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We established a comprehensive variation map for 1379 European cattle from nine breeds using a pangenome graph. Although SV and SNP distributions were similar genome\u2010wide, 19.3% of SVs exhibited low linkage disequilibrium (\n                    <jats:italic>r<\/jats:italic>\n                    \u00b2\u2009&lt;\u20090.2) with nearby SNPs. These non\u2010SNP\u2010tagged SVs are preferentially localized to chromosome ends and promoters, and play crucial roles in artificial selection for production traits. Integrated analyses of large\u2010scale chromosomal recombination data and transposon\u2010mediated SV events revealed that terminal chromosomal recombination and strong selection on recurrent young SVs are likely to prevent SNP tagging. For SVs tagged by SNPs, they were found to play a dominant role in haplotype diversity and inter\u2010population differences. Genome\u2010wide association studies of over 50,000 dairy bulls using imputed SV\u2009+\u2009SNP data identified functional SVs missed by standard analysis, including an SV (chr6:32,772,14\u201332,772,409) showing strong milk yield association (\n                    <jats:italic>p<\/jats:italic>\n                    \u2009&lt;\u20091\u2009\u00d7\u200910\n                    <jats:sup>\u2212<\/jats:sup>\n                    <jats:sup>10<\/jats:sup>\n                    ) and divergent selection between dairy and beef breeds, demonstrating SVs' unique contribution to complex trait architecture. Overall, our study illustrates the independent or dominant roles of SV in the breeding processes of the European cattle, facilitating the use of pangenome SVs to recover missing heritability from SNP\u2010based research.\n                  <\/jats:p>","DOI":"10.1002\/imo2.70095","type":"journal-article","created":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T01:30:55Z","timestamp":1775439055000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pangenome variation analysis uncovers the impacts of SNP\u2010independent structural variations in modern European cattle breeding"],"prefix":"10.1002","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3976-0033","authenticated-orcid":false,"given":"Shoulu","family":"Dai","sequence":"first","affiliation":[{"name":"Yazhouwan National Laboratory Sanya China"},{"name":"Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of 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