A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.

Koch, Caroline Tina; Bruggmann, Rémy; Tetens, Jens; Drögemüller, Cord (2013). A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle. PLoS ONE, 8(10), e77841. Public Library of Science 10.1371/journal.pone.0077841

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Highland cattle with congenital crop ears have notches of variable size on the tips of both ears. In some cases, cartilage deformation can be seen and occasionally the external ears are shortened. We collected 40 cases and 80 controls across Switzerland. Pedigree data analysis confirmed a monogenic autosomal dominant mode of inheritance with variable expressivity. All affected animals could be traced back to a single common ancestor. A genome-wide association study was performed and the causative mutation was mapped to a 4 Mb interval on bovine chromosome 6. The H6 family homeobox 1 (HMX1) gene was selected as a positional and functional candidate gene. By whole genome re-sequencing of an affected Highland cattle, we detected 6 non-synonymous coding sequence variants and two variants in an ultra-conserved element at the HMX1 locus with respect to the reference genome. Of these 8 variants, only a non-coding 76 bp genomic duplication (g.106720058_106720133dup) located in the conserved region was perfectly associated with crop ears. The identified copy number variation probably results in HMX1 misregulation and possible gain-of-function. Our findings confirm the role of HMX1 during the development of the external ear. As it is sometimes difficult to phenotypically diagnose Highland cattle with slight ear notches, genetic testing can now be used to improve selection against this undesired trait.

Item Type:

Journal Article (Original Article)


05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
08 Faculty of Science > Department of Biology > Bioinformatics and Computational Biology

UniBE Contributor:

Koch, Caroline, Bruggmann, Rémy, Drögemüller, Cord


500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture




Public Library of Science




Susanne Portner

Date Deposited:

04 Jul 2014 11:42

Last Modified:

05 Dec 2022 14:29

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