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Research article2021Peer reviewedOpen access

Introgression contributes to distribution of structural variations in cattle

Upadhyay, Maulik; Derks, Martijn F. L.; Andersson, Goran; Medugorac, Ivica; Groenen, Martien A. M.; Crooijmans, Richard P. M. A.


Structural variations (SVs) are an important source of phenotypic diversity in cattle. Here, 72 whole genome sequences representing taurine and zebu cattle were used to identify SVs. Applying multiple approaches, 16,738 SVs were identified. A comparison against the Database of Genomic Variants archives revealed that 1575 SVs were novel in our data. A novel duplication covering the entire GALNT15 gene, was observed only in N'Dama. A duplication, which was previously reported only in zebu and associated with navel length, was also observed in N'Dama. Investigation of a novel deletion located upstream of CAST13 gene and identified only in Italian cattle and zebu, revealed its introgressed origin in the former. Overall, our data highlights how the SVs distribution in cattle is also shaped by forces such as demographical differences and gene flow. The cattle SVs of this study and its meta-data can be visualized on an interactive genome browser at


Structural variations; Whole genome sequences; Taurine; Indicine; Introgression; GALNT15

Published in

2021, Volume: 113, number: 5, pages: 3092-3102

      SLU Authors

    • Upadhyay, Maulik

      • Department of Animal Biosciences, Swedish University of Agricultural Sciences
      • Ludwig Maximilian University Munich (LMU)
      • Wageningen University & Research Centre (Wageningen UR)
    • UKÄ Subject classification

      Animal and Dairy Science

      Publication identifier


      Permanent link to this page (URI)