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Thorsrud JA, Huson HJ. Description of breed ancestry and genetic health traits in arctic sled dog breeds. Canine Med Genet 2021; 8:8. [PMID: 34544496 PMCID: PMC8454093 DOI: 10.1186/s40575-021-00108-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Background This study describes the presence and frequency of health traits among three populations of dogs traditionally used for sledding and explores their ancestry and breed composition as provided by the commercially available Embark dog DNA test. The three populations include the purebred Siberian Husky and the admixed populations of Alaskan sled dogs and Polar Huskies. While the Siberian Husky represents a well-established breed with extensive historical and health data, the Alaskan sled dog is less studied but has been the subject of nutritional, physiological, and genetic studies related to ancestry and performance. In contrast, the Polar Husky is a relatively obscure and rare group of dogs used for arctic exploration with very little-known information. The three populations were compared using Embark results, providing new insight into the health traits circulating within the populations and the potential ancestral linkage of the health traits between the sledding populations. Embark results are based upon 228,588 single-nucleotide polymorphisms (SNPs) spanning the canine genome, characterized using a custom-designed Illumina beadchip array. Results Specifically, breed composition was summarized for the two admixed populations with most of the dogs being predominantly categorized as Alaskan husky- type dog or “Supermutt”. Mitochondrial and Y chromosome haplogroups and haplotypes were found with Alaskan sled dogs carrying most of the haplogroups and types found in Siberian and Polar Huskies. Genomic principal component analysis reflected population structure corresponding to breed and substructure within the Alaskan sled dogs related to sprint or distance competition. Genetic markers associated with Alanine Aminotransferase activity, Alaskan Husky Encephalopathy, dilated cardiomyopathy, Collie eye anomaly, degenerative myelopathy, ichthyosis, and factor VII deficiency were identified in the populations of sledding breeds. Conclusion These results provide a preliminary description of genetic characteristics found in sledding breeds, improving the understanding and care of working sled dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-021-00108-z.
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Affiliation(s)
- Joseph A Thorsrud
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, 201 Morrison Hall, 507 Tower Road, Ithaca, NY, 14853, USA
| | - Heather J Huson
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, 201 Morrison Hall, 507 Tower Road, Ithaca, NY, 14853, USA.
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102
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Benítez-Burraco A, Pörtl D, Jung C. Did Dog Domestication Contribute to Language Evolution? Front Psychol 2021; 12:695116. [PMID: 34589022 PMCID: PMC8473740 DOI: 10.3389/fpsyg.2021.695116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
Different factors seemingly account for the emergence of present-day languages in our species. Human self-domestication has been recently invoked as one important force favoring language complexity mostly via a cultural mechanism. Because our self-domestication ultimately resulted from selection for less aggressive behavior and increased prosocial behavior, any evolutionary or cultural change impacting on aggression levels is expected to have fostered this process. Here, we hypothesize about a parallel domestication of humans and dogs, and more specifically, about a positive effect of our interaction with dogs on human self-domestication, and ultimately, on aspects of language evolution, through the mechanisms involved in the control of aggression. We review evidence of diverse sort (ethological mostly, but also archeological, genetic, and physiological) supporting such an effect and propose some ways of testing our hypothesis.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Daniela Pörtl
- Psychiatric Department, Saale-Unstrut Klinikum, Teaching Hospital Leipzig and Jena Universities, Naumburg, Germany
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103
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Best practices for analyzing imputed genotypes from low-pass sequencing in dogs. Mamm Genome 2021; 33:213-229. [PMID: 34498136 PMCID: PMC8913487 DOI: 10.1007/s00335-021-09914-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Although DNA array-based approaches for genome-wide association studies (GWAS) permit the collection of thousands of low-cost genotypes, it is often at the expense of resolution and completeness, as SNP chip technologies are ultimately limited by SNPs chosen during array development. An alternative low-cost approach is low-pass whole genome sequencing (WGS) followed by imputation. Rather than relying on high levels of genotype confidence at a set of select loci, low-pass WGS and imputation rely on the combined information from millions of randomly sampled low-confidence genotypes. To investigate low-pass WGS and imputation in the dog, we assessed accuracy and performance by downsampling 97 high-coverage (> 15×) WGS datasets from 51 different breeds to approximately 1× coverage, simulating low-pass WGS. Using a reference panel of 676 dogs from 91 breeds, genotypes were imputed from the downsampled data and compared to a truth set of genotypes generated from high-coverage WGS. Using our truth set, we optimized a variant quality filtering strategy that retained approximately 80% of 14 M imputed sites and lowered the imputation error rate from 3.0% to 1.5%. Seven million sites remained with a MAF > 5% and an average imputation quality score of 0.95. Finally, we simulated the impact of imputation errors on outcomes for case-control GWAS, where small effect sizes were most impacted and medium-to-large effect sizes were minorly impacted. These analyses provide best practice guidelines for study design and data post-processing of low-pass WGS-imputed genotypes in dogs.
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104
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Axelsson E, Ljungvall I, Bhoumik P, Conn LB, Muren E, Ohlsson Å, Olsen LH, Engdahl K, Hagman R, Hanson J, Kryvokhyzha D, Pettersson M, Grenet O, Moggs J, Del Rio-Espinola A, Epe C, Taillon B, Tawari N, Mane S, Hawkins T, Hedhammar Å, Gruet P, Häggström J, Lindblad-Toh K. The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels. PLoS Genet 2021; 17:e1009726. [PMID: 34473707 PMCID: PMC8412370 DOI: 10.1371/journal.pgen.1009726] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity. As a consequence of selective breeding, specific disease-causing mutations have become more frequent in certain dog breeds. Whether the breeding practice also resulted in a general increase in the overall number of disease-causing mutations per dog genome is however not clear. To address this question, we compare the amount of harmful, potentially disease-causing, mutations in dogs from eight common breeds that have experienced varying degrees of intense selective breeding. We find that individuals belonging to the breed affected by the most intense breeding—cavalier King Charles spaniel (cKCs)—carry more harmful variants than other breeds, indicating that past breeding practices may have increased the overall levels of harmful genetic variation in dogs. The most common disease in cKCs is myxomatous mitral valve disease (MMVD). To identify variants linked to this disease we next characterize mutations that are common in cKCs, but rare in other breeds, and then investigate if these mutations can predict MMVD in dachshunds. We find that variants that regulate the expression of the gene NEBL in papillary muscles may increase the risk of the disease, indicating that loss of papillary muscle integrity could contribute to the development of MMVD.
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Affiliation(s)
- Erik Axelsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Priyasma Bhoumik
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Laura Bas Conn
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Muren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lisbeth Høier Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karolina Engdahl
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ragnvi Hagman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jeanette Hanson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Dmytro Kryvokhyzha
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Olivier Grenet
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jonathan Moggs
- Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Christian Epe
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Bruce Taillon
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Nilesh Tawari
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Shrinivas Mane
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Troy Hawkins
- Elanco Animal Health, Greenfield, Indiana, United States of America
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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105
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Is the Prevalence of Leishmania infantum Linked to Breeds in Dogs? Characterization of Seropositive Dogs in Ibiza. Animals (Basel) 2021; 11:ani11092579. [PMID: 34573545 PMCID: PMC8466328 DOI: 10.3390/ani11092579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Leishmaniosis is an important zoonotic protozoan disease. Leishmania infantum is a protozoan species that accounts for the majority of cases in the Mediterranean. In this study, we analyzed the prevalence of infection in different dog breeds from Ibizan Island. Our results showed that the Doberman Pinscher and Boxer breeds present a higher prevalence of infection, and the relationship between antibodies’ serum titer and staging of disease was confirmed. Differences between age and sex were not found. Abstract Leishmaniosis is an important zoonotic protozoan disease primarily spread to the Mediterranean region by Leishmania infantum, the predominant protozoan species, which accounts for the majority of cases. Development of disease depends on the immune response of the definitive host and, predictably, their genetic background. Recent studies have revealed breed-typical haplotypes that are susceptible to the spread of the protozoan parasite. The objective of this study was to analyze the prevalence of leishmaniosis on a Mediterranean island and determine the relationship between disease prevalence and breed. In addition, information on seropositive animals was recorded to characterize animals affected by the disease. To study the prevalence, a total of 3141 dogs were analyzed. Of these, the 149 infected animals were examined for age, sex, antibody titer, and disease stage. We observed a prevalence of 4.74%, which varied between breeds (p < 0.05). The Doberman Pinscher and Boxer breeds had the highest prevalence of leishmaniosis. Significant differences were observed between breeds with common ancestors, emphasizing the important genetic component. Finally, regarding the characterization of seropositive animals, the distribution is similar to other studies. We discovered a relationship (p < 0.05) between the number of antibody titers and the clinical disease stage, which was also present in Leishmania infantum, suggesting that the development of the disease depends on the humoral or Th2 immune response with ineffective antibodies.
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106
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Hecht EE, Zapata I, Alvarez CE, Gutman DA, Preuss TM, Kent M, Serpell JA. Neurodevelopmental scaling is a major driver of brain-behavior differences in temperament across dog breeds. Brain Struct Funct 2021; 226:2725-2739. [PMID: 34455497 DOI: 10.1007/s00429-021-02368-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022]
Abstract
Behavioral traits like aggression, anxiety, and trainability differ significantly across dog breeds and are highly heritable. However, the neural bases of these differences are unknown. Here we analyzed structural MRI scans of 62 dogs in relation to breed-average scores for the 14 major dimensions in the Canine Behavioral Assessment and Research Questionnaire, a well-validated measure of canine temperament. Several behavior categories showed significant relationships with morphologically covarying gray matter networks and regional volume changes. Networks involved in social processing and the flight-or-fight response were associated with stranger-directed fear and aggression, putatively the main behaviors under selection pressure during wolf-to-dog domestication. Trainability was significantly associated with expansion in broad regions of cortex, while fear, aggression, and other "problem" behaviors were associated with expansion in distributed subcortical regions. These results closely overlapped with regional volume changes with total brain size, in striking correspondence with models of developmental constraint on brain evolution. This suggests that the established link between dog body size and behavior is due at least in part to disproportionate enlargement of later-developing regions in larger brained dogs. We discuss how this may explain the known correlation of increasing reactivity with decreasing body size in dogs.
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Affiliation(s)
- E E Hecht
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave., Cambridge, MA, 02138, USA.
| | - I Zapata
- Department of Biomedical Sciences, Rocky Vista University, Parker, CO, 80134, USA
| | - C E Alvarez
- Center for Clinical and Translational Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.,Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210, USA
| | - D A Gutman
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, 30029, USA
| | - T M Preuss
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30029, USA
| | - M Kent
- College of Veterinary Medicine, University of Georgia at Athens, Athens, GA, 30602, USA
| | - J A Serpell
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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107
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Geiger M, Schoenebeck JJ, Schneider RA, Schmidt MJ, Fischer MS, Sánchez-Villagra MR. Exceptional Changes in Skeletal Anatomy under Domestication: The Case of Brachycephaly. Integr Org Biol 2021; 3:obab023. [PMID: 34409262 PMCID: PMC8366567 DOI: 10.1093/iob/obab023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/06/2021] [Accepted: 07/08/2021] [Indexed: 01/17/2023] Open
Abstract
"Brachycephaly" is generally considered a phenotype in which the facial part of the head is pronouncedly shortened. While brachycephaly is characteristic for some domestic varieties and breeds (e.g., Bulldog, Persian cat, Niata cattle, Anglo-Nubian goat, Middle White pig), this phenotype can also be considered pathological. Despite the superficially similar appearance of "brachycephaly" in such varieties and breeds, closer examination reveals that "brachycephaly" includes a variety of different cranial modifications with likely different genetic and developmental underpinnings and related with specific breed histories. We review the various definitions and characteristics associated with brachycephaly in different domesticated species. We discern different types of brachycephaly ("bulldog-type," "katantognathic," and "allometric" brachycephaly) and discuss morphological conditions related to brachycephaly, including diseases (e.g., brachycephalic airway obstructive syndrome). Further, we examine the complex underlying genetic and developmental processes and the culturally and developmentally related reasons why brachycephalic varieties may or may not be prevalent in certain domesticated species. Knowledge on patterns and mechanisms associated with brachycephaly is relevant for domestication research, veterinary and human medicine, as well as evolutionary biology, and highlights the profound influence of artificial selection by humans on animal morphology, evolution, and welfare.
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Affiliation(s)
- M Geiger
- Paleontological Institute and Museum, University of Zurich,
Karl-Schmid-Str. 4, 8006 Zurich, Switzerland
| | - J J Schoenebeck
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University
of Edinburgh, Easter Bush Campus, Midlothian EH25
9RG, UK
| | - R A Schneider
- Department of Orthopaedic Surgery, University of California at San
Francisco, 513 Parnassus Avenue, S-1164, San Francisco, CA
94143-0514, USA
| | - M J Schmidt
- Clinic for Small Animals—Neurosurgery, Neuroradiology and Clinical
Neurology, Justus Liebig University Giessen, Frankfurter Str.
114, 35392 Giessen, Germany
| | - M S Fischer
- Institute of Zoology and Evolutionary Research, Friedrich-Schiller
University Jena, Erbertstr. 1, 07743 Jena,
Germany
| | - M R Sánchez-Villagra
- Paleontological Institute and Museum, University of Zurich,
Karl-Schmid-Str. 4, 8006 Zurich, Switzerland
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108
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Ohta J, Konishi-Kato Y, Minegishi S, Sakurada K. Oral bacterial DNA-based discrimination of human and canine saliva for the analysis of indistinct bite marks. Forensic Sci Int Genet 2021; 54:102566. [PMID: 34332321 DOI: 10.1016/j.fsigen.2021.102566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/28/2022]
Abstract
Analyzing ambiguous bite marks using conventional morphological approaches to identify attackers is difficult; thus, applying molecular biological methods for identifying an attacker from their saliva is a possible approach in a forensic investigation. This study aimed to establish oral bacterial DNA-based human and canine saliva markers and develop a practical method for their discrimination. We considered Streptococcus oralis and Pasteurella canis as human and canine saliva marker candidates, respectively. Duplex bacterial DNA detection using melting curve analysis was designed and evaluated for forensic applicability using proof-of-concept experiments. S. oralis DNA was detected from human saliva samples from 30 out of 30 individuals, and P. canis DNA was detected from canine saliva samples from 73 out of 77 individuals (26 dog breeds). Additionally, both bacterial DNA markers were accurately detected from human blood-contaminated saliva samples and mock indistinct bite marks. Our results indicate that both bacterial DNA markers were sensitive, robust, and discriminating saliva markers. We consider that our duplex bacterial DNA examination is a simple, practical, and useful method for the detection of saliva from indistinct bite marks and discrimination between human and canine saliva.
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Affiliation(s)
- Jun Ohta
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Scientific Crime Laboratory, Kanagawa Prefectural Police, 155-1 Yamashita-cho, Naka-ku, Yokohama, Kanagawa 231-0023, Japan.
| | - Yuko Konishi-Kato
- Forensic Science Laboratory, Hyogo Prefectural Police Headquarters, 5-4-1, Shimoyamatedo-ri, Chuo-ku, Kobe, Hyogo 650-8510, Japan
| | - Saki Minegishi
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Koichi Sakurada
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Stevanovic V, Tabain I, Vilibic-Cavlek T, Mauric Maljkovic M, Benvin I, Hruskar Z, Kovac S, Smit I, Miletic G, Hadina S, Staresina V, Radin L, Plichta V, Skrlin B, Vrbanac Z, Brkljacic M, Cvetnic M, Habus J, Martinkovic K, Zecevic I, Jurkic G, Ferencak I, Stritof Z, Perharic M, Bucic L, Barbic L. The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome. Viruses 2021; 13:1430. [PMID: 34452296 PMCID: PMC8402787 DOI: 10.3390/v13081430] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
Over a year into the COVID-19 pandemic, there is growing evidence that SARS-CoV-2 infections among dogs are more common than previously thought. In this study, the prevalence of SARS-CoV-2 antibodies was investigated in two dog populations. The first group was comprised of 1069 dogs admitted to the Veterinary Teaching Hospital for any given reason. The second group included dogs that shared households with confirmed COVID-19 cases in humans. This study group numbered 78 dogs. In COVID-19 infected households, 43.9% tested ELISA positive, and neutralising antibodies were detected in 25.64% of dogs. Those data are comparable with the secondary attack rate in the human population. With 14.69% of dogs in the general population testing ELISA positive, there was a surge of SARS-CoV-2 infections within the dog population amid the second wave of the pandemic. Noticeably seroprevalence of SARS-CoV-2 in the dog and the human population did not differ at the end of the study period. Male sex, breed and age were identified as significant risk factors. This study gives strong evidence that while acute dog infections are mostly asymptomatic, they can pose a significant risk to dog health. Due to the retrospective nature of this study, samples for viral isolation and PCR were unavailable. Still, seropositive dogs had a 1.97 times greater risk for developing central nervous symptoms.
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Affiliation(s)
- Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
| | - Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Maja Mauric Maljkovic
- Department for Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Iva Benvin
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Zeljka Hruskar
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
| | - Snjezana Kovac
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
| | - Iva Smit
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Gorana Miletic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
| | - Suzana Hadina
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Vilim Staresina
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
| | - Lada Radin
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Valentina Plichta
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Branimir Skrlin
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Zoran Vrbanac
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Mirna Brkljacic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Marija Cvetnic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Josipa Habus
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Kresimir Martinkovic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Iva Zecevic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Gabrijela Jurkic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Ivana Ferencak
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
| | - Zinka Stritof
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Matko Perharic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Lovro Bucic
- Department of Epidemiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia;
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
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110
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Lyu G, Feng C, Zhu S, Ren S, Dang W, Irwin DM, Wang Z, Zhang S. Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds. Front Genet 2021; 12:671686. [PMID: 34335687 PMCID: PMC8317602 DOI: 10.3389/fgene.2021.671686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the "Mame Shiba Inu" breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including F ST, H p and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.
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Affiliation(s)
- Guangqi Lyu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Feng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shiyu Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuang Ren
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Wanyi Dang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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111
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José‐López R, Gutierrez‐Quintana R, de la Fuente C, Manzanilla EG, Suñol A, Pi Castro D, Añor S, Sánchez‐Masian D, Fernández‐Flores F, Ricci E, Marioni‐Henry K, Mascort J, Matiasek LA, Matiasek K, Brennan PM, Pumarola M. Clinical features, diagnosis, and survival analysis of dogs with glioma. J Vet Intern Med 2021; 35:1902-1917. [PMID: 34117807 PMCID: PMC8295679 DOI: 10.1111/jvim.16199] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Gliomas in dogs remain poorly understood. OBJECTIVES To characterize the clinicopathologic findings, diagnostic imaging features and survival of a large sample of dogs with glioma using the Comparative Brain Tumor Consortium diagnostic classification. ANIMALS Ninety-one dogs with histopathological diagnosis of glioma. METHODS Multicentric retrospective case series. Signalment, clinicopathologic findings, diagnostic imaging characteristics, treatment, and outcome were used. Tumors were reclassified according to the new canine glioma diagnostic scheme. RESULTS No associations were found between clinicopathologic findings or survival and tumor type or grade. However, definitive treatments provided significantly (P = .03) improved median survival time (84 days; 95% confidence interval [CI], 45-190) compared to palliative treatment (26 days; 95% CI, 11-54). On magnetic resonance imaging (MRI), oligodendrogliomas were associated with smooth margins and T1-weighted hypointensity compared to astrocytomas (odds ratio [OR], 42.5; 95% CI, 2.42-744.97; P = .04; OR, 45.5; 95% CI, 5.78-333.33; P < .001, respectively) and undefined gliomas (OR, 84; 95% CI, 3.43-999.99; P = .02; OR, 32.3; 95% CI, 2.51-500.00; P = .008, respectively) and were more commonly in contact with the ventricles than astrocytomas (OR, 7.47; 95% CI, 1.03-53.95; P = .049). Tumor spread to neighboring brain structures was associated with high-grade glioma (OR, 6.02; 95% CI, 1.06-34.48; P = .04). CONCLUSIONS AND CLINICAL IMPORTANCE Dogs with gliomas have poor outcomes, but risk factors identified in survival analysis inform prognosis and the newly identified MRI characteristics could refine diagnosis of tumor type and grade.
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Affiliation(s)
- Roberto José‐López
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUK
- Department of Animal Medicine and Surgery, Veterinary FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Rodrigo Gutierrez‐Quintana
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUK
| | - Cristian de la Fuente
- Department of Animal Medicine and Surgery, Veterinary FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Edgar G. Manzanilla
- School of Veterinary Medicine, University College DublinDublinIreland
- TEAGASC, The Irish Food and Agriculture AuthorityCorkIreland
| | - Anna Suñol
- ARS VeterinariaBarcelonaSpain
- Present address:
Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUK
| | - Dolors Pi Castro
- Department of Animal Medicine and Surgery, Veterinary FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER‐BBN), Universitat Autònoma de BarcelonaBarcelonaSpain
- Present address:
Anicura Arvivet Hospital VeterinariBarcelonaSpain
| | - Sonia Añor
- Department of Animal Medicine and Surgery, Veterinary FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Daniel Sánchez‐Masian
- Institute of Veterinary Science, University of LiverpoolNestonUK
- Present address:
Anderson Moores Veterinary SpecialistsWinchesterUK
| | | | - Emanuele Ricci
- Institute of Veterinary Science, University of LiverpoolNestonUK
| | - Katia Marioni‐Henry
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of EdinburghEdinburghUK
| | | | - Lara A. Matiasek
- Tierklinik HaarHaarGermany
- Present address:
Anicura Small Animal ClinicBabenhausenGermany
| | - Kaspar Matiasek
- Centre for Clinical Veterinary Medicine, Ludwig‐Maximilians‐UniversitaetMunichGermany
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of EdinburghEdinburghUK
| | - Martí Pumarola
- Department of Animal Medicine and Surgery, Veterinary FacultyUniversitat Autònoma de BarcelonaBarcelonaSpain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER‐BBN), Universitat Autònoma de BarcelonaBarcelonaSpain
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112
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Boone JM, Bond R, Loeffler A, Ferguson EA, Hendricks A. Malassezia otitis unresponsive to primary care: outcome in 59 dogs. Vet Dermatol 2021; 32:441-e119. [PMID: 34189776 DOI: 10.1111/vde.12995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 02/22/2021] [Accepted: 04/01/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Otitis externa (OE) is a common disorder in dogs. Infection by the commensal yeast, Malassezia pachydermatis, may result in chronic disease that does not respond to standard primary care. Chronic infectious OE may be associated with otitis media (OM). HYPOTHESIS/OBJECTIVE To report medical management, clinical outcomes and frequency of middle ear involvement, in dogs with Malassezia otitis unresponsive to primary care. ANIMALS Fifty-nine dogs from one referral veterinary hospital from January 2007 to September 2018. METHODS AND MATERIALS Retrospective analysis of medical records of dogs referred with chronic otitis and treated for Malassezia otitis at a referral veterinary hospital. RESULTS Chronic Malassezia OE was treated successfully in 91% of ears, in 87% of these cases with one ear flush intervention. Median time-to-resolution was 27 days after ear flush intervention. Neither duration of otitis, presence of neutrophils in aural discharge nor administration of oral itraconazole affected clinical outcome. Malassezia OM occurred concurrently in 17% of ears. CONCLUSIONS AND CLINICAL RELEVANCE These findings assist clinicians and carers of affected dogs in decision-making, by documenting that most cases of canine Malassezia otitis that have not resolved with standard primary care, can be treated successfully with a well-staged and intense medical treatment plan. Malassezia OM should be suspected to occur concurrently in around a fifth of affected ears.
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Affiliation(s)
- Johann M Boone
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Ross Bond
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Anette Loeffler
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Ewan A Ferguson
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Anke Hendricks
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA, UK
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113
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Brown JD, Podadera J, Ward M, Goldsmid S, Simpson DJ. The presence, morphology and clinical significance of vertebral body malformations in an Australian population of French Bulldogs and Pugs. Aust Vet J 2021; 99:378-387. [PMID: 34137021 DOI: 10.1111/avj.13094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To describe the incidence, morphology and clinical significance of congenital vertebral malformations (CVM) in two breeds of brachycephalic dogs presenting to a referral veterinary hospital. DESIGN Prospective cohort study series. MATERIALS AND METHODS Forty-nine French Bulldogs and Pugs were prospectively evaluated and placed in one of two groups based on whether or not they presented for neurological signs referable to spinal cord disease. A computed tomography (CT) of their entire spine was obtained and the presence and classification of CVM along with the degree of spinal kyphosis recorded for all dogs. Statistical analysis was performed to identify clinical associations between these factors (P < 0.05). RESULTS CVM were prevalent across both breeds with the French Bulldog having more malformations than the Pug (Kruskal-Wallis nonparametric analysis of variance, P < 0.0001). Breed associated vertebral malformation subtypes included butterfly subtype in French Bulldogs (Chi-square, P = 0.0002), and transitional subtype in Pugs (odds ratio, 22.7; P = 0.000). A new subtype, dorsal wedge, was observed in 12 cases. The presence, number and subtype of vertebral malformation were not reliable for predicting the development of neurological signs across both breeds (Chi-square, P > 0.05). However, spinal kyphosis >35° calculated via Cobb angle was associated with Pugs that had neurological deficits (Chi-square, P = 0.028). CONCLUSIONS Congenital vertebral malformations largely appear to be incidental findings in this population of French Bulldogs but are of more significance in the Pug breed when spinal kyphosis is >35°. French Bulldogs that have spinal cord disease and CVM are more likely to have pathology distant to CVM with intervertebral disc herniation most common.
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Affiliation(s)
- J D Brown
- Surgery Department, Animal Referral Hospital, Homebush, New South Wales, Australia
| | - J Podadera
- Sydney School of Veterinary Science, The University of Sydney, Camden, New South Wales, Australia
| | - M Ward
- Sydney School of Veterinary Science, The University of Sydney, Camden, New South Wales, Australia
| | - S Goldsmid
- Surgery Department, Animal Referral Hospital, Homebush, New South Wales, Australia
| | - D J Simpson
- Surgery Department, Animal Referral Hospital, Homebush, New South Wales, Australia
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114
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Berger C, Heinrich J, Berger B, Hecht W, Parson W. Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs. Genes (Basel) 2021; 12:genes12060908. [PMID: 34208207 PMCID: PMC8230911 DOI: 10.3390/genes12060908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.
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Affiliation(s)
- Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Correspondence: ; Tel.: +43-512-9003-70640
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35390 Giessen, Germany;
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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Evans JM, Parker HG, Rutteman GR, Plassais J, Grinwis GCM, Harris AC, Lana SE, Ostrander EA. Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in retriever dog breeds. PLoS Genet 2021; 17:e1009543. [PMID: 33983928 PMCID: PMC8118335 DOI: 10.1371/journal.pgen.1009543] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/12/2021] [Indexed: 12/18/2022] Open
Abstract
Histiocytic sarcoma is an aggressive hematopoietic malignancy of mature tissue histiocytes with a poorly understood etiology in humans. A histologically and clinically similar counterpart affects flat-coated retrievers (FCRs) at unusually high frequency, with 20% developing the lethal disease. The similar clinical presentation combined with the closed population structure of dogs, leading to high genetic homogeneity, makes dogs an excellent model for genetic studies of cancer susceptibility. To determine the genetic risk factors underlying histiocytic sarcoma in FCRs, we conducted multiple genome-wide association studies (GWASs), identifying two loci that confer significant risk on canine chromosomes (CFA) 5 (Pwald = 4.83x10-9) and 19 (Pwald = 2.25x10-7). We subsequently undertook a multi-omics approach that has been largely unexplored in the canine model to interrogate these regions, generating whole genome, transcriptome, and chromatin immunoprecipitation sequencing. These data highlight the PI3K pathway gene PIK3R6 on CFA5, and proximal candidate regulatory variants that are strongly associated with histiocytic sarcoma and predicted to impact transcription factor binding. The CFA5 association colocalizes with susceptibility loci for two hematopoietic malignancies, hemangiosarcoma and B-cell lymphoma, in the closely related golden retriever breed, revealing the risk contribution this single locus makes to multiple hematological cancers. By comparison, the CFA19 locus is unique to the FCR and harbors risk alleles associated with upregulation of TNFAIP6, which itself affects cell migration and metastasis. Together, these loci explain ~35% of disease risk, an exceptionally high value that demonstrates the advantages of domestic dogs for complex trait mapping and genetic studies of cancer susceptibility. We have identified two regions of the canine genome that explain a striking 35% of risk for developing histiocytic sarcoma in FCRs. The disease is uniformly lethal, affects 20% of FCRs, and parallels a cancer of the same name in humans. Both regions harbor genes involved in cell migration and cancer-related pathways. The first includes variants in regulatory regions at the tumor suppressor PIK3R6 locus that are strongly associated with histiocytic sarcoma and likely confer risk for other hematopoietic cancers. FCRs with risk alleles at the second locus demonstrate increased expression of TNFAIP6, which correlates with poor prognosis in multiple human cancers. In identifying genomic differences between affected and unaffected dogs, we advance our understanding of both canine and human health biology and set the stage for the development of diagnostic and therapeutic strategies.
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Affiliation(s)
- Jacquelyn M. Evans
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Heidi G. Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gerard R. Rutteman
- Department of Clinical Sciences, division Internal Medicine of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Guy C. M. Grinwis
- Department Biomedical Health Sciences, division Pathology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Alexander C. Harris
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan E. Lana
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Abstract
Subvalvular aortic stenosis (SAS) is one of the most common congenital heart defects of dogs. The disease is characterized by obstruction of the left ventricular outflow tract, resulting in pressure overload on the left ventricle. The etiology of obstruction is a fibromuscular nodule, ridge, or ring of tissue that increases aortic outflow tract velocity. This review is focused on the prevalence, inheritance pattern, and current genetic insights of canine SAS. The prevalence of this disease was reported at 4.7 % in a large veterinary referral hospital. The mode of inheritance for this disease has also been described in breeds with a high disease prevalence such as the Bullmastiff, Bouvier des Flandres, Dogue de Bordeaux, Golden Retriever, Newfoundland, and Rottweiler. Genetic investigations seeking to identify causative mutations for SAS are lacking with only a single published variant associated with SAS in Newfoundlands.
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117
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Salonen M, Mikkola S, Hakanen E, Sulkama S, Puurunen J, Lohi H. Reliability and Validity of a Dog Personality and Unwanted Behavior Survey. Animals (Basel) 2021; 11:1234. [PMID: 33923262 PMCID: PMC8147106 DOI: 10.3390/ani11051234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 12/20/2022] Open
Abstract
Dogs have distinct, consistent personalities, but the structure of dog personality is still unclear. Dog personality and unwanted behavior are often studied with behavioral questionnaires. Even though many questionnaires are reliable and valid measures of behavior, all new questionnaire tools should be extensively validated. Here, we examined the structure of personality and six unwanted behavior questionnaire sections: noise sensitivity, fearfulness, aggression, fear of surfaces and heights, separation anxiety and impulsivity/inattention with factor analyses. Personality consisted of seven factors: Insecurity, Training focus, Energy, Aggressiveness/dominance, Human sociability, Dog sociability and Perseverance. Most unwanted behavior sections included only one factor, but the impulsivity/inattention section divided into two factors (Hyperactivity/impulsivity and Inattention) and the aggression section into four factors (Barking, Stranger directed aggression, Owner directed aggression and Dog directed aggression). We also examined the internal consistency, test-retest reliability, inter-rater reliability and convergent validity of the 17 personality and unwanted behavior traits and discovered excellent reliability and validity. Finally, we investigated the discriminant validity of the personality traits, which was good. Our findings indicate that this personality and unwanted behavior questionnaire is a reliable and valid tool that can be used to study personality and behavior extensively.
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Affiliation(s)
- Milla Salonen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland; (M.S.); (S.M.); (E.H.); (S.S.); (J.P.)
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Salla Mikkola
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland; (M.S.); (S.M.); (E.H.); (S.S.); (J.P.)
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Emma Hakanen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland; (M.S.); (S.M.); (E.H.); (S.S.); (J.P.)
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Sini Sulkama
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland; (M.S.); (S.M.); (E.H.); (S.S.); (J.P.)
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Jenni Puurunen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland; (M.S.); (S.M.); (E.H.); (S.S.); (J.P.)
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland; (M.S.); (S.M.); (E.H.); (S.S.); (J.P.)
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
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Karakus E, Prinzinger C, Leiting S, Geyer J. Sequencing of the Canine Cytochrome P450 CYP2C41 Gene and Genotyping of Its Polymorphic Occurrence in 36 Dog Breeds. Front Vet Sci 2021; 8:663175. [PMID: 33969041 PMCID: PMC8100205 DOI: 10.3389/fvets.2021.663175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/25/2021] [Indexed: 12/27/2022] Open
Abstract
Cytochrome P450 (CYP) drug metabolizing enzymes play an important role in efficient drug metabolism and elimination. Many CYPs are polymorphic and, thereby, drug metabolism can vary between individuals. In the case of canine CYP2C41, gene polymorphism was identified. However, as the first available canine genome sequences all were CYP2C41 negative, this polymorphism could not be clarified at the genomic level. The present study provides an exact characterization of the CYP2C41 gene deletion polymorphism at the genomic level and presents a PCR-based genotyping method that was used for CYP2C41 genotyping of 1,089 individual subjects from 36 different dog breeds. None of the Bearded Collie, Bernese Mountain, Boxer, Briard, French Bulldog or Irish Wolfhound subjects had the CYP2C41 gene in their genomes. In contrast, in the Chinese Char-Pei, Siberian Husky, Schapendoes and Kangal breeds, the CYP2C41 allele frequency was very high, with values of 67, 57, 43, and 34%, respectively. Interestingly, the site of gene deletion was identical for all CYP2C41 negative dogs, and all CYP2C41 positive dogs showed highly homologous sequence domains upstream and downstream from the CYP2C41 gene. CYP2C41 genotyping can now be routinely used in future pharmacokinetic studies in canines, in order to identify genetically-based poor or extensive drug metabolizers. This, together with more extensive in vitro drug screening for CYP2C41 substrates will help to determine the clinical relevance of CYP2C41, and to optimize drug treatment. Although the relative abundance of the CYP2C41 protein in the canine liver seems to not be very high, this CYP could substantially contribute to hepatic drug metabolism in dogs expressing CYP2C41 from both alleles and, when CYP2C41 shows higher catalytic activity to a given drug than other hepatic metabolic enzymes.
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Affiliation(s)
- Emre Karakus
- Faculty of Veterinary Medicine, Institute of Pharmacology and Toxicology, Justus Liebig University Giessen, Giessen, Germany
| | - Clarissa Prinzinger
- Faculty of Veterinary Medicine, Institute of Pharmacology and Toxicology, Justus Liebig University Giessen, Giessen, Germany
| | - Silke Leiting
- Faculty of Veterinary Medicine, Institute of Pharmacology and Toxicology, Justus Liebig University Giessen, Giessen, Germany
| | - Joachim Geyer
- Faculty of Veterinary Medicine, Institute of Pharmacology and Toxicology, Justus Liebig University Giessen, Giessen, Germany
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119
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Long-term stress in dogs is related to the human-dog relationship and personality traits. Sci Rep 2021; 11:8612. [PMID: 33883667 PMCID: PMC8060293 DOI: 10.1038/s41598-021-88201-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/06/2021] [Indexed: 02/01/2023] Open
Abstract
Previously, we found that dogs belonging to the herding breed group, selected for human cooperation, synchronise their long-term stress levels with their owners. The aim of the current study was to investigate features that could influence long-term stress levels in ancient dog breeds, genetically closer to wolves, and dogs specifically selected to work independently of their owner. Twenty-four ancient breed dogs and 18 solitary hunting dogs were recruited and hair samples were obtained from both dogs and owners from which hair cortisol concentration (HCC) was analysed. Additionally, the owners completed lifestyle surveys, the Monash Dog Owner Relationship Scale (MDORS) on human–dog relationship, and both dog and owner personality questionnaires (Dog Personality questionnaire and Big Five Inventory survey). The results from the MDORS indicate that the subscale Perceived cost correlated to the dog HCC of tested breed groups: solitary hunting breeds (χ2 = 4.95, P = 0.026, β = 0.055), ancient breeds (χ2 = 2.74, P = 0.098, β = 0.027), and herding dogs included from a previous study (χ2 = 6.82, P = 0.009, β = − 0.061). The HCC of the solitary hunting dogs was also related to the owner personality traits Agreeableness (χ2 = 12.30, P < 0.001, β = − 0.060) and Openness (χ2 = 9.56, P = 0.002, β = 0.048) suggesting a more substantial influence of the owner on the solitary hunting dog’s HCC compared to the ancient breeds. No effect of owner HCC on dog HCC was found in either ancient or in solitary hunting breeds. Hence, the long-term stress synchronisation is likely to be a trait in breeds selected for human cooperation. In conclusion, dog HCC is often related to the owners’ personality, but is primarily influenced by the owner-dog relationship.
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120
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Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 2021; 31:762-774. [PMID: 33863806 PMCID: PMC8092016 DOI: 10.1101/gr.266049.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 02/26/2021] [Indexed: 01/02/2023]
Abstract
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Carlos Morcillo-Suarez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Juan
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08201, Spain
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Abstract
Dogs and humans have coexisted together for thousands of years, but it was not until the Victorian Era that humans practiced selective breeding to produce the modern standards we see today. Strong artificial selection during the breed formation period has simplified the genetic architecture of complex traits and caused an enrichment of identity-by-descent (IBD) segments in the dog genome. This study demonstrates the value of IBD segments and utilizes them to infer the recent demography of canids, predict case-control status for complex traits, locate regions of the genome potentially linked to inbreeding depression, and to identify understudied breeds where there is potential to discover new disease-associated variants. Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.
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122
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Jiang F, Lin R, Xiao C, Xie T, Jiang Y, Chen J, Ni P, Sung WK, Han J, Du X, Li S. Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations. Genet Sel Evol 2021; 53:35. [PMID: 33849442 PMCID: PMC8042899 DOI: 10.1186/s12711-021-00627-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/26/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. RESULTS Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). CONCLUSIONS Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.
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Affiliation(s)
- Fan Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Ruiyi Lin
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Changyi Xiao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Tanghui Xie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yaoxin Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianhai Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute for Systems Genetics, West China Hospital, Auspiciousness Peace Center, Gaopeng Avenue, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wing-Kin Sung
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Department of Computer Science, National University of Singapore, Singapore, 117417 Singapore
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People’s Republic of China
| | - Xiaoyong Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Shijun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
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Gutierrez‐Quintana R, Decker S. Tail end of the brachycephalic problem: diagnostic and treatment options for spinal malformations. IN PRACTICE 2021. [DOI: 10.1002/inpr.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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124
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Kawakami T, Jensen MK, Slavney A, Deane PE, Milano A, Raghavan V, Ford B, Chu ET, Sams AJ, Boyko AR. R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. PLoS One 2021; 16:e0248233. [PMID: 33755696 PMCID: PMC7987146 DOI: 10.1371/journal.pone.0248233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/22/2021] [Indexed: 11/18/2022] Open
Abstract
Structural variations (SVs) represent a large fraction of all genetic diversity, but how this genetic diversity is translated into phenotypic and organismal diversity is unclear. Explosive diversification of dog coat color and patterns after domestication can provide a unique opportunity to explore this question; however, the major obstacle is to efficiently collect a sufficient number of individuals with known phenotypes and genotypes of hundreds of thousands of markers. Using customer-provided information about coat color and patterns of dogs tested on a commercial canine genotyping platform, we identified a genomic region on chromosome 38 that is strongly associated with a mottled coat pattern (roaning) by genome-wide association study. We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835–11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. The tandem duplication is in an intronic region of usherin gene (USH2A), which was perfectly associated with roaning but absent in non-roaned dogs. We detected strong selection signals in this region characterized by reduced nucleotide diversity (π), increased runs of homozygosity, and extended haplotype homozygosity in Wirehaired Pointing Griffons and Australian Cattle Dogs (typically roaned breeds), as well as elevated genetic difference (FST) between Wirehaired Pointing Griffon (roaned) and Labrador Retriever (non-roaned). Surprisingly, all Dalmatians (N = 262) carried the duplication embedded in identical or similar haplotypes with roaned dogs, indicating this region as a shared target of selection during the breed’s formation. We propose that the Dalmatian’s unique spots were a derived coat pattern by establishing a novel epistatic interaction between roaning “R-locus” on chromosome 38 and an uncharacterized modifier locus. These results highlight the utility of consumer-oriented genotype and phenotype data in the discovery of genomic regions contributing to phenotypic diversity in dogs.
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Affiliation(s)
- Takeshi Kawakami
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- * E-mail: (ARB); (TK)
| | - Meghan K. Jensen
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Andrea Slavney
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Petra E. Deane
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Ausra Milano
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Vandana Raghavan
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Brett Ford
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Erin T. Chu
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Aaron J. Sams
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Adam R. Boyko
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ARB); (TK)
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125
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Soh PXY, Hsu WT, Khatkar MS, Williamson P. Evaluation of genetic diversity and management of disease in Border Collie dogs. Sci Rep 2021; 11:6243. [PMID: 33737533 PMCID: PMC7973533 DOI: 10.1038/s41598-021-85262-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/28/2021] [Indexed: 01/31/2023] Open
Abstract
Maintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis. Molecular estimates revealed a mean multi-locus heterozygosity (MLH) of 0.311 (SD 0.027), 20.79% of the genome consisted of runs of homozygosity (ROH ) > 1 Mb, effective population size (Ne) was 84.7, and mean inbreeding (F) was 0.052 (SD 0.083). For 227 genotyped Border Collies that had available pedigree information (GenoPed), molecular and pedigree estimates of diversity were compared. A reference population (dogs born between 2005 and 2015, inclusive; N = 13,523; RefPop) and their ancestors (N = 12,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a Ne of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (fe), 28 effective ancestors (fa) and 10.65 (SD 2.82) founder genomes (Ng). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH > 1 Mb, MLH, heterozygosity), however, there was a loss of > 10% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of > 5% for 5 SNPs around the NCL mutation (maximum 5.18%). A common ancestor was identified for 38 TNS-affected dogs and 64 TNS carriers, and a different common ancestor was identified for 33 NCL-affected dogs and 28 carriers, with some overlap of prominent individuals between both pedigrees. Overall, Border Collies have a high level of genetic diversity compared to other breeds.
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Affiliation(s)
- Pamela Xing Yi Soh
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Wei Tse Hsu
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Mehar Singh Khatkar
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Peter Williamson
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
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126
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Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen J, Rosen BD, Johnson GS, Rice ES, Hillier LD, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC, Ballard JWO. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 2021; 22:188. [PMID: 33726677 PMCID: PMC7962210 DOI: 10.1186/s12864-021-07493-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/28/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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Affiliation(s)
- Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878 Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - James M. Ferguson
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str, 27 06484 Quedlinburg, Germany
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705 USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211 USA
| | - Edward S. Rice
- Department of Surgery, University of Missouri, Columbia, MO 65211 USA
| | | | - Jillian M. Hammond
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010 Australia
| | - Ozren Bogdanovic
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765 Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
- Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009 Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Wesley C. Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211 Australia
| | - J. William O. Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086 Australia
- School of Biosciences, University of Melbourne, Parkville, Victoria 3052 Australia
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Edmunds GL, Smalley MJ, Beck S, Errington RJ, Gould S, Winter H, Brodbelt DC, O'Neill DG. Dog breeds and body conformations with predisposition to osteosarcoma in the UK: a case-control study. Canine Med Genet 2021; 8:2. [PMID: 33750475 PMCID: PMC7944903 DOI: 10.1186/s40575-021-00100-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/30/2021] [Indexed: 11/16/2022] Open
Abstract
Background Osteosarcoma is an aggressive and painful bone neoplasm in dogs. Previous studies have reported epidemiological associations suggesting that large body mass, long bone length and the genetics of certain breeds including the Rottweiler are associated with elevated osteosarcoma risk. However, these studies were often limited by selection bias and confounding factors, and have rarely offered insights into breed-associated protection for osteosarcoma. The current study includes 1756 appendicular and axial osteosarcoma cases presenting to VPG Histology (Bristol, UK) compared against a control population of 905,211 dogs without osteosarcoma from primary care electronic patient records in the VetCompass™ dataset. Methods and study design Retrospective, case-control study. Multivariable logistic regression analysis explored associations between demographic risk factors (including breed, chondrodystrophy, age, sex/neuter status, skull-shape, and body mass) and osteosarcoma of all anatomical sites. Results We identified several breeds with increased and reduced odds of osteosarcoma. At highest risk were the Rottweiler and Great Dane, with > 10 times the odds of osteosarcoma compared with crossbreds, and the Rhodesian Ridgeback, which has not featured in previous lists of at-risk breeds for osteosarcoma, and had an odds ratio of 11.31 (95% confidence interval 7.37–17.35). Breeds at lowest risk of osteosarcoma (protected breeds) included the Bichon Frise, the French Bulldog and the Cavalier King Charles Spaniel, all with odd ratios of less than 0.30 compared with crossbreds. Body mass was strongly associated with osteosarcoma risk; dogs over 40 kg exhibited osteosarcoma odds of 45.44 (95% confidence interval 33.74–61.20) compared with dogs less than 10 kg. Chondrodystrophic breeds had an osteosarcoma odds ratio of 0.13 (95% confidence interval 0.11–0.16) compared with non-chondrodystrophic breeds. Conclusions This study provides evidence of strong breed-associated osteosarcoma risk and protection, suggesting a genetic basis for osteosarcoma pathogenesis. It highlights that breeds selected for long legs/large body mass are generally overrepresented amongst at-risk breeds, whilst those selected for short leg length/small body mass are generally protected. These findings could inform genetic studies to identify osteosarcoma risk alleles in canines and humans; as well as increasing awareness amongst veterinarians and owners, resulting in improved breeding practices and clinical management of osteosarcoma in dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-021-00100-7.
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Affiliation(s)
- Grace L Edmunds
- Bristol Veterinary School, Langford House, Langford, Bristol, BS40 5DU, UK.
| | - Matthew J Smalley
- European Cancer Stem Cell Research Institute and School of Biosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Sam Beck
- VPG Histology (formerly Bridge), Horner Court, 637 Gloucester Road, Horfield, Bristol, BS7 0BJ, UK
| | - Rachel J Errington
- Division of Cancer and Genetics, School of Medicine, Academic Avenue, Cardiff University, Cardiff, CF62 3LF, UK
| | - Sara Gould
- Langford Veterinary Services, Langford House Langford, Bristol, BS40 5DU, UK
| | | | - Dave C Brodbelt
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts, AL9 7TA, UK
| | - Dan G O'Neill
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts, AL9 7TA, UK
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128
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Baker LA, Momen M, McNally R, Berres ME, Binversie EE, Sample SJ, Muir P. Biologically Enhanced Genome-Wide Association Study Provides Further Evidence for Candidate Loci and Discovers Novel Loci That Influence Risk of Anterior Cruciate Ligament Rupture in a Dog Model. Front Genet 2021; 12:593515. [PMID: 33763109 PMCID: PMC7982834 DOI: 10.3389/fgene.2021.593515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/01/2021] [Indexed: 11/20/2022] Open
Abstract
Anterior cruciate ligament (ACL) rupture is a common condition that disproportionately affects young people, 50% of whom will develop knee osteoarthritis (OA) within 10 years of rupture. ACL rupture exhibits both hereditary and environmental risk factors, but the genetic basis of the disease remains unexplained. Spontaneous ACL rupture in the dog has a similar disease presentation and progression, making it a valuable genomic model for ACL rupture. We leveraged the dog model with Bayesian mixture model (BMM) analysis (BayesRC) to identify novel and relevant genetic variants associated with ACL rupture. We performed RNA sequencing of ACL and synovial tissue and assigned single nucleotide polymorphisms (SNPs) within differentially expressed genes to biological prior classes. SNPs with the largest effects were on chromosomes 3, 5, 7, 9, and 24. Selection signature analysis identified several regions under selection in ACL rupture cases compared to controls. These selection signatures overlapped with genome-wide associations with ACL rupture as well as morphological traits. Notable findings include differentially expressed ACSF3 with MC1R (coat color) and an association on chromosome 7 that overlaps the boundaries of SMAD2 (weight and body size). Smaller effect associations were within or near genes associated with regulation of the actin cytoskeleton and the extracellular matrix, including several collagen genes. The results of the current analysis are consistent with previous work published by our laboratory and others, and also highlight new genes in biological pathways that have not previously been associated with ACL rupture. The genetic associations identified in this study mirror those found in human beings, which lays the groundwork for development of disease-modifying therapies for both species.
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Affiliation(s)
- Lauren A Baker
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Rachel McNally
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark E Berres
- Bioinformatics Resource Center, Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Emily E Binversie
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Susannah J Sample
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Peter Muir
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
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129
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Metabolomics shows the Australian dingo has a unique plasma profile. Sci Rep 2021; 11:5245. [PMID: 33664285 PMCID: PMC7933249 DOI: 10.1038/s41598-021-84411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 01/02/2023] Open
Abstract
Dingoes occupy a wide range of the Australian mainland and play a crucial role as an apex predator with a generalist omnivorous feeding behaviour. Dingoes are ecologically, phenotypically and behaviourally distinct from modern breed dogs and have not undergone artificial selection since their arrival in Australia. In contrast, humans have selected breed dogs for novel and desirable traits. First, we examine whether the distinct evolutionary histories of dingoes and domestic dogs has lead to differences in plasma metabolomes. We study metabolite composition differences between dingoes (n = 15) and two domestic dog breeds (Basenji n = 9 and German Shepherd Dog (GSD) n = 10). Liquid chromatography mass spectrometry, type II and type III ANOVA with post-hoc tests and adjustments for multiple comparisons were used for data evaluation. After accounting for within group variation, 62 significant metabolite differences were detected between dingoes and domestic dogs, with the majority of differences in protein (n = 14) and lipid metabolites (n = 12), mostly lower in dingoes. Most differences were observed between dingoes and domestic dogs and fewest between the domestic dog breeds. Next, we collect a second set of data to investigate variation between pure dingoes (n = 10) and dingo-dog hybrids (n = 10) as hybridisation is common in regional Australia. We detected no significant metabolite differences between dingoes and dingo-dog hybrids after Bonferroni correction. However, power analysis showed that increasing the sample size to 15 could result in differences in uridine 5′-diphosphogalactose (UDPgal) levels related to galactose metabolism. We suggest this may be linked to an increase in Amylase 2B copy number in hybrids. Our study illustrates that the dingo metabolome is significantly different from domestic dog breeds and hybridisation is likely to influence carbohydrate metabolism.
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130
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Pacheco G, van Grouw H, Shapiro MD, Gilbert MTP, Vieira FG. Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biol Evol 2021; 12:136-150. [PMID: 32053199 PMCID: PMC7144551 DOI: 10.1093/gbe/evaa027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.
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Affiliation(s)
- George Pacheco
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark.,The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, Hertfordshire, United Kingdom
| | | | - Marcus Thomas P Gilbert
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark.,The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Denmark.,NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Filipe Garrett Vieira
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Denmark
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131
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Whitehouse-Tedd K, Richards N, Parker M. Dogs and Conservation: emerging themes and considerations. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.e2004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Katherine Whitehouse-Tedd
- Nottingham Trent University, School of Animal, Rural and Environmental Sciences, Southwell, United Kingdom; e-mail:
| | - Ngaio Richards
- Working Dogs for Conservation, Missoula, Montana, United States; e-mail: ,
| | - Megan Parker
- Working Dogs for Conservation, Missoula, Montana, United States; e-mail: ,
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132
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Saver A, Lulich JP, Van Buren S, Furrow E. Calcium oxalate urolithiasis in juvenile dogs. Vet Rec 2021; 189:e141. [PMID: 34357620 DOI: 10.1002/vetr.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 11/10/2020] [Accepted: 01/26/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND The features of juvenile-onset calcium oxalate urolithiasis in dogs have not been previously reported. METHODS Calcium oxalate urolith submissions to the Minnesota Urolith Center between 2012 and 2016 were analyzed to identify those originating from juvenile (≤2 years, n = 510) or mature (7-9 years, n = 39,093) dogs. Breed, sex, urolith salt type and urolith location were compared between groups. Breeds represented in both groups were also compared with respect to sex, urolith salt type and urolith location. RESULTS French (odds ratios [OR] = 14.7, p < 0.001) and English (OR = 14.3, p < 0.001) Bulldogs were overrepresented in juvenile submissions. All juvenile French and English Bulldogs were male. Across all breeds, juvenile dogs were more likely to be male (89%, p < 0.001) than mature dogs (79%). Juvenile dogs were also more likely to form dihydrate stones compared to mature dogs (33% versus 14%, respectively; p < 0.001). Breed differences were discovered in sex, urolith salt type and stone location. CONCLUSIONS French and English Bulldogs comprise a greater proportion of juvenile calcium oxalate urolith submissions than expected based on their rarity in mature submissions. Inherited risk factors, particularly X chromosome variants, should be investigated due to the strong breed and sex predispositions identified.
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Affiliation(s)
- Alexander Saver
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jody P Lulich
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Samantha Van Buren
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Eva Furrow
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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133
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Genetics of canine diabetes mellitus part 1: Phenotypes of disease. Vet J 2021; 270:105611. [PMID: 33641807 DOI: 10.1016/j.tvjl.2021.105611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 01/09/2023]
Abstract
This two-part article discusses the mechanisms by which genetic variation can influence the risk of complex diseases, with a focus on canine diabetes mellitus. In Part 1, presented here, the importance of accurate methods for classifying different types of diabetes will be discussed, since this underpins the selection of cases and controls for genetic studies. Part 2 will focus on our current understanding of the genes involved in diabetes risk, and the way in which new genome sequencing technologies are poised to reveal new diabetes genes in veterinary species.
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134
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Liotta L, Bionda A, Cortellari M, Negro A, Crepaldi P. From phenotypical to genomic characterisation of the mannara dog: an italian shepherd canine resource. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1972852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Messina, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Veterinarie, University of Messina, Messina, Italy
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milano, Milano, Italy
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milano, Milano, Italy
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milano, Milano, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia, University of Milano, Milano, Italy
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135
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Conte A, Bernardini M, De Decker S, Ricco C, Behr S, Sanchez-Masian D, Cherubini GB, De Risio L, Gutierrez-Quintana R. Thoracic Vertebral Canal Stenosis Associated with Vertebral Arch Anomalies in Small Brachycephalic Screw-Tail Dog Breeds. Vet Comp Orthop Traumatol 2020; 34:191-199. [PMID: 33285597 DOI: 10.1055/s-0040-1721375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVE The aim of this study was to describe clinical and imaging features of thoracic vertebral canal stenosis secondary to the hypertrophy of the vertebral lamina and articular processes in screw-tail brachycephalic dog breeds, to evaluate the prevalence of the malformation in a large group of screw-tail dog breeds and to determine if degree of stenosis is associated with presence of neurological signs. STUDY DESIGN This is a retrospective multicentric study. MATERIALS AND METHODS Clinical records of 185 screw-tail brachycephalic dogs (French Bulldogs, English Bulldogs, Boston Terriers) and Pugs were reviewed. Ten dogs with neurological deficits secondary to thoracic vertebral canal stenosis diagnosed on magnetic resonance imaging were identified (Group 1). Neurologically normal dogs (n = 175) of the same breeds underwent computed tomographic imaging of the thoracic vertebral column for other medical reasons (Group 2). Cross-sectional measurements were used to calculate a stenotic ratio. RESULTS Group 1 consisted of three French Bulldogs, six English Bulldogs and one Pug. Eight were males. Most dogs presented with progressive non-painful pelvic limbs ataxia and paresis. Twenty stenotic sites were identified with the most common being T4-T5. Three of ten dogs were treated surgically and all had a good long-term outcome. In Group 2, 33 of 175 dogs had one or more stenotic sites with the most common being T2-T3. The degree of the stenosis was significantly higher in Group 1 (p = 0.019). A stenotic ratio of 0.56 had sensitivity and specificity of 67% to differentiate between dogs with and without neurological signs. CONCLUSION Cranial thoracic vertebral canal stenosis is observed predominantly in young male Bulldogs, but not all stenoses are clinically relevant.
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Affiliation(s)
| | - Marco Bernardini
- Ospedale Veterinario "I Portoni Rossi", Zola Pedrosa, Italy.,Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Steven De Decker
- Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Cristoforo Ricco
- Willows Veterinary Centre & Referral Service, Solihull, United Kingdom
| | - Sebastien Behr
- Willows Veterinary Centre & Referral Service, Solihull, United Kingdom
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136
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Letko A, Minor KM, Friedenberg SG, Shelton GD, Salvador JP, Mandigers PJJ, Leegwater PAJ, Winkler PA, Petersen-Jones SM, Stanley BJ, Ekenstedt KJ, Johnson GS, Hansen L, Jagannathan V, Mickelson JR, Drögemüller C. A CNTNAP1 Missense Variant Is Associated with Canine Laryngeal Paralysis and Polyneuropathy. Genes (Basel) 2020; 11:E1426. [PMID: 33261176 PMCID: PMC7761076 DOI: 10.3390/genes11121426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Laryngeal paralysis associated with a generalized polyneuropathy (LPPN) most commonly exists in geriatric dogs from a variety of large and giant breeds. The purpose of this study was to discover the underlying genetic and molecular mechanisms in a younger-onset form of this neurodegenerative disease seen in two closely related giant dog breeds, the Leonberger and Saint Bernard. Neuropathology of an affected dog from each breed showed variable nerve fiber loss and scattered inappropriately thin myelinated fibers. Using across-breed genome-wide association, haplotype analysis, and whole-genome sequencing, we identified a missense variant in the CNTNAP1 gene (c.2810G>A; p.Gly937Glu) in which homozygotes in both studied breeds are affected. CNTNAP1 encodes a contactin-associated protein important for organization of myelinated axons. The herein described likely pathogenic CNTNAP1 variant occurs in unrelated breeds at variable frequencies. Individual homozygous mutant LPPN-affected Labrador retrievers that were on average four years younger than dogs affected by geriatric onset laryngeal paralysis polyneuropathy could be explained by this variant. Pathologic changes in a Labrador retriever nerve biopsy from a homozygous mutant dog were similar to those of the Leonberger and Saint Bernard. The impact of this variant on health in English bulldogs and Irish terriers, two breeds with higher CNTNAP1 variant allele frequencies, remains unclear. Pathogenic variants in CNTNAP1 have previously been reported in human patients with lethal congenital contracture syndrome and hypomyelinating neuropathy, including vocal cord palsy and severe respiratory distress. This is the first report of contactin-associated LPPN in dogs characterized by a deleterious variant that most likely predates modern breed establishment.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - Katie M. Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA;
| | - G. Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Jill Pesayco Salvador
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Paul J. J. Mandigers
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Peter A. J. Leegwater
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Paige A. Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Simon M. Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Kari J. Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Liz Hansen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
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Kortekaas K, Kotrschal K. Social Context Influences Resting Physiology in Dogs. Animals (Basel) 2020; 10:E2214. [PMID: 33255961 PMCID: PMC7760264 DOI: 10.3390/ani10122214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 12/05/2022] Open
Abstract
Domestication has affected the social life of dogs. They seem to be less dependent on their pack members than wolves, potentially causing dogs to be more alert towards their environment, especially when resting. Such a response has been found in dogs resting alone compared to wolves in the same situation. However, as this may be influenced by social context, we compared alertness (i.e., degree of activation along the sleep-wake continuum-measured via cardiac parameters) of pack-living and enclosure-kept dogs in two conditions: (1) alone, and (2) with pack members, and in two states of activation: (1) inactive wakefulness, and (2) resting. We found that when dogs were resting alone, alertness was higher than when resting in the pack; individual alertness was potentially influenced by social rank. However, alertness was similar in the two conditions during inactive wakefulness. Thus, depending on social context, familiar conspecifics may still provide support in dogs; i.e., domestication has probably only partly shifted the social orientation of dogs from conspecifics to humans. We suggest that cardiac responses of dogs may be more flexible than those of wolves because of their adaptation to the more variable presence of humans and conspecifics in their environment.
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Affiliation(s)
- Kim Kortekaas
- Department of Cognitive Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Department of Behavioral Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria;
- Wolf Science Center, Domestication Lab, Konrad-Lorenz Institute of Ethology, University of Veterinary Medicine, Savoyenstrasse 1a, 1160 Vienna, Austria
| | - Kurt Kotrschal
- Department of Behavioral Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria;
- Wolf Science Center, Domestication Lab, Konrad-Lorenz Institute of Ethology, University of Veterinary Medicine, Savoyenstrasse 1a, 1160 Vienna, Austria
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138
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Bird DJ, Jacquemetton C, Buelow SA, Evans AW, Van Valkenburgh B. Domesticating olfaction: Dog breeds, including scent hounds, have reduced cribriform plate morphology relative to wolves. Anat Rec (Hoboken) 2020; 304:139-153. [PMID: 33205623 DOI: 10.1002/ar.24518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/26/2020] [Accepted: 06/12/2020] [Indexed: 11/08/2022]
Abstract
The domestic dog is assumed by nearly everyone to be the consummate smeller. Within the species Canis familiaris individual breeds, such as the bloodhound or beagle, are known as olfactory stars. These are "scent breeds," a grouping variably defined as a genetic clade or breed class commonly used for scent detection tasks. Previous work suggests that the dog has a more robust olfactory anatomy than many mammal species. Now we undertake a closer investigation of the dog's olfactory system, both in relationship to its closest wild relatives, the wolf and coyote, and across individual breeds. First, we seek to resolve whether the dog has lost olfactory capacity through its domestication from the wolf lineage. Second, we test the inertial lore that among dogs, "scent breeds," have a superior olfactory facility. As a measure of relative olfactory capacity, we look to the cribriform plate (CP), a bony cup in the posterior nasal cavity perforated by passageways for all olfactory nerve bundles streaming from the periphery to the brain. Using high-resolution computed tomography (CT) scans and digital quantification, we compare relative CP size in 46 dog breeds, the coyote and gray wolf. Results show the dog has a reduced CP surface area relative to the wolf and coyote. Moreover, we found no significant differences between CP size of "scent" and "non-scent" breeds. Our study suggests that the dog lost olfactory capacity as a result of domestication and this loss was not recovered in particular breed groupings through directed artificial selection for increased olfactory facility.
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Affiliation(s)
- Deborah J Bird
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Christiane Jacquemetton
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Sophie A Buelow
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Andrew W Evans
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
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Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding. G3-GENES GENOMES GENETICS 2020; 10:4001-4011. [PMID: 32900902 PMCID: PMC7642940 DOI: 10.1534/g3.120.401269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and modern parents provided one example of this phenomenon. The recent cultivar contains the Rht-B1b green revolution semi-dwarfing allele and compensatory alleles that reduce its negative effects. However, improvements in traits other than plant height were due to pleiotropic loci with favorable effects on traits and to favorable loci with no detectable pleiotropic effects. Wheat breeding appears to tolerate mutations at conserved nucleotide sites and to only select for alleles with both favorable and unfavorable effects on traits in exceptional situations.
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140
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Djurkin Kušec I, Bošković I, Zorc M, Gvozdanović K, Škorput D, Dovč P, Kušec G. Genomic Characterization of the Istrian Shorthaired Hound. Animals (Basel) 2020; 10:ani10112013. [PMID: 33139624 PMCID: PMC7693797 DOI: 10.3390/ani10112013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.
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Affiliation(s)
- Ivona Djurkin Kušec
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia; (I.D.K.); (I.B.); (K.G.); (G.K.)
| | - Ivica Bošković
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia; (I.D.K.); (I.B.); (K.G.); (G.K.)
| | - Minja Zorc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
- Correspondence:
| | - Kristina Gvozdanović
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia; (I.D.K.); (I.B.); (K.G.); (G.K.)
| | - Dubravko Škorput
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
| | - Goran Kušec
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia; (I.D.K.); (I.B.); (K.G.); (G.K.)
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141
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Kriangwanich W, Nganvongpanit K, Buddhachat K, Siengdee P, Chomdej S, Ponsuksili S, Thitaram C. Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis. PeerJ 2020; 8:e10215. [PMID: 33194413 PMCID: PMC7605226 DOI: 10.7717/peerj.10215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/28/2020] [Indexed: 12/28/2022] Open
Abstract
The identification of differing physical characteristics of dogs is an uncomplicated and straightforward way to categorize dog breeds. However, many dog owners and veterinarians still struggle to distinguish between pure breed and mixed variations in certain breeds of dogs. Presently, the absence of the tools and methods needed to confirm a pure breed dog is a significant problem since the only method available to validate pure or mongrel breeds is the official pedigree system. Inter-simple sequence repeat markers have been successfully used to assess genetic variations and differentiations. Notably, inter-simple sequence repeat markers coupled with high resolution melting analysis were effectively used for the breed identification of 43 breeds of dogs (total 463 dogs). The 10 primers chosen for analysis resulted in a range of 31-78.6% of breed discrimination when using one primer, while a combination of two primers was able to successfully discriminate between all of the 43 dog breeds (100%). Shannon's index information (I = 2.586 ± 0.034) and expected heterozygosity (H e = 0.908 ± 0.003) indicated a high level of genetic diversity among breeds. The fixation index (F st ) revealed a value of 10.4%, demonstrating that there was a high level of genetic subdivision between populations. This study showed that inter-simple sequence repeat marker analysis was effective in demonstrating high genetic diversity among varying breeds of dogs, while a combination of Inter-simple sequence repeat marker analysis and high resolution melting analysis could provide an optional technique for researchers to effectively identify breeds through genetic variations.
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Affiliation(s)
- Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Puntita Siengdee
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | - Chatchote Thitaram
- Center of Excellence in Elephant and Wildlife Research, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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142
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Bergström A, Frantz L, Schmidt R, Ersmark E, Lebrasseur O, Girdland-Flink L, Lin AT, Storå J, Sjögren KG, Anthony D, Antipina E, Amiri S, Bar-Oz G, Bazaliiskii VI, Bulatović J, Brown D, Carmagnini A, Davy T, Fedorov S, Fiore I, Fulton D, Germonpré M, Haile J, Irving-Pease EK, Jamieson A, Janssens L, Kirillova I, Horwitz LK, Kuzmanovic-Cvetković J, Kuzmin Y, Losey RJ, Dizdar DL, Mashkour M, Novak M, Onar V, Orton D, Pasarić M, Radivojević M, Rajković D, Roberts B, Ryan H, Sablin M, Shidlovskiy F, Stojanović I, Tagliacozzo A, Trantalidou K, Ullén I, Villaluenga A, Wapnish P, Dobney K, Götherström A, Linderholm A, Dalén L, Pinhasi R, Larson G, Skoglund P. Origins and genetic legacy of prehistoric dogs. Science 2020; 370:557-564. [PMID: 33122379 PMCID: PMC7116352 DOI: 10.1126/science.aba9572] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022]
Abstract
Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Ryan Schmidt
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- CIBIO-InBIO, University of Porto, Campus de Vairão, Portugal
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
| | - Ophelie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- Liverpool John Moores University, Liverpool, UK
| | - Audrey T Lin
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - David Anthony
- Hartwick College, Oneonta, NY, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ekaterina Antipina
- Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Sarieh Amiri
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | | | | | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tom Davy
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | - Ivana Fiore
- Bioarchaeology Service, Museo delle Civiltà, Rome, Italy
- Environmental and Evolutionary Biology Doctoral Program, Sapienza University of Rome, Rome, Italy
| | | | | | - James Haile
- University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Lundbeck GeoGenetics Centre, The Globe Institute, Copenhagen, Denmark
| | - Alexandra Jamieson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | | | | | | | - Yaroslav Kuzmin
- Sobolev Institute of Geology and Mineralogy of the Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
- Tomsk State University, Tomsk, Russian Federation
| | | | | | - Marjan Mashkour
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Paris, France
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Vedat Onar
- Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | | | - Maja Pasarić
- Institute of Ethnology and Folklore Research, Zagreb, Croatia
| | | | | | | | - Hannah Ryan
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | | | | | - Katerina Trantalidou
- Hellenic Ministry of Culture & Sports, Athens, Greece
- University of Thessaly, Argonauton & Philellinon, Volos, Greece
| | - Inga Ullén
- National Historical Museums, Stockholm, Sweden
| | - Aritza Villaluenga
- Consolidated Research Group on Prehistory (IT-1223-19), University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Paula Wapnish
- Pennsylvania State University, University Park, PA, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
- School of Philosophical and Historical Inquiry, Faculty of Arts and Social Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
- Stockholm University, Stockholm, Sweden
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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143
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Sundman AS, Pértille F, Lehmann Coutinho L, Jazin E, Guerrero-Bosagna C, Jensen P. DNA methylation in canine brains is related to domestication and dog-breed formation. PLoS One 2020; 15:e0240787. [PMID: 33119634 PMCID: PMC7595415 DOI: 10.1371/journal.pone.0240787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/02/2020] [Indexed: 11/19/2022] Open
Abstract
Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 ± 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 ± 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.
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Affiliation(s)
- Ann-Sofie Sundman
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Fábio Pértille
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/ Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Carlos Guerrero-Bosagna
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Per Jensen
- AVIAN Behaviour Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- * E-mail:
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144
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Surbakti S, Parker HG, McIntyre JK, Maury HK, Cairns KM, Selvig M, Pangau-Adam M, Safonpo A, Numberi L, Runtuboi DYP, Davis BW, Ostrander EA. New Guinea highland wild dogs are the original New Guinea singing dogs. Proc Natl Acad Sci U S A 2020; 117:24369-24376. [PMID: 32868416 PMCID: PMC7533868 DOI: 10.1073/pnas.2007242117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
New Guinea singing dogs (NGSD) are identifiable by their namesake vocalizations, which are unlike any other canid population. Their novel behaviors and potential singular origin during dog domestication make them an attractive, but elusive, subject for evolutionary and conservation study. Although once plentiful on the island of New Guinea (NG), they were presumed to currently exist only in captivity. This conclusion was based on the lack of sightings in the lowlands of the island and the concurrent expansion of European- and Asian-derived dogs. We have analyzed the first nuclear genomes from a canid population discovered during a recent expedition to the highlands of NG. The extreme altitude (>4,000 m) of the highland wild dogs' (HWD) observed range and confirmed vocalizations indicate their potential to be a wild NGSD population. Comparison of single-nucleotide polymorphism genotypes shows strong similarity between HWD and the homogeneous captive NGSD, with the HWD showing significantly higher genetic diversity. Admixture analyses and estimation of shared haplotypes with phylogenetically diverse populations also indicates the HWD is a novel population within the distinct evolutionary lineage of Oceanic canids. Taken together, these data indicate the HWD possesses a distinct potential to aid in the conservation of NGSD both in the wild and under human care.
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Affiliation(s)
- Suriani Surbakti
- Department of Biology, Universitas Cenderawasih, Jayapura, Papua 99224, Indonesia
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD 20892
| | - James K McIntyre
- New Guinea Highland Wild Dog Foundation, Fernandina Beach, FL 32034
| | - Hendra K Maury
- Department of Biology, Universitas Cenderawasih, Jayapura, Papua 99224, Indonesia
| | - Kylie M Cairns
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Meagan Selvig
- Department of Conservation Biology, University of Göttingen, 37073 Göttingen Germany
| | - Margaretha Pangau-Adam
- Department of Biology, Universitas Cenderawasih, Jayapura, Papua 99224, Indonesia
- Department of Conservation Biology, University of Göttingen, 37073 Göttingen Germany
| | - Apolo Safonpo
- Department of Biology, Universitas Cenderawasih, Jayapura, Papua 99224, Indonesia
| | - Leonardo Numberi
- Department of Biology, Universitas Cenderawasih, Jayapura, Papua 99224, Indonesia
| | - Dirk Y P Runtuboi
- Department of Biology, Universitas Cenderawasih, Jayapura, Papua 99224, Indonesia
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University College of Veterinary Medicine, College Station, TX 77843
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD 20892;
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145
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Mui ML, Famula TR, Henthorn PS, Hess RS. Heritability and complex segregation analysis of naturally-occurring diabetes in Australian Terrier Dogs. PLoS One 2020; 15:e0239542. [PMID: 32970763 PMCID: PMC7514011 DOI: 10.1371/journal.pone.0239542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/09/2020] [Indexed: 11/18/2022] Open
Abstract
The Australian Terrier breed is the breed at highest risk for naturally-occurring diabetes mellitus in the United States, where it is 32 times more likely to develop diabetes compared to mixed breed dogs. However, the heritability and mode of inheritance of spontaneous diabetes in Australian Terriers has not been reported. The aim of this study was therefore to investigate the heritability and mode of inheritance of diabetes in Australian Terriers. A cohort of related Australian Terriers including 383 Australian Terriers without diabetes, 86 Australian Terriers with spontaneous diabetes, and 14 Australian Terriers with an unknown phenotype, was analyzed. A logistic regression model including the effects of sex was formulated to evaluate the heritability of diabetes. The inheritance pattern of spontaneous diabetes in Australian Terriers was investigated by use of complex segregation analysis. Six possible inheritance models were studied, and the Akaike Information Criterion was used to determine the best model for diabetes inheritance in Australian Terriers, among the models deemed biologically feasible. Heritability of diabetes in Australian Terriers was estimated at 0.18 (95% confidence interval 0.0-0.67). There was no significant difference in the effect of males and females on disease outcome. Complex segregation analysis suggested that the mode of diabetes inheritance in Australian Terriers is polygenic, with no evidence for a large effect single gene influencing diabetes. It is concluded that in the population of Australian Terriers bred in the United States, a relatively small degree of genetic variation contributes to spontaneous diabetes. A genetic uniformity for diabetes-susceptible genes within the population of Australian Terriers bred in the Unites States could increase the risk of diabetes in this cohort. These findings hold promise for future genetic studies of canine diabetes focused on this particular breed.
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Affiliation(s)
- Mei Lun Mui
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas R. Famula
- Department of Animal Science, University of California–Davis, Davis, California, United States of America
| | - Paula S. Henthorn
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rebecka S. Hess
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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146
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Kolm N, Temrin H, Miklósi Á, Kubinyi E, Garamszegi LZ. The link between selection for function and human-directed play behaviour in dogs. Biol Lett 2020; 16:20200366. [PMID: 32961091 PMCID: PMC7532715 DOI: 10.1098/rsbl.2020.0366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human-directed play behaviour is a distinct behavioural feature of domestic dogs. But the role that artificial selection for contemporary dog breeds has played for human-directed play behaviour remains elusive. Here, we investigate how human-directed play behaviour has evolved in relation to the selection for different functions, considering processes of shared ancestry and gene flow among the different breeds. We use the American Kennel Club (AKC) breed group categorization to reflect the major functional differences and combine this with observational data on human-directed play behaviour for over 132 breeds across 89 352 individuals from the Swedish Dog Mentality Assessment project. Our analyses demonstrate that ancestor dogs already showed intermediate levels of human-directed play behaviour, levels that are shared with several modern breed types. Herding and Sporting breeds display higher levels of human-directed play behaviour, statistically distinguishable from Non-sporting and Toy breeds. Our results suggest that human-directed play behaviour played a role in the early domestication of dogs and that subsequent artificial selection for function has been important for contemporary variation in a behavioural phenotype mediating the social bond with humans.
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Affiliation(s)
- Niclas Kolm
- Department of Zoology, Stockholm University, Svante Arrhenius väg 18B, 10691 Stockholm, Sweden
| | - Hans Temrin
- Department of Zoology, Stockholm University, Svante Arrhenius väg 18B, 10691 Stockholm, Sweden
| | - Ádám Miklósi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Enikő Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - László Zsolt Garamszegi
- Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary.,MTA-ELTE, Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
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147
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Variants in FtsJ RNA 2'-O-Methyltransferase 3 and Growth Hormone 1 are associated with small body size and a dental anomaly in dogs. Proc Natl Acad Sci U S A 2020; 117:24929-24935. [PMID: 32958658 DOI: 10.1073/pnas.2009500117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Domesticated dogs show unparalleled diversity in body size across breeds, but within breeds variation is limited by selective breeding. Many heritable diseases of dogs are found among breeds of similar sizes, suggesting that as in humans, alleles governing growth have pleiotropic effects. Here, we conducted independent genome-wide association studies in the small Shetland Sheepdog breed and discovered a locus on chromosome 9 that is associated with a dental abnormality called maxillary canine-tooth mesioversion (MCM) (P = 1.53 × 10-7) as well as two body size traits: height (P = 1.67 × 10-5) and weight (P = 1.16 × 10-7). Using whole-genome resequencing data, we identified variants in two proximal genes: FTSJ3, encoding an RNA methyltransferase, and GH1, encoding growth hormone. A substitution in FTSJ3 and a splice donor insertion in GH1 are strongly associated with MCM and reduced body size in Shetland Sheepdogs. We demonstrated in vitro that the GH1 variant leads to exon 3 skipping, predicting a mutant protein known to cause human pituitary dwarfism. Statistical modeling, however, indicates that the FTSJ3 variant is the stronger predictor of MCM and that each derived allele reduces body size by about 1 inch and 5 pounds. In a survey of 224 breeds, both FTSJ3 and GH1 variants are frequent among very small "toy" breeds and absent from larger breeds. Our findings indicate that a chromosome 9 locus harboring tightly linked variants in FTSJ3 and GH1 reduces growth in the Shetland Sheepdog and toy breed dogs and confers risk for MCM through vertical pleiotropy.
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148
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Comparing the tractability of young hand-raised wolves (Canis lupus) and dogs (Canis familiaris). Sci Rep 2020; 10:14678. [PMID: 32895422 PMCID: PMC7477132 DOI: 10.1038/s41598-020-71687-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/19/2020] [Indexed: 11/08/2022] Open
Abstract
Dogs live in 45% of households, integrated into various human groups in various societies. This is certainly not true for wolves. We suggest that dogs' increased tractability (meant as individual dogs being easier to control, handle and direct by humans, in contrast to trainability defined as performance increase due to training) makes a crucial contribution to this fundamental difference. In this study, we assessed the development of tractability in hand-raised wolves and similarly raised dogs. We combined a variety of behavioural tests: fetching, calling, obeying a sit signal, hair brushing and walking in a muzzle. Wolf (N = 16) and dog (N = 11) pups were tested repeatedly, between the ages of 3-24 weeks. In addition to hand-raised wolves and dogs, we also tested mother-raised family dogs (N = 12) for fetching and calling. Our results show that despite intensive socialization, wolves remained less tractable than dogs, especially in contexts involving access to a resource. Dogs' tractability appeared to be less context dependent, as they followed human initiation of action in more contexts than wolves. We found no evidence that different rearing conditions (i.e. intensive socialization vs. mother rearing) would affect tractability in dogs. This suggests that during domestication dogs might have been selected for increased tractability, although based on the current data we cannot exclude that the differential speed of development of dogs and wolves or the earlier relocation of wolves to live as a group explains some of the differences we found.
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Ali MB, Evans JM, Parker HG, Kim J, Pearce-Kelling S, Whitaker DT, Plassais J, Khan QM, Ostrander EA. Genetic analysis of the modern Australian labradoodle dog breed reveals an excess of the poodle genome. PLoS Genet 2020; 16:e1008956. [PMID: 32911491 PMCID: PMC7482835 DOI: 10.1371/journal.pgen.1008956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
The genomic diversity of the domestic dog is an invaluable resource for advancing understanding of mammalian biology, evolutionary biology, morphologic variation, and behavior. There are approximately 350 recognized breeds in the world today, many established through hybridization and selection followed by intense breeding programs aimed at retaining or enhancing specific traits. As a result, many breeds suffer from an excess of particular diseases, one of many factors leading to the recent trend of "designer breed" development, i.e. crossing purebred dogs from existing breeds in the hope that offspring will be enriched for desired traits and characteristics of the parental breeds. We used a dense panel of 150,106 SNPs to analyze the population structure of the Australian labradoodle (ALBD), to understand how such breeds are developed. Haplotype and admixture analyses show that breeds other than the poodle (POOD) and Labrador retriever (LAB) contributed to ALBD formation, but that the breed is, at the genetic level, predominantly POOD, with all small and large varieties contributing to its construction. Allele frequency analysis reveals that the breed is enhanced for variants associated with a poodle-like coat, which is perceived by breeders to have an association with hypoallergenicity. We observed little enhancement for LAB-specific alleles. This study provides a blueprint for understanding how dog breeds are formed, highlighting the limited scope of desired traits in defining new breeds.
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Affiliation(s)
- Muhammad Basil Ali
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Punjab, Pakistan
| | - Jacquelyn M. Evans
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
| | - Heidi G. Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
| | - Jaemin Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
| | - Susan Pearce-Kelling
- OptiGen, LLC Cornell Business and Technology Park, Ithaca, NY, United States of America
| | - D. Thad Whitaker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
| | - Qaiser M. Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Punjab, Pakistan
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda MD, United States of America
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150
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Hess R, Henthorn P, Devoto M, Wang F, Feng R. An Exploratory Association Analysis of the Insulin Gene Region With Diabetes Mellitus in Two Dog Breeds. J Hered 2020; 110:793-800. [PMID: 31587057 PMCID: PMC6916661 DOI: 10.1093/jhered/esz059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Samoyeds and Australian Terriers are the 2 dog breeds at highest risk (>10-fold) for diabetes mellitus in the United States. It is unknown if the insulin (INS) gene is involved in the pathophysiology of diabetes in Samoyeds and Australian Terriers. It was hypothesized that the INS gene region provides a common genetic causality for diabetes in Samoyeds and Australian Terriers. We conducted a 2-stage genetic association study involving both breeds. In the discovery stage (Stage 1), Samoyeds with and without diabetes were compared in the frequencies of 447 tagging single-nucleotide polymorphisms (SNPs) within 2.5 megabases (Mb) up- and downstream of the INS gene on the Illumina CanineHD BeadChip. SNPs yielding a P-value < 0.005 were selected for further follow-up. In the validation stage (Stage 2), Australian Terriers with and without diabetes were compared in the SNPs genotyped by the Affymetrix GeneChip Canine Genome 2.0 Array and within 1 Mb up- and downstream of the selected SNPs from Stage 1. Two SNPs that were in high linkage disequilibrium (LD, r2 = 0.7) were selected from Stage 1. In Stage 2, among the 76 SNPs examined, 5 were significantly associated with diabetes after Bonferroni's correction for multiple comparisons. Three of these 5 SNPs were in complete LD (r2 = 1 for all associations) and the 2 remaining SNPs were in moderate LD (r2 = 0.4). In conclusion, an association between the INS gene region and diabetes was suggested in 2 dog breeds of different clades. This region could have importance in diabetes in other breeds or in canine diabetes at large.
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Affiliation(s)
- Rebecka Hess
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Paula Henthorn
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Translational and Precision Medicine, University of Rome Sapienza, Rome, Italy
| | - Fan Wang
- Department of Molecular Cardiology, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Rui Feng
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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