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...

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Autores principales:	Caroline Tina Koch, Rémy Bruggmann, Jens Tetens, Cord Drögemüller
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b892748e73094ebc870264dc84e9ba05
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spelling	oai:doaj.org-article:b892748e73094ebc870264dc84e9ba052021-11-18T08:49:47ZA non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.1932-620310.1371/journal.pone.0077841https://doaj.org/article/b892748e73094ebc870264dc84e9ba052013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24194898/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Highland 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.Caroline Tina KochRémy BruggmannJens TetensCord DrögemüllerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e77841 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Caroline Tina Koch Rémy Bruggmann Jens Tetens Cord Drögemüller A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
description	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.
format	article
author	Caroline Tina Koch Rémy Bruggmann Jens Tetens Cord Drögemüller
author_facet	Caroline Tina Koch Rémy Bruggmann Jens Tetens Cord Drögemüller
author_sort	Caroline Tina Koch
title	A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
title_short	A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
title_full	A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
title_fullStr	A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
title_full_unstemmed	A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
title_sort	non-coding genomic duplication at the hmx1 locus is associated with crop ears in highland cattle.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b892748e73094ebc870264dc84e9ba05
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A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.

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