Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs
Bernese mountain dogs are a large dog breed formed in the early 1900s in Switzerland. While originally farm dogs that were used for pulling carts, guarding, and driving cattle, today they are considered multi-purpose companion and family dogs. The breed is predisposed to several complex diseases, su...
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MDPI AG
2023-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/3/650 |
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| author | Anna Letko Benoît Hédan Anna Snell Alexander C. Harris Vidhya Jagannathan Göran Andersson Bodil S. Holst Elaine A. Ostrander Pascale Quignon Catherine André Tosso Leeb |
| author_facet | Anna Letko Benoît Hédan Anna Snell Alexander C. Harris Vidhya Jagannathan Göran Andersson Bodil S. Holst Elaine A. Ostrander Pascale Quignon Catherine André Tosso Leeb |
| author_sort | Anna Letko |
| collection | DOAJ |
| description | Bernese mountain dogs are a large dog breed formed in the early 1900s in Switzerland. While originally farm dogs that were used for pulling carts, guarding, and driving cattle, today they are considered multi-purpose companion and family dogs. The breed is predisposed to several complex diseases, such as histiocytic sarcoma, degenerative myelopathy, or hip dysplasia. Using whole-genome sequencing (WGS) data, we assessed the genomic architecture of 33 unrelated dogs from four countries: France, Sweden, Switzerland, and the United States. Analysis of runs of homozygosity (ROH) identified 12,643 ROH with an average length of 2.29 Mb and an average inbreeding coefficient of 0.395. Multidimensional scaling analysis of the genetic relatedness revealed limited clustering of European versus USA dogs, suggesting exchanges of breeding stock between continents. Furthermore, only two mtDNA haplotypes were detected in the 33 studied dogs, both of which are widespread throughout multiple dog breeds. WGS-based ROH analyses revealed several fixed or nearly fixed regions harboring discreet morphological trait-associated as well as disease-associated genetic variants. Several genes involved in the regulation of immune cells were found in the ROH shared by all dogs, which is notable in the context of the breed’s strong predisposition to hematopoietic cancers. High levels of inbreeding and relatedness, strongly exaggerated in the last 30 years, have likely led to the high prevalence of specific genetic disorders in this breed. |
| first_indexed | 2024-03-11T06:30:31Z |
| format | Article |
| id | doaj.art-e5982a079c024a539b75e69c0603cc2c |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T06:30:31Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-e5982a079c024a539b75e69c0603cc2c2023-11-17T11:17:32ZengMDPI AGGenes2073-44252023-03-0114365010.3390/genes14030650Genomic Diversity and Runs of Homozygosity in Bernese Mountain DogsAnna Letko0Benoît Hédan1Anna Snell2Alexander C. Harris3Vidhya Jagannathan4Göran Andersson5Bodil S. Holst6Elaine A. Ostrander7Pascale Quignon8Catherine André9Tosso Leeb10Institut de Génétique et Développement de Rennes (IGDR)–UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, FranceInstitut de Génétique et Développement de Rennes (IGDR)–UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, FranceDepartment of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, SwedenNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20984, USAInstitute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, SwitzerlandDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, SwedenDepartment of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, SwedenNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20984, USAInstitut de Génétique et Développement de Rennes (IGDR)–UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, FranceInstitut de Génétique et Développement de Rennes (IGDR)–UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, FranceInstitute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, SwitzerlandBernese mountain dogs are a large dog breed formed in the early 1900s in Switzerland. While originally farm dogs that were used for pulling carts, guarding, and driving cattle, today they are considered multi-purpose companion and family dogs. The breed is predisposed to several complex diseases, such as histiocytic sarcoma, degenerative myelopathy, or hip dysplasia. Using whole-genome sequencing (WGS) data, we assessed the genomic architecture of 33 unrelated dogs from four countries: France, Sweden, Switzerland, and the United States. Analysis of runs of homozygosity (ROH) identified 12,643 ROH with an average length of 2.29 Mb and an average inbreeding coefficient of 0.395. Multidimensional scaling analysis of the genetic relatedness revealed limited clustering of European versus USA dogs, suggesting exchanges of breeding stock between continents. Furthermore, only two mtDNA haplotypes were detected in the 33 studied dogs, both of which are widespread throughout multiple dog breeds. WGS-based ROH analyses revealed several fixed or nearly fixed regions harboring discreet morphological trait-associated as well as disease-associated genetic variants. Several genes involved in the regulation of immune cells were found in the ROH shared by all dogs, which is notable in the context of the breed’s strong predisposition to hematopoietic cancers. High levels of inbreeding and relatedness, strongly exaggerated in the last 30 years, have likely led to the high prevalence of specific genetic disorders in this breed.https://www.mdpi.com/2073-4425/14/3/650population structureinbreedingwhole-genome sequencingimmune systemcancer |
| spellingShingle | Anna Letko Benoît Hédan Anna Snell Alexander C. Harris Vidhya Jagannathan Göran Andersson Bodil S. Holst Elaine A. Ostrander Pascale Quignon Catherine André Tosso Leeb Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs Genes population structure inbreeding whole-genome sequencing immune system cancer |
| title | Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs |
| title_full | Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs |
| title_fullStr | Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs |
| title_full_unstemmed | Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs |
| title_short | Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs |
| title_sort | genomic diversity and runs of homozygosity in bernese mountain dogs |
| topic | population structure inbreeding whole-genome sequencing immune system cancer |
| url | https://www.mdpi.com/2073-4425/14/3/650 |
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