Abstract
Cotton domestication has driven remarkable improvements in fiber quality; however, the integrative roles of structural variation (SV), 3D genome architecture, and epigenetic regulation in this process remain poorly understood. Here, the genome assembly of wild (yucatanense, Yuc) and cultivated cotton (Xinluzao 61, XLZ61) is first reported. A total of 35 050 InDels and 165 inversions are identified, and 86.6% of these SVs are accumulated in differential topologically associating domain regions, indicating the important role of SV in 3D genome remodeling. Comparative analysis also yielded 199 359 differential DNA methylation regions and 2 092 787 differential RNA methylation loci, collectively affecting 44.7% of differentially expressed genes. Notably, SV-associated methylation changes had stronger effects on gene expression than epigenetic modifications alone. Construction of an ultra-dense genetic map comprising 13 602 620 SNP loci and QTL mapping further revealed SVs and 3D genome remodeling-driven DNA/RNA methylation divergence to contribute to fiber length in domesticated cotton, demonstrating how SV reshapes trait variation. Collectively, these findings elucidated the crucial role of the "SVs-3D genome remodeling-epigenetic modifications-gene expression" cascade regulatory network in cotton fiber domestication, offering both a theoretical foundation and genetic resources for molecular design breeding in fiber crops.