Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies

Structural variations (SVs ≥ 50 bp) are a critical but underexplored source of genetic diversity in cattle, shaping traits vital for productivity, adaptability, and health. Advances in long-read sequencing, pangenome graph construction, and near-complete genome assemblies now allow accurate SV detection and genotyping. These innovations overcome the limitations of single-reference genomes, enabling the discovery of complex SVs, including nested and overlapping variants, and providing access to previously inaccessible genomic regions such as centromeres and telomeres. This review highlights the current landscape of cattle SV research, with emphasis on integrating long-read sequencing and pangenome frameworks to uncover breed-specific and population-level variation. While many SVs are linked to economically important traits such as feed efficiency and disease resistance, their broader regulatory impacts remain an active area of investigation. Emerging functional genomics approaches, including transcriptomics, epigenomics, and genome editing, will clarify how SVs influence gene regulation and phenotype. Looking forward, the integration of SV catalogs with multi-omics data, imputation resources, and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications. Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics, enabling precision selection and sustainable agriculture despite challenges in cost, data sharing, and functional validation.