Sequencing & Pangenomes

The diversity and evolutionary history of structural variation in European cattle genomes

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Abstract

The diversification of cattle (Bos taurus) has been shaped by extensive admixture both among breeds and with other Bos species. Although gene flow within the Bos species complex has been well characterized at the level of single nucleotide variation (SNV), its impact on structural variant (SV) diversity remains poorly understood, largely due to the technical difficulties and high cost associated with generating long read data required to detect SVs. However, SVs are likely to have played an important role in domestication and adaptation given their substantial impacts on genome evolution and gene expression. In this study, we used a pangenomics approach to explore the diversity and evolutionary history of SVs across European cattle breeds. We integrated 56 high-quality cattle assemblies (mean NG50: 73.04 ± 22.96 Mb; mean USCO completeness: 97.95 ± 1.32%) of 27 diverse European breeds into a pangenome with Minigraph-Cactus, a reference-guided framework for graph construction from multiple whole-genome alignments. By mapping publicly available short read whole genome sequencing data of more than 1,000 samples, we genotyped ~ 120,000 SVs with the variation graph toolkit (vg call) across 89 taurine breeds, wisent (Bison bonasus) and the extinct aurochs (Bos primigenius). The resulting SV genotypes reveal substantial diversity and breed (group) specific clustering, mirroring previous findings with SNVs. We also explored how previously hypothesized introgression events among domestic taurine cattle (European and North African), wisent and aurochs shaped the landscape of structural variation in current breeds alongside selection. We put a particular emphasis on known quantitative trait loci of economic importance. Our work provides the most comprehensive catalog of SVs in European cattle to date, offering a valuable reference for future breed-focused studies. It also elucidates the evolutionary history of SVs in European cattle - highlighting the roles of introgression and selection - and demonstrates how high-quality pangenome references enable leveraging short read data to analyze structural variation.

Keywords: 2026

How to Cite:

van Elst, T., Leonard, A., Rosen, B., Smith, T., Low, L. & Pausch, H., (2026) “The diversity and evolutionary history of structural variation in European cattle genomes”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284656. doi: https://doi.org/10.31274/wcgalp.23608

Rights: 1