Abstract
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.
Highlights
Isolated congenital malformations of the external ear are known in humans and different animal species [1,2,3]
A previous study in Highland cattle reported the presence of very short ears, almost rudimentary, and graded these into a separate third class [8]
We found a 76 bp genomic duplication downstream of the bovine homeobox 1 (HMX1) gene associated with dominantly inherited crop ears in Highland cattle
Summary
Isolated congenital malformations of the external ear are known in humans and different animal species [1,2,3]. Isolated external ear anomalies are known in Scottish breeds such as Ayrshire and Highland cattle, and in Irish Dexter cattle [5,6,7,8,9]. Monogenic autosomal dominant inheritance with variable expressivity has been suggested by several authors [5,6,7,8] Another probably dominantly inherited non-syndromic ear anomaly was reported in British Jersey cattle, in which the notch is located at the lower edge of the ear and looks like the artificially placed ‘‘underbite’’ mark by breeders [10]. A quantitative trait locus for floppy versus erect ears was recently mapped on canine chromosome 10 by genome-wide association [12]
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