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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\u2019s 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.<\/jats:p>","DOI":"10.3390\/genes14030650","type":"journal-article","created":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T05:18:43Z","timestamp":1678079923000},"page":"650","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6521-1285","authenticated-orcid":false,"given":"Anna","family":"Letko","sequence":"first","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et D\u00e9veloppement de Rennes (IGDR)\u2013UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2418-1868","authenticated-orcid":false,"given":"Beno\u00eet","family":"H\u00e9dan","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et D\u00e9veloppement de Rennes (IGDR)\u2013UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Snell","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander C.","family":"Harris","sequence":"additional","affiliation":[{"name":"National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20984, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidhya","family":"Jagannathan","sequence":"additional","affiliation":[{"name":"Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5131-3144","authenticated-orcid":false,"given":"G\u00f6ran","family":"Andersson","sequence":"additional","affiliation":[{"name":"Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7623-7141","authenticated-orcid":false,"given":"Bodil S.","family":"Holst","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6075-9738","authenticated-orcid":false,"given":"Elaine A.","family":"Ostrander","sequence":"additional","affiliation":[{"name":"National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20984, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascale","family":"Quignon","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et D\u00e9veloppement de Rennes (IGDR)\u2013UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Andr\u00e9","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et D\u00e9veloppement de Rennes (IGDR)\u2013UMR6290, University Rennes 1, CNRS-INSERM, 35000 Rennes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0553-4880","authenticated-orcid":false,"given":"Tosso","family":"Leeb","sequence":"additional","affiliation":[{"name":"Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,4]]},"reference":[{"key":"ref_1","unstructured":"(2022, June 01). 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