A Non-Coding Genomic Duplication at the HMX1 Locus Is Associated with Crop Ears in Highland Cattle

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.患有先天性耳缺畸形（congenital crop ears）的高地牛，其双耳耳尖会出现大小不一的缺刻。部分病例可见软骨变形，偶见外耳缩短的情况。我们在瑞士境内收集了40份病例样本与80份对照样本。系谱数据分析证实，该性状呈单基因常染色体显性遗传模式，且表现度存在差异。所有患病个体均可追溯至同一个共同祖先。我们开展了全基因组关联分析（genome-wide association study），将致病突变定位至牛6号染色体上一段4 Mb的区间内。H6同源框家族成员1（H6 family homeobox 1, HMX1）基因被选为位置-功能候选基因。通过对1头患病高地牛进行全基因组重测序，我们相对于参考基因组，在HMX1基因座处检测到6个错义编码序列变异以及2个位于超保守元件内的变异。在上述8个变异中，仅1个位于保守区域内的非编码76 bp基因组重复序列（g.106720058_106720133dup）与耳缺畸形性状呈完全关联。该拷贝数变异可能会导致HMX1基因表达失调，并可能产生功能获得性效应。本研究结果证实了HMX1在外耳发育过程中的作用。由于部分仅存在轻微耳尖缺刻的高地牛难以通过表型诊断，如今可借助基因检测优化对该不良性状的选育淘汰工作。