showed significant differences in the number of isomers and splicing patterns (Shahzad et al., 2024). These differences are not merely minor variations but bring about linea-specific expression patterns and even new functions. Interestingly, the isomer changes triggered by SV are not confined to the developmental stage; they are also involved in regulating fiber growth and sometimes affect cotton's responsiveness under stress. 4 SVs and Phenotypic Traits in Upland and Pima Cotton 4.1 Fiber length, strength, and fineness The difference in fiber quality between Gossypium hirsutum and Gossypium barbadense has long been well known, but it is not easy to explain the genetic basis of this difference. Researchers are increasingly inclined to believe that structural variations (SVs) play a key role in this. According to the results of genome-wide association studies (GWAS) and pan-genome studies, many variations significantly associated with traits such as fiber length, strength, and fineness are concentrated in the D subgenome (Chen et al., 2022). These variations are usually distributed near the genes that regulate fiber development. Their effects may not be direct, but they often accumulate continuously during the development process. Interestingly, although some mutations can bring about superior traits, they may not be retained. Take the GhROPGEF5 gene as an example. The deletion of one of its bases can significantly increase fiber length and strength. However, this allele is not common in upland cotton because it may lead to a decrease in yield (Wang et al., 2024). In contrast, researchers are more inclined to adopt a "leveraging" approach-introducing the high-quality gene fragments of Pima cotton into upland cotton to improve the fiber properties. Through QTL mapping and transcriptome analysis, multiple candidate genes and their regulatory networks have been identified (Li et al., 2024). It is worth noting that many differences in fibrous traits that SNP analysis fails to capture are often caused by these structural variations deeply hidden in the genome. 4.2 Stress tolerance and environmental adaptation The performance of upland cotton and Pima cotton in responding to environmental pressure is also not the same, and this difference is closely related to structural variation. In certain gene families, such as the NDA family, there is a significant association between internal structural variations or presence/absence variations (PAVs) and enhanced salt-alkali tolerance (Fan et al., 2022). In comparative genomic studies, the structural variation density of the D subgenome is higher, which may explain why terrestrial cotton (G. hirsutum) can adapt to a wider range of environments. Unlike Pima cotton, which is mainly concentrated in tropical and subtropical regions, upland cotton can even maintain a stable yield in high-latitude areas. Some studies have pointed out that this adaptability also benefits from the combined effect of gene infiltration and structural variation, which provide upland cotton with stronger disease resistance, such as resistance to Fusarium wilt (Wang et al., 2022). In addition, in many areas where cis-type elements related to light, hormones and environmental signal responses are located, structural variations often occur, enabling plants to adjust their physiological responses more flexibly to adapt to complex environments. 4.3 Yield components and plant architecture Yield is not the result determined by a single gene, but rather a combination of traits influenced by structural variations. A large number of structural variations found in the A subgenome are closely related to traits such as cotton boll weight, cotton fluff rate and seed index. GWAS analysis has identified nearly a hundred SVS significantly associated with yield traits, many of which directly affect genes regulating plant type or reproductive development (Jiang et al., 2024). There is a typical example: by introducing the sub-okra leaf shape gene of sea island cotton into upland cotton, the canopy structure of short-season cotton varieties was optimized, the
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