Cotton Genomics and Genetics 2025, Vol.16, No.6, 259-268 http://cropscipublisher.com/index.php/cgg 259 Review and Progress Open Access Structural Variations Drive Phenotypic Divergence in Upland and Pima Cotton Pingping Yang, Xian Zhang, Shujuan Wang Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: shujuan.wang@hitar.org Cotton Genomics and Genetics, 2025, Vol.16, No.6 doi: 10.5376/cgg.2025.16.0026 Received: 01 Sep., 2025 Accepted: 11 Oct., 2025 Published: 02 Nov., 2025 Copyright © 2025 Yang et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Yang P.P., Zhang X., and Wang S.J., 2025, Structural variations drive phenotypic divergence in upland and pima cotton, Cotton Genomics and Genetics, 16(6): 259-268 (doi: 10.5376/cgg.2025.16.0026) Abstract Structural variations (SVs) are major genomic alterations that contribute to species diversity and phenotypic differentiation. In this review, we explored how SVs drive the phenotypic divergence between Upland cotton (Gossypium hirsutum) and Pima cotton (Gossypium barbadense), two economically significant species with distinct fiber characteristics. We first summarized advances in sequencing technologies that facilitate the detection and characterization of SVs and analyzed their types, frequency, and lineage-specific patterns across cotton genomes. We then discussed the functional impact of SVs on gene expression, dosage, and regulation, emphasizing their role in modifying fiber traits, stress tolerance, yield, and plant architecture. Mechanistic insights revealed that transposable elements, homologous recombination, and epigenetic modifications are key forces shaping SV formation and genome plasticity. A case study on a major inversion on chromosome A07 further demonstrated how SVs influence fiber quality and provide new opportunities for marker-assisted selection. Finally, we highlighted the integration of SV data into breeding and genome-editing programs to enhance cotton improvement. This review underscores the central role of structural variations in cotton evolution and breeding innovation, offering a genomic foundation for future research on trait diversification and molecular breeding strategies. Keywords Structural variations; Gossypium hirsutum; Gossypium barbadense; Fiber quality; Genomic evolution 1Introduction In global cotton production, upland cotton (Gossypium hirsutum) and Pima cotton (Gossypium barbadense) almost occupy the entire market. The former is highly productive and hardy, and is the main force of the world's cotton. The latter has earned the reputation of "high-end cotton" by virtue of its long fibers and high strength. However, its output is not large and its market share is relatively limited (Lu et al., 2022). Interestingly, the story of these two types of cotton dates back over A million years-when an ancient polyploidization event led to the "fusion" of the ancestors of the A genome and the D genome, and then each embarked on an independent path of domestication, eventually forming the two types with distinct traits today (Yang et al., 2019). When it comes to the diversity of cotton, the concept of "structural variation" (SVs) cannot be avoided. Insertions, deletions, inversions and translocations, these seemingly trivial changes, are precisely the key forces driving the genetic diversity of plants. They not only influenced the evolution of cotton, but also determined the quality of fibers, yield and even disease resistance (Jin et al., 2023). With the continuous improvement of sequencing technology, a large number of structural variations between upland cotton and island cotton, as well as within the same species, have been gradually revealed. These variations will rewrite the expression mode of genes and reshape the regulatory network, thereby causing differences among phenotypes (Ma et al., 2021). It is particularly worth noting that many of these variations are hidden in regions that are difficult for single nucleotide polymorphisms (SNPS) to reach-that is to say, they explain the traits that SNP analyses often "overlook". This study focuses on a core issue: How exactly does structural variation drive the differentiation of land-based cotton and Pima cotton in terms of morphology and agronomic characteristics? We have integrated the achievements of high-quality genome assembly, pan-genome and genome-wide association studies to sort out the formation, function and potential value of SV in breeding from different perspectives. The focus is on how they affect fiber quality, yield performance and stress resistance, with the aim of providing new clues for future cotton improvement.
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