Pingping Yang , Xian Zhang , Shujuan Wang

Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China
Author    Correspondence author
Cotton Genomics and Genetics, 2025, Vol. 16, No. 6   doi: 10.5376/cgg.2025.16.0026
Received: 07 Sep., 2025    Accepted: 11 Oct., 2025    Published: 02 Nov., 2025

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.

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)

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.

Structural variations; Gossypium hirsutum; Gossypium barbadense; Fiber quality; Genomic evolution