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Kieler IN, Persson SM, Hagman R, Marinescu VD, Hedhammar Å, Strandberg E, Lindblad-Toh K, Arendt ML. Genome wide association study in Swedish Labrador retrievers identifies genetic loci associated with hip dysplasia and body weight. Sci Rep 2024; 14:6090. [PMID: 38480780 PMCID: PMC10937653 DOI: 10.1038/s41598-024-56060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Genome wide association studies (GWAS) have been utilized to identify genetic risk loci associated with both simple and complex inherited disorders. Here, we performed a GWAS in Labrador retrievers to identify genetic loci associated with hip dysplasia and body weight. Hip dysplasia scores were available for 209 genotyped dogs. We identified a significantly associated locus for hip dysplasia on chromosome 24, with three equally associated SNPs (p = 4.3 × 10-7) in complete linkage disequilibrium located within NDRG3, a gene which in humans has been shown to be differentially expressed in osteoarthritic joint cartilage. Body weight, available for 85 female dogs, was used as phenotype for a second analysis. We identified two significantly associated loci on chromosome 10 (p = 4.5 × 10-7) and chromosome 31 (p = 2.5 × 10-6). The most associated SNPs within these loci were located within the introns of the PRKCE and CADM2 genes, respectively. PRKCE has been shown to play a role in regulation of adipogenesis whilst CADM2 has been associated with body weight in multiple human GWAS. In summary, we identified credible candidate loci explaining part of the genetic inheritance for hip dysplasia and body weight in Labrador retrievers with strong candidate genes in each locus previously implicated in the phenotypes investigated.
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Affiliation(s)
- Ida Nordang Kieler
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofia Malm Persson
- Department for Breeding and Health, Swedish Kennel Club, Stockholm, Sweden
| | - Ragnvi Hagman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala, Sweden
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maja Louise Arendt
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- SciLifeLab, Uppsala, Sweden.
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2
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Herb M. NADPH Oxidase 3: Beyond the Inner Ear. Antioxidants (Basel) 2024; 13:219. [PMID: 38397817 PMCID: PMC10886416 DOI: 10.3390/antiox13020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Reactive oxygen species (ROS) were formerly known as mere byproducts of metabolism with damaging effects on cellular structures. The discovery and description of NADPH oxidases (Nox) as a whole enzyme family that only produce this harmful group of molecules was surprising. After intensive research, seven Nox isoforms were discovered, described and extensively studied. Among them, the NADPH oxidase 3 is the perhaps most underrated Nox isoform, since it was firstly discovered in the inner ear. This stigma of Nox3 as "being only expressed in the inner ear" was also used by me several times. Therefore, the question arose whether this sentence is still valid or even usable. To this end, this review solely focuses on Nox3 and summarizes its discovery, the structural components, the activating and regulating factors, the expression in cells, tissues and organs, as well as the beneficial and detrimental effects of Nox3-mediated ROS production on body functions. Furthermore, the involvement of Nox3-derived ROS in diseases progression and, accordingly, as a potential target for disease treatment, will be discussed.
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Affiliation(s)
- Marc Herb
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany;
- German Centre for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
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3
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Tomé I, Alves-Pimenta S, Sargo R, Pereira J, Colaço B, Brancal H, Costa L, Ginja M. Mechanical osteoarthritis of the hip in a one medicine concept: a narrative review. BMC Vet Res 2023; 19:222. [PMID: 37875898 PMCID: PMC10599070 DOI: 10.1186/s12917-023-03777-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Human and veterinary medicine have historically presented many medical areas of potential synergy and convergence. Mechanical osteoarthritis (MOA) is characterized by a gradual complex imbalance between cartilage production, loss, and derangement. Any joint instability that results in an abnormal overload of the joint surface can trigger MOA. As MOA has a prevailing mechanical aetiology, treatment effectiveness can only be accomplished if altered joint mechanics and mechanosensitive pathways are normalized and restored. Otherwise, the inflammatory cascade of osteoarthritis will be initiated, and the changes may become irreversible. The management of the disease using non-steroidal anti-inflammatory drugs, analgesics, physical therapy, diet changes, or nutraceuticals is conservative and less effective. MOA is a determinant factor for the development of hip dysplasia in both humans and dogs. Hip dysplasia is a hereditary disease with a high incidence and, therefore, of great clinical importance due to the associated discomfort and significant functional limitations. Furthermore, on account of analogous human and canine hip dysplasia disease and under the One Medicine concept, unifying veterinary and human research could improve the well-being and health of both species, increasing the acknowledgement of shared diseases. Great success has been accomplished in humans regarding preventive conservative management of hip dysplasia and following One Medicine concept, similar measures would benefit dogs. Moreover, animal models have long been used to better understand the different diseases' mechanisms. Current research in animal models was addressed and the role of rabbit models in pathophysiologic studies and of the dog as a spontaneous animal model were highlighted, denoting the inexistence of rabbit functional models to investigate therapeutic approaches in hip MOA.
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Affiliation(s)
- I Tomé
- Department of Veterinary Sciences, University of Trás-Os-Montes E Alto Douro, Vila Real, 5000-801, Portugal.
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal.
| | - S Alves-Pimenta
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
- Department of Animal Science, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
| | - R Sargo
- Department of Veterinary Sciences, University of Trás-Os-Montes E Alto Douro, Vila Real, 5000-801, Portugal
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
| | - J Pereira
- Department of Veterinary Sciences, University of Trás-Os-Montes E Alto Douro, Vila Real, 5000-801, Portugal
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
| | - B Colaço
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
- Department of Animal Science, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
| | - H Brancal
- Clínica Veterinária da Covilhã, Covilhã, 6200-289, Portugal
| | - L Costa
- Department of Veterinary Sciences, University of Trás-Os-Montes E Alto Douro, Vila Real, 5000-801, Portugal
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
| | - M Ginja
- Department of Veterinary Sciences, University of Trás-Os-Montes E Alto Douro, Vila Real, 5000-801, Portugal
- CECAV, Centre for Animal Sciences and Veterinary Studies, Associate Laboratory for Animal and Veterinary Science - AL4AnimalS, University of Trás-Os-Montes E Alto Douro, Vila Real, Portugal
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4
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Hayward JJ, Todhunter RJ. Common Orthopedic Traits and Screening for Breeding Programs. Vet Clin North Am Small Anim Pract 2023:S0195-5616(23)00066-9. [PMID: 37225647 DOI: 10.1016/j.cvsm.2023.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Orthopedic diseases are complex traits, meaning genetics and environmental factors affect risk, making identification of genetic associations difficult. In the United States, hip and elbow scores, patellar luxation scores, Legg-Calvé-Perthes disease, and shoulder osteochondrosis affectedness are available in the Orthopedic Foundation for Animals registry. Distraction indices and extended, ventrodorsal hip conformation scores are recorded by PennHIP. Application of estimated breeding values for hip and elbow dysplasia in breeder selection reduces the severity and prevalence of these traits. Genomic prediction and whole-genome sequence technologies and methods should improve knowledge of genetics underlying orthopedic diseases, leading to improved canine orthopedic genetic quality.
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Affiliation(s)
- Jessica J Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rory J Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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5
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Leeb T, Bannasch D, Schoenebeck JJ. Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases. Annu Rev Anim Biosci 2023; 11:183-205. [PMID: 36322969 DOI: 10.1146/annurev-animal-050622-055534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland;
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California, Davis, California, USA;
| | - Jeffrey J Schoenebeck
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom;
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6
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Whole exome sequencing of 28 families of Danish descent reveals novel candidate genes and pathways in developmental dysplasia of the hip. Mol Genet Genomics 2023; 298:329-342. [PMID: 36454308 PMCID: PMC9938029 DOI: 10.1007/s00438-022-01980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022]
Abstract
Developmental dysplasia of the hip (DDH) is a common condition involving instability of the hip with multifactorial etiology. Early diagnosis and treatment are critical as undetected DDH is an important cause of long-term hip complications. Better diagnostics may be achieved through genetic methods, especially for patients with positive family history. Several candidate genes have been reported but the exact molecular etiology of the disease is yet unknown. In the present study, we performed whole exome sequencing of DDH patients from 28 families with at least two affected first-degree relatives. Four genes previously not associated with DDH (METTL21B, DIS3L2, PPP6R2, and TM4SF19) were identified with the same variants shared among affected family members, in more than two families. Among known association genes, we found damaging variants in DACH1, MYH10, NOTCH2, TBX4, EVC2, OTOG, and SHC3. Mutational burden analysis across the families identified 322 candidate genes, and enriched pathways include the extracellular matrix, cytoskeleton, ion-binding, and detection of mechanical stimulus. Taken altogether, our data suggest a polygenic mode of inheritance for DDH, and we propose that an impaired transduction of the mechanical stimulus is involved in the etiopathological mechanism. Our findings refine our current understanding of candidate causal genes in DDH, and provide a foundation for downstream functional studies.
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7
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Binversie EE, Momen M, Rosa GJM, Davis BW, Muir P. Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing. Front Genet 2022; 13:913354. [PMID: 36531249 PMCID: PMC9755188 DOI: 10.3389/fgene.2022.913354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mehdi Momen
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Guilherme J. M. Rosa
- Department of Animal and Dairy Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Peter Muir,
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8
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Jiang L, Li Z, Hayward JJ, Hayashi K, Krotscheck U, Todhunter RJ, Tang Y, Huang M. Genomic Prediction of Two Complex Orthopedic Traits Across Multiple Pure and Mixed Breed Dogs. Front Genet 2021; 12:666740. [PMID: 34630503 PMCID: PMC8492927 DOI: 10.3389/fgene.2021.666740] [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: 02/10/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
Canine hip dysplasia (CHD) and rupture of the cranial cruciate ligament (RCCL) are two complex inherited orthopedic traits of dogs. These two traits may occur concurrently in the same dog. Genomic prediction of these two diseases would benefit veterinary medicine, the dog’s owner, and dog breeders because of their high prevalence, and because both traits result in painful debilitating osteoarthritis in affected joints. In this study, 842 unique dogs from 6 breeds with hip and stifle phenotypes were genotyped on a customized Illumina high density 183 k single nucleotide polymorphism (SNP) array and also analyzed using an imputed dataset of 20,487,155 SNPs. To implement genomic prediction, two different statistical methods were employed: Genomic Best Linear Unbiased Prediction (GBLUP) and a Bayesian method called BayesC. The cross-validation results showed that the two methods gave similar prediction accuracy (r = 0.3–0.4) for CHD (measured as Norberg angle) and RCCL in the multi-breed population. For CHD, the average correlation of the AUC was 0.71 (BayesC) and 0.70 (GBLUP), which is a medium level of prediction accuracy and consistent with Pearson correlation results. For RCCL, the correlation of the AUC was slightly higher. The prediction accuracy of GBLUP from the imputed genotype data was similar to the accuracy from DNA array data. We demonstrated that the genomic prediction of CHD and RCCL with DNA array genotype data is feasible in a multiple breed population if there is a genetic connection, such as breed, between the reference population and the validation population. Albeit these traits have heritability of about one-third, higher accuracy is needed to implement in a natural population and predicting a complex phenotype will require much larger number of dogs within a breed and across breeds. It is possible that with higher accuracy, genomic prediction of these orthopedic traits could be implemented in a clinical setting for early diagnosis and treatment, and the selection of dogs for breeding. These results need continuous improvement in model prediction through ongoing genotyping and data sharing. When genomic prediction indicates that a dog is susceptible to one of these orthopedic traits, it should be accompanied by clinical and radiographic screening at an acceptable age with appropriate follow-up.
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Affiliation(s)
- Liping Jiang
- College of Mathematics, Jilin University, Changchun, China.,Electrical and Information Engineering College, Jilin Agricultural Science and Technology University, Jilin, China
| | - Zhuo Li
- Electrical and Information Engineering College, Jilin Agricultural Science and Technology University, Jilin, China
| | - Jessica J Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Kei Hayashi
- Department of Clinical Sciences and Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Ursula Krotscheck
- Department of Clinical Sciences and Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Rory J Todhunter
- Department of Clinical Sciences and Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - You Tang
- Electrical and Information Engineering College, Jilin Agricultural Science and Technology University, Jilin, China
| | - Meng Huang
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, United States
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9
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Wang S, Strandberg E, Arvelius P, Clements DN, Wiener P, Friedrich J. Genome-wide association studies for canine hip dysplasia in single and multiple populations - implications and potential novel risk loci. BMC Genomics 2021; 22:636. [PMID: 34474664 PMCID: PMC8414704 DOI: 10.1186/s12864-021-07945-z] [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: 02/11/2021] [Accepted: 08/17/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems across countries. In this study, we incorporated routinely assessed CHD records and genotype data of German Shepherd dogs from two countries (UK and Sweden) to perform genome-wide association studies (GWAS) within populations using different variations of CHD phenotypes. As phenotypes, dogs were either classified into cases and controls based on the Fédération Cynologique Internationale (FCI) five-level grading of the worst hip or the FCI grade was treated as an ordinal trait. In a subsequent meta-analysis, we added publicly available data from a Finnish population and performed the GWAS across all populations. Genetic associations for the CHD phenotypes were evaluated in a linear mixed model using 62,089 SNPs. RESULTS Multiple SNPs with genome-wide significant and suggestive associations were detected in single-population GWAS and the meta-analysis. Few of these SNPs overlapped between populations or between single-population GWAS and the meta-analysis, suggesting that many CHD-related QTL are population-specific. More significant or suggestive SNPs were identified when FCI grades were used as phenotypes in comparison to the case-control approach. MED13 (Chr 9) and PLEKHA7 (Chr 21) emerged as novel positional candidate genes associated with hip dysplasia. CONCLUSIONS Our findings confirm the complex genetic nature of hip dysplasia in dogs, with multiple loci associated with the trait, most of which are population-specific. Routinely assessed CHD information collected across countries provide an opportunity to increase sample sizes and statistical power for association studies. While the lack of standardisation of CHD assessment schemes across countries poses a challenge, we showed that conversion of traits can be utilised to overcome this obstacle.
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Affiliation(s)
- Shizhi Wang
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden
| | - Per Arvelius
- Swedish Armed Forces Dog Training Centre, Box 194, SE-195 24, Märsta, Sweden
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Pamela Wiener
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Juliane Friedrich
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.
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10
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Mikkola L, Kyöstilä K, Donner J, Lappalainen AK, Hytönen MK, Lohi H, Iivanainen A. An across-breed validation study of 46 genetic markers in canine hip dysplasia. BMC Genomics 2021; 22:68. [PMID: 33478395 PMCID: PMC7818755 DOI: 10.1186/s12864-021-07375-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/07/2021] [Indexed: 12/30/2022] Open
Abstract
Background Canine hip dysplasia (CHD) is a common disease, with a complex genetic background. Dogs with severe CHD sometimes also suffer from osteoarthritis (OA), an inflammatory, often painful and incurable condition. Previous studies have reported breed-specific genetic loci associated with different hip dysplasia and OA phenotypes. However, the independent replication of the known associations within or across breeds has been difficult due to variable phenotype measures, inadequate sample sizes and the existence of population specific variants. Results We execute a validation study of 46 genetic markers in a cohort of nearly 1600 dogs from ten different breeds. We categorize the dogs into cases and controls according to the hip scoring system defined by the Fédération Cynologique Internationale (FCI). We validate 21 different loci associated on fourteen chromosomes. Twenty of these associated with CHD in specific breeds, whereas one locus is unique to the across-breed study. We show that genes involved in the neddylation pathway are enriched among the genes in the validated loci. Neddylation contributes to many cellular functions including inflammation. Conclusions Our study successfully replicates many loci and highlights the complex genetic architecture of CHD. Further characterisation of the associated loci could reveal CHD-relevant genes and pathways for improved understanding of the disease pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07375-x.
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Affiliation(s)
- Lea Mikkola
- Department of Veterinary Biosciences, University of Helsinki, P.O. BOX 66 (Agnes Sjöbergin katu 2), 00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Helsinki, Finland
| | - Kaisa Kyöstilä
- Department of Veterinary Biosciences, University of Helsinki, P.O. BOX 66 (Agnes Sjöbergin katu 2), 00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Helsinki, Finland
| | | | - Anu K Lappalainen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Marjo K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, P.O. BOX 66 (Agnes Sjöbergin katu 2), 00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, P.O. BOX 66 (Agnes Sjöbergin katu 2), 00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Helsinki, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, University of Helsinki, P.O. BOX 66 (Agnes Sjöbergin katu 2), 00014, Helsinki, Finland.
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11
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Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats. Int J Genomics 2020; 2020:6035694. [PMID: 32802828 PMCID: PMC7403911 DOI: 10.1155/2020/6035694] [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: 04/08/2020] [Accepted: 07/07/2020] [Indexed: 11/26/2022] Open
Abstract
This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate ≥ 0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.
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12
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Bruun CS, Bank A, Ström A, Proschowsky HF, Fredholm M. Validation of DNA test for hip dysplasia failed in Danish Labrador Retrievers. Anim Genet 2020; 51:617-619. [PMID: 32432791 DOI: 10.1111/age.12951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Canine hip dysplasia is characterized by poor hip joint conformation and laxity. The disease is a complex trait influenced by both genetics and environment. Diagnosis and quantification of hip dysplasia are performed by radiographic examination of the hip joint and the diagnosis is used for making breeding decisions in many breeds. A prognostic genetic test (the Dysgen test) based on seven associated SNPs has been developed in a study based on Spanish Labrador Retrievers. In our study this test has been evaluated in 39 Danish Labrador Retrievers with known radiographic hip score: 14 with hip dysplasia (grade D or E) and 25 without hip dysplasia (grade A or B). There was no significant correlation between the Dysgen test results and the radiographic hip status (P = 0.3203) in these dogs, indicating that Dysgen test results obtained for Danish Labrador Retrievers have no prognostic value.
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Affiliation(s)
- C S Bruun
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, 1870, Denmark
| | - A Bank
- Evidensia Specialistdjursjukhuset, Helsingborg, 254 66, Sweden
| | - A Ström
- Evidensia Specialistdjursjukhuset, Helsingborg, 254 66, Sweden
| | | | - M Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, 1870, Denmark
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13
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Merca R, Bockstahler B, Vezzoni A, Tichy A, Boano S, Vidoni B. Canine hip dysplasia screening: Comparison of early evaluation to final grading in 231 dogs with Fédération Cynologique Internationale A and B. PLoS One 2020; 15:e0233257. [PMID: 32421701 PMCID: PMC7233575 DOI: 10.1371/journal.pone.0233257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 05/02/2020] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES This study aimed to verify if a significant difference exists between parameters in the early evaluation of normal and near-normal hip joints, to evaluate the influence of age and breed on the parameters, and to clarify the usefulness of a total score for differentiating between Fédération Cynologique Internationale (FCI) grade A and B hips. METHODS A total of 231 dogs were classified according to whether they had FCI A or B hips at adulthood, with measurements obtained at 14-28 weeks of age. The total score was calculated by the summation of the following quantitative parameters: angle of subluxation (AS), angle of reduction (AR), laxity index (LI), and dorsal acetabular rim slope (DARS). Logistic regression analysis was performed to establish the probability of the study population to develop an FCI B hip based on the total score. This was repeated for the highest score in combination with the worst-rated hip and once more for breeds. RESULTS No correlation between age and the parameters was found in the cohort, or for FCI A and B. The values of all the parameters were significantly lower in the FCI A group than in the FCI B group (AR: 4.42° ± 6.0° vs 7.62° ± 7.2°; AS: 0.45° ± 1.9° vs 1.55° ± 3.8°; LI: 0.32 ± 0.1 vs 0.36 ± 0.1; DARS: 3.30° ± 1.8° vs 3.77° ± 1.9°; TS: 11.47 ± 8.3 vs 16.65 ± 10.9). Labrador Retrievers and Golden Retrievers showed significant differences between parameters for both FCI grades. The range, where FCI A and B hips can be predicted on the basis of the total score, was different when assessed for the entire cohort, Labrador Retrievers, and Golden Retrievers. CLINICAL SIGNIFICANCE Our results show that even in normal and near-normal hips, the parameters significantly differed in the early evaluation. Moreover, cutoff values should be set for different breeds in the prediction of the FCI grade during early evaluation for a better breeding selection regarding canine hip dysplasia, one of the most common orthopedic diseases among large and giant breed dogs.
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Affiliation(s)
- Roxana Merca
- Department for Companion Animals and Horses, University Clinic for Small Animals, Small Animal Surgery, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Bockstahler
- Department for Companion Animals and Horses, University Clinic for Small Animals, Small Animal Surgery, University of Veterinary Medicine, Vienna, Austria
| | | | - Alexander Tichy
- Department for Companion Animals and Horses, University Clinic for Small Animals, Small Animal Surgery, University of Veterinary Medicine, Vienna, Austria
| | | | - Britta Vidoni
- Department for Companion Animals and Horses, University Clinic for Small Animals, Small Animal Surgery, University of Veterinary Medicine, Vienna, Austria
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14
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Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D. Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 2020; 9:giaa027. [PMID: 32236524 PMCID: PMC7111595 DOI: 10.1093/gigascience/giaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. FINDINGS Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. CONCLUSIONS GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, QLD 4878, Australia
- John Curtin School of Medical Research, Australian National University, Garran Rd, Canberra, ACT 2600, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, MD 20705, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
| | - Eva K F Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Andre E Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Kirston Barton
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Ruth J Lyons
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
- Central Clinical School, University of Sydney, Parramatta Road, Camperdown, NSW 2050, Australia
| | - Arina D. Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Martin A Smith
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
- Broad Institute of MIT and Harvard, Main St, Cambridge, MA 02142, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, ShanghaiTech University, Huaxia Middle Rd, Pudong 201210, China
| | - Timothy P L Smith
- US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA
| | - Robert A Zammit
- Vineyard Veterinary Hospital, Windsor Rd, Vineyard, NSW 2765, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
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15
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Meeson RL, Todhunter RJ, Blunn G, Nuki G, Pitsillides AA. Spontaneous dog osteoarthritis - a One Medicine vision. Nat Rev Rheumatol 2020; 15:273-287. [PMID: 30953036 PMCID: PMC7097182 DOI: 10.1038/s41584-019-0202-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Osteoarthritis (OA) is a global disease that, despite extensive research, has limited treatment options. Pet dogs share both an environment and lifestyle attributes with their owners, and a growing awareness is developing in the public and among researchers that One Medicine, the mutual co-study of animals and humans, could be beneficial for both humans and dogs. To that end, this Review highlights research opportunities afforded by studying dogs with spontaneous OA, with a view to sharing this active area of veterinary research with new audiences. Similarities and differences between dog and human OA are examined, and the proposition is made that suitably aligned studies of spontaneous OA in dogs and humans, in particular hip and knee OA, could highlight new avenues of discovery. Developing cross-species collaborations will provide a wealth of research material and knowledge that is relevant to human OA and that cannot currently be obtained from rodent models or experimentally induced dog models of OA. Ultimately, this Review aims to raise awareness of spontaneous dog OA and to stimulate discussion regarding its exploration under the One Medicine initiative to improve the health and well-being of both species. Osteoarthritis occurs spontaneously in pet dogs, which often share environmental and lifestyle risk-factors with their owners. This Review aims to stimulate cooperation between medical and veterinary research under the One Medicine initiative to improve the welfare of dogs and humans. Dogs have many analogous spontaneous diseases that result in end-stage osteoarthritis (OA). Inbreeding and the predisposition of certain dog breeds for OA enable easier identification of candidate genetic associations than in outbred humans. Dog OA subtypes offer a potential stratification rationale for aetiological differences and alignment to analogous human OA phenotypes. The relatively compressed time course of spontaneous dog OA offers longitudinal research opportunities. Collaboration with veterinary researchers can provide tissue samples from early-stage OA and opportunities to evaluate new therapeutics in a spontaneous disease model. Awareness of the limitations and benefits of using clinical veterinary patients in research is important.
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Affiliation(s)
- Richard L Meeson
- Skeletal Biology Group, Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK.,Department of Clinical Services and Sciences, Royal Veterinary College, University of London, London, UK.,Institute of Orthopaedics and Musculoskeletal Science, University College London, London, UK
| | - Rory J Todhunter
- Department of Clinical Sciences, Cornell University, Ithaca, NY, USA.,Cornell Veterinary Biobank, Cornell University, Ithaca, NY, USA
| | - Gordon Blunn
- Institute of Orthopaedics and Musculoskeletal Science, University College London, London, UK.,School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - George Nuki
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew A Pitsillides
- Skeletal Biology Group, Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK.
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16
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James HK, McDonnell F, Lewis TW. Effectiveness of Canine Hip Dysplasia and Elbow Dysplasia Improvement Programs in Six UK Pedigree Breeds. Front Vet Sci 2020; 6:490. [PMID: 32010712 PMCID: PMC6974481 DOI: 10.3389/fvets.2019.00490] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
Hip and elbow dysplasia are common disorders in larger dog breeds and crosses, and a known contributory factor to osteoarthritis, lameness and reduced mobility. Screening schemes evaluating the severity of hip and elbow dysplasia in the UK are administered by the British Veterinary Association (BVA) and the Kennel Club (KC). The BVA/KC Hip Dysplasia scoring scheme is over 50 years old, having originated in 1965, and has operated in its current form since 1983. The BVA/KC Elbow Dysplasia grading scheme commenced more recently in 1998 and is based on the International Elbow Working Group guidelines. Hip score and elbow grade data on a considerable number of dogs in the UK have been generated from these two screening schemes. This study analyses data from dogs of six breeds scored from 1990 to present, to establish any determinable trends in hip score and elbow grade parameters, and to examine whether the implementation of such schemes has had a positive influence on hip and elbow health. A range of criteria, including the rate of participation in the screening schemes, hip score and elbow grade parameters (e.g., median, mean, standard deviation), and estimated breeding values (EBVs) were analyzed, both in the overall population and also among breeding animals. The results show a general decline in hip score parameters (median, mean, standard deviation, and 75th percentile), revealing a reduction in the prevalence and severity of hip dysplasia. There was a more modest decline in mean elbow grade within breeds. The proportion of sires and dams (of dogs born per year) with no hip score or elbow grade fell substantially over time, demonstrating good participation in the screening schemes. In most breeds, the scores of sires and dams are demonstrably improving. There is a declining genetic trend as ascertained by EBVs for both hip scores and elbow grades in most breeds, implying that the improvement observed is due in part to selection for improvement in hip and elbow health as described by the respective screening schemes.
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Affiliation(s)
| | | | - Thomas W. Lewis
- The Kennel Club, London, United Kingdom
- School of Veterinary Medicine and Science, The University of Nottingham, Nottingham, United Kingdom
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17
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Akis I, Ates A, Atmaca G, Oztabak KO, Esen Gursel F, Yardibi H, Altunatmaz K, Eravci Yalin E, Karabagli M. The association of genetic polymorphisms of bone formation genes with canine hip dysplasia. IRANIAN JOURNAL OF VETERINARY RESEARCH 2020; 21:40-45. [PMID: 32368224 PMCID: PMC7183374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 05/28/2019] [Accepted: 07/08/2019] [Indexed: 06/11/2023]
Abstract
BACKGROUND Canine hip dysplasia (CHD) is an orthopedic disorder characterized by abnormal laxity of the hip joint. It is considered multifactorial and polygenic and affects predominantly medium and large sized dog breeds. AIMS The aim of this study was to identify CHD associated polymorphisms in chromosomal regions on CFA19, CFA24, CFA26, and CFA34. METHODS Blood samples from 60 dogs of different breeds were collected and genotyped, including 46 cases and 14 controls. After sequencing and single nucleotide polymorphism (SNP) determination of the target regions, an individual SNP analysis with a 2 statistic was performed based on the comparison of allele frequencies in cases and controls. RESULTS A significant association was observed between CHD and a T/C SNP on CFA19, which harbors genes involved in bone metabolism. No other significant association was found in the study and previously identified SNPs cannot be validated as related to CHD. CONCLUSION Further research is warranted to identify CHD-associated polymorphisms in order to develop a genotype-based diagnosis and selection approach.
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Affiliation(s)
- I. Akis
- Department of Basic Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - A. Ates
- Department of Basic Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - G. Atmaca
- Ph.D. Student in Biochemistry, Department of Basic Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - K. O. Oztabak
- Department of Basic Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - F. Esen Gursel
- Department of Basic Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - H. Yardibi
- Department of Basic Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - K. Altunatmaz
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - E. Eravci Yalin
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
| | - M. Karabagli
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34320, Avcilar, Istanbul, Turkey
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18
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Ajadi RA, Sanni JL, Sobayo EF, Ijaopo OK. Evaluation of plasma trace elements and oxidant/antioxidant status in Boerboel dogs with hip dysplasia. BULGARIAN JOURNAL OF VETERINARY MEDICINE 2020. [DOI: 10.15547/bjvm.2185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Changes in plasma concentrations of trace elements and oxidants/antioxidants were evaluated in twenty healthy Boerboels of both sexes and median age of 2 years. Antero-posterior and flexed lateral radiographs of the hip were obtained using digital x-ray machine and hip grading was done according to Fédération Cynologique Internationale (FCI) system. Blood was collected from the cephalic vein for determination of plasma concentrations of manganese (Mn), magnesium (Mg), copper (Cu), cobalt (Co), malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), glutathione peroxidase (GPX) and Vitamin E. Correlation between the parameters was done using Pearson’s correlation. Eleven (11/20) of the Boerboel dogs had hip dysplasia (HD), comprising five (5/9) males and six (6/11) females. Plasma Mn, Cu and Co were insignificantly higher in Boerboels with normal hips than those with HD. MDA concentration was significantly (p<0.05) lower in Boerboels with normal hips (0.75 ± 0.84 µmol/L) than in dogs with HD (1.77 ± 0.78 µmol/L), while SOD was significantly (p<0.05) higher in Boerboels with normal hips (0.65 ± 0.22 U/ml) than with HD (0.32 ± 0.16 U/ml). It was concluded that there were differences in plasma oxidants/antioxidants between Boerboel dogs with normal hips and those with hip dysplasia suggesting their role in the pathogenesis of canine hip dysplasia
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19
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Mikkola L, Holopainen S, Pessa-Morikawa T, Lappalainen AK, Hytönen MK, Lohi H, Iivanainen A. Genetic dissection of canine hip dysplasia phenotypes and osteoarthritis reveals three novel loci. BMC Genomics 2019; 20:1027. [PMID: 31881848 PMCID: PMC6935090 DOI: 10.1186/s12864-019-6422-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/22/2019] [Indexed: 12/15/2022] Open
Abstract
Background Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can cause a severe impairment of the quality of life. In Finland, the complex condition is categorized to five classes from normal to severe dysplasia, but the categorization includes several sub-traits: congruity of the joint, Norberg angle, subluxation degree of the joint, shape and depth of the acetabulum, and osteoarthritis. Hip dysplasia and osteoarthritis have been proposed to have separate genetic etiologies. Results Using Fédération Cynologique Internationale -standardized ventrodorsal radiographs, German shepherds were rigorously phenotyped for osteoarthritis, and for joint incongruity by Norberg angle and femoral head center position in relation to dorsal acetabular edge. The affected dogs were categorized into mild, moderate and severe dysplastic phenotypes using official hip scores. Three different genome-wide significant loci were uncovered. The strongest candidate genes for hip joint incongruity were noggin (NOG), a bone and joint developmental gene on chromosome 9, and nanos C2HC-type zinc finger 1 (NANOS1), a regulator of matrix metalloproteinase 14 (MMP14) on chromosome 28. Osteoarthritis mapped to a long intergenic region on chromosome 1, between genes encoding for NADPH oxidase 3 (NOX3), an intriguing candidate for articular cartilage degradation, and AT-rich interactive domain 1B (ARID1B) that has been previously linked to joint laxity. Conclusions Our findings highlight the complexity of canine hip dysplasia phenotypes. In particular, the results of this study point to the potential involvement of specific and partially distinct loci and genes or pathways in the development of incongruity, mild dysplasia, moderate-to-severe dysplasia and osteoarthritis of canine hip joints. Further studies should unravel the unique and common mechanisms for the various sub-traits.
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Affiliation(s)
- Lea Mikkola
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66 (Mustialankatu 1), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Saila Holopainen
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66 (Mustialankatu 1), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Pessa-Morikawa
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66 (Mustialankatu 1), FI-00014, Helsinki, Finland
| | - Anu K Lappalainen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Marjo K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66 (Mustialankatu 1), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66 (Mustialankatu 1), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66 (Mustialankatu 1), FI-00014, Helsinki, Finland.
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20
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Ohlerth S, Geiser B, Flückiger M, Geissbühler U. Prevalence of Canine Hip Dysplasia in Switzerland Between 1995 and 2016-A Retrospective Study in 5 Common Large Breeds. Front Vet Sci 2019; 6:378. [PMID: 31709271 PMCID: PMC6821640 DOI: 10.3389/fvets.2019.00378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
Canine hip dysplasia (CHD) is a genetic disease, modulated by epigenetic and environmental factors. To decrease the prevalence of CHD, the hip joints of many pure breed dogs are radiographed to identify dysplastic dogs not qualified for breeding. It has been shown that both, prevalence and severity of CHD may be reduced on the basis of phenotypic i.e., radiographic selection of breeding animals. The method has been used in many countries for over 50 years. In the present study, severity and prevalence of CHD in five common large breeds in Switzerland were evaluated since 1995. Both, prevalence and severity of CHD dropped in each breed between the periods 1995-1999 and 2010-2016. The prevalence decreased in Golden Retrievers from 25 to 9% and in Labrador Retrievers from 16 to 3%, respectively. In the Flat-Coated Retriever, prevalence in general was low, decreasing from 6 to 3%. In the Bernese mountain dog and the German shepherd dog, a decrease from 21 to 12% and from 46 to 18%, respectively, was observed. However, the rather low overall rate of radiographed dogs (Retrievers: 11 to 18%, Bernese Mountain dogs: 23% and German Shepherd dogs: 31%) does not allow to draw reliable conclusions regarding the true prevalence of CHD for the entire population of these breeds in Switzerland.
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Affiliation(s)
- Stefanie Ohlerth
- Clinic for Diagnostic Imaging, Department of Clinical Services and Diagnostics, University of Zurich, Zurich, Switzerland
| | - Britta Geiser
- Section of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Mark Flückiger
- Clinic for Diagnostic Imaging, Department of Clinical Services and Diagnostics, University of Zurich, Zurich, Switzerland
| | - Urs Geissbühler
- Section of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
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21
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Mikkola LI, Holopainen S, Lappalainen AK, Pessa-Morikawa T, Augustine TJP, Arumilli M, Hytönen MK, Hakosalo O, Lohi H, Iivanainen A. Novel protective and risk loci in hip dysplasia in German Shepherds. PLoS Genet 2019; 15:e1008197. [PMID: 31323019 PMCID: PMC6668854 DOI: 10.1371/journal.pgen.1008197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/31/2019] [Accepted: 05/14/2019] [Indexed: 12/15/2022] Open
Abstract
Canine hip dysplasia is a common, non-congenital, complex and hereditary disorder. It can inflict severe pain via secondary osteoarthritis and lead to euthanasia. An analogous disorder exists in humans. The genetic background of hip dysplasia in both species has remained ambiguous despite rigorous studies. We aimed to investigate the genetic causes of this disorder in one of the high-risk breeds, the German Shepherd. We performed genetic analyses with carefully phenotyped case-control cohorts comprising 525 German Shepherds. In our genome-wide association studies we identified four suggestive loci on chromosomes 1 and 9. Targeted resequencing of the two loci on chromosome 9 from 24 affected and 24 control German Shepherds revealed deletions of variable sizes in a putative enhancer element of the NOG gene. NOG encodes for noggin, a well-described bone morphogenetic protein inhibitor affecting multiple developmental processes, including joint development. The deletion was associated with the healthy controls and mildly dysplastic dogs suggesting a protective role against canine hip dysplasia. Two enhancer variants displayed a decreased activity in a dual luciferase reporter assay. Our study identifies novel loci and candidate genes for canine hip dysplasia, with potential regulatory variants in the NOG gene. Further research is warranted to elucidate how the identified variants affect the expression of noggin in canine hips, and what the potential effects of the other identified loci are.
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Affiliation(s)
- Lea I. Mikkola
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Saila Holopainen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Anu K. Lappalainen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Meharji Arumilli
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Marjo K. Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Osmo Hakosalo
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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22
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Ahner CE, Stoker AM, Bozynski CC, Cook CR, Leary EV, Kuroki K, Cruz CN, Cook JL. Protein biomarkers in serum and urine for determining presence or absence of hip dysplasia in a canine model. J Orthop Res 2019; 37:916-920. [PMID: 30720210 DOI: 10.1002/jor.24242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/25/2019] [Indexed: 02/04/2023]
Abstract
This study compares serum and urine concentrations of relevant protein biomarkers among adult dogs with or without radiographic canine hip dysplasia (CHD). Adult (≥2 years of age), client-owned dogs (n = 74) radiographically categorized as having at least "good" hips (n = 49) or having "mild," "moderate," or "severe" hip dysplasia (n = 25) by the Orthopedic Foundation for Animals (OFA). Urine and serum samples were obtained from each dog at a single time-point and processed and analyzed for relevant protein biomarkers. Urinary concentrations of CTX-II (p < 0.001) and TIMP-1 (p = 0.002) were significantly lower in dogs with CHD compared to dogs with no CHD. ROC curve analyses were successful in establishing a panel of four biomarkers (urinary CTX-I and II, serum MMP-9, and serum PIICP) with high discriminatory capability for the presence or absence of hip dysplasia in adult dogs (AUC = 0.89). Urine and serum biomarkers can distinguish adult dogs with radiographic CHD from those with no CHD with a sensitivity of 0.95 and specificity of 0.77 using ROC analysis with AUC 0.89. Clinical Significance: This finding suggests that this simple, minimally invasive diagnostic technique has potential for discriminating dysplastic dogs from dogs with normal hips, with possible translational application to humans based on similar etiopathogenesis. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 9999:1-5, 2019.
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Affiliation(s)
- Carin E Ahner
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri.,Division of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Aaron M Stoker
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri
| | - Chantelle C Bozynski
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri
| | - Cristi R Cook
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri
| | - Emily V Leary
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri.,Department of Orthopaedic Surgery, University of Missouri, 1100 Virginia Ave., Columbia, Missouri, 65212
| | - Keiichi Kuroki
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri
| | - Carissa N Cruz
- College of Veterinary Medicine and Surgery, University of Missouri, Columbia, Missouri.,Villa Park Animal Clinic, Los Angeles, California
| | - James L Cook
- Thompson Laboratory for Regenerative Orthopaedics, University of Missouri, Columbia, Missouri.,Department of Orthopaedic Surgery, University of Missouri, 1100 Virginia Ave., Columbia, Missouri, 65212
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23
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Friedrich J, Antolín R, Edwards SM, Sánchez‐Molano E, Haskell MJ, Hickey JM, Wiener P. Accuracy of genotype imputation in Labrador Retrievers. Anim Genet 2018; 49:303-311. [PMID: 29974966 PMCID: PMC6055857 DOI: 10.1111/age.12677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
Abstract
The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular interest to analyse the effect of factors like single nucleotide polymorphism (SNP) density of genotyping arrays and relatedness between dogs on imputation accuracy due to the acknowledged genetic and pedigree structure of dog breeds. In this study, we simulated different genotyping strategies based on data from 1179 Labrador Retriever dogs. The study involved 5826 SNPs on chromosome 1 representing the high density (HighD) array; the low-density (LowD) array was simulated by masking different proportions of SNPs on the HighD array. The correlations between true and imputed genotypes for a realistic masking level of 87.5% ranged from 0.92 to 0.97, depending on the scenario used. A correlation of 0.92 was found for a likely scenario (10% of dogs genotyped using HighD, 87.5% of HighD SNPs masked in the LowD array), which indicates that genotype imputation in Labrador Retrievers can be a valuable tool to reduce experimental costs while increasing sample size. Furthermore, we show that genotype imputation can be performed successfully even without pedigree information and with low relatedness between dogs in the reference and validation sets. Based on these results, the impact of genotype imputation was evaluated in a genome-wide association analysis and genomic prediction in Labrador Retrievers.
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Affiliation(s)
- J. Friedrich
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianEH25 9RGUK
| | - R. Antolín
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianEH25 9RGUK
| | - S. M. Edwards
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianEH25 9RGUK
| | - E. Sánchez‐Molano
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianEH25 9RGUK
| | - M. J. Haskell
- Animal and Veterinary Sciences GroupScotland's Rural CollegeEdinburghEH9 3JGUK
| | - J. M. Hickey
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianEH25 9RGUK
| | - P. Wiener
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianEH25 9RGUK
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24
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Edwards SM, Woolliams JA, Hickey JM, Blott SC, Clements DN, Sánchez-Molano E, Todhunter RJ, Wiener P. Joint Genomic Prediction of Canine Hip Dysplasia in UK and US Labrador Retrievers. Front Genet 2018; 9:101. [PMID: 29643866 PMCID: PMC5883867 DOI: 10.3389/fgene.2018.00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/13/2018] [Indexed: 01/11/2023] Open
Abstract
Canine hip dysplasia, a debilitating orthopedic disorder that leads to osteoarthritis and cartilage degeneration, is common in several large-sized dog breeds and shows moderate heritability suggesting that selection can reduce prevalence. Estimating genomic breeding values require large reference populations, which are expensive to genotype for development of genomic prediction tools. Combining datasets from different countries could be an option to help build larger reference datasets without incurring extra genotyping costs. Our objective was to evaluate genomic prediction based on a combination of UK and US datasets of genotyped dogs with records of Norberg angle scores, related to canine hip dysplasia. Prediction accuracies using a single population were 0.179 and 0.290 for 1,179 and 242 UK and US Labrador Retrievers, respectively. Prediction accuracies changed to 0.189 and 0.260, with an increased bias of genomic breeding values when using a joint training set (biased upwards for the US population and downwards for the UK population). Our results show that in this study of canine hip dysplasia, little or no benefit was gained from using a joint training set as compared to using a single population as training set. We attribute this to differences in the genetic background of the two populations as well as the small sample size of the US dataset.
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Affiliation(s)
- Stefan M Edwards
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
| | - John A Woolliams
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
| | - Sarah C Blott
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Dylan N Clements
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
| | - Enrique Sánchez-Molano
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
| | - Rory J Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
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25
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Wiener P, Sánchez-Molano E, Clements DN, Woolliams JA, Haskell MJ, Blott SC. Genomic data illuminates demography, genetic structure and selection of a popular dog breed. BMC Genomics 2017; 18:609. [PMID: 28806925 PMCID: PMC5557481 DOI: 10.1186/s12864-017-3933-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/09/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. RESULTS We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. CONCLUSIONS This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Enrique Sánchez-Molano
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Dylan N. Clements
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - John A. Woolliams
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
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26
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Abstract
First identified in 1935, canine hip dysplasia is thought to be the most common orthopedic condition diagnosed in the dog. It is most prevalent in large and giant breed dogs, with a complex polygenic mode of inheritance, and relatively low heritability. External factors including caloric intake when growing have a significant effect on phenotypic expression. Initial joint laxity progresses to osteoarthritis due to subluxation and abnormal wearing. Selective breeding programs to attempt to decrease prevalence have shown modest results so far.
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Affiliation(s)
- Michael D King
- Department of Surgery, Canada West Veterinary Specialists & Critical Care Hospital, 1988 Kootenay Street, Vancouver, British Columbia V5M 4Y3, Canada.
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27
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Abstract
The genetic architecture of behavioral traits in dogs is of great interest to owners, breeders, and professionals involved in animal welfare, as well as to scientists studying the genetics of animal (including human) behavior. The genetic component of dog behavior is supported by between-breed differences and some evidence of within-breed variation. However, it is a challenge to gather sufficiently large datasets to dissect the genetic basis of complex traits such as behavior, which are both time-consuming and logistically difficult to measure, and known to be influenced by nongenetic factors. In this study, we exploited the knowledge that owners have of their dogs to generate a large dataset of personality traits in Labrador Retrievers. While accounting for key environmental factors, we demonstrate that genetic variance can be detected for dog personality traits assessed using questionnaire data. We identified substantial genetic variance for several traits, including fetching tendency and fear of loud noises, while other traits revealed negligibly small heritabilities. Genetic correlations were also estimated between traits; however, due to fairly large SEs, only a handful of trait pairs yielded statistically significant estimates. Genomic analyses indicated that these traits are mainly polygenic, such that individual genomic regions have small effects, and suggested chromosomal associations for six of the traits. The polygenic nature of these traits is consistent with previous behavioral genetics studies in other species, for example in mouse, and confirms that large datasets are required to quantify the genetic variance and to identify the individual genes that influence behavioral traits.
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28
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Oberbauer AM, Keller GG, Famula TR. Long-term genetic selection reduced prevalence of hip and elbow dysplasia in 60 dog breeds. PLoS One 2017; 12:e0172918. [PMID: 28234985 PMCID: PMC5325577 DOI: 10.1371/journal.pone.0172918] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/10/2017] [Indexed: 11/24/2022] Open
Abstract
Canine hip dysplasia (CHD) and elbow dysplasia (ED) impact the health and welfare of all dogs. The first formally organized assessment scheme to improve canine health centered on reducing the prevalence of these orthopedic disorders. Phenotypic screening of joint conformation remains the currently available strategy for breeders to make selection decisions. The present study evaluated the efficacy of employing phenotypic selection on breed improvement of hips and elbows using the Orthopedic Foundation for Animals complete database spanning the 1970–2015 time period. Sixty breeds having more than 1000 unique hip evaluations and 500 elbow evaluations (1,056,852 and 275,129 hip and elbow records, respectively) were interrogated to derive phenotypic improvement, sex and age at time of assessment effects, correlation between the two joints, heritability estimates, estimated breeding values (EBV), and effectiveness of maternal/paternal selection. The data demonstrated that there has been overall improvement in hip and elbow conformation with a reduction in EBV for disease liability, although the breeds differed in the magnitude of the response to selection. Heritabilities also differed substantially across the breeds as did the correlation of the joints; in the absence of a universal association of these differences with breed size, popularity, or participation in screening, it appears that the breeds themselves vary in genetic control. There was subtle, though again breed specific, impact of sex and older ages on CHD and ED. There was greater paternal impact on a reduction of CHD. In the absence of direct genetic tests for either of these two diseases, phenotypic selection has proven to be effective. Furthermore, the data underscore that selection schemes must be breed specific and that it is likely the genetic profiles will be unique across the breeds for these two conditions. Despite the advances achieved with phenotypic selection, incorporation of EBVs into selection schemes should accelerate advances in hip and elbow improvement.
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Affiliation(s)
- A M Oberbauer
- Department of Animal Science, University of California, Davis, Davis, CA United States of America
| | - G G Keller
- Orthopedic Foundation for Animals, Columbia, MO United States of America
| | - T R Famula
- Department of Animal Science, University of California, Davis, Davis, CA United States of America
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29
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Hoffman AM, Dow SW. Concise Review: Stem Cell Trials Using Companion Animal Disease Models. Stem Cells 2016; 34:1709-29. [PMID: 27066769 DOI: 10.1002/stem.2377] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/26/2016] [Indexed: 12/13/2022]
Abstract
Studies to evaluate the therapeutic potential of stem cells in humans would benefit from more realistic animal models. In veterinary medicine, companion animals naturally develop many diseases that resemble human conditions, therefore, representing a novel source of preclinical models. To understand how companion animal disease models are being studied for this purpose, we reviewed the literature between 2008 and 2015 for reports on stem cell therapies in dogs and cats, excluding laboratory animals, induced disease models, cancer, and case reports. Disease models included osteoarthritis, intervertebral disc degeneration, dilated cardiomyopathy, inflammatory bowel diseases, Crohn's fistulas, meningoencephalomyelitis (multiple sclerosis-like), keratoconjunctivitis sicca (Sjogren's syndrome-like), atopic dermatitis, and chronic (end-stage) kidney disease. Stem cells evaluated in these studies included mesenchymal stem-stromal cells (MSC, 17/19 trials), olfactory ensheathing cells (OEC, 1 trial), or neural lineage cells derived from bone marrow MSC (1 trial), and 16/19 studies were performed in dogs. The MSC studies (13/17) used adipose tissue-derived MSC from either allogeneic (8/13) or autologous (5/13) sources. The majority of studies were open label, uncontrolled studies. Endpoints and protocols were feasible, and the stem cell therapies were reportedly safe and elicited beneficial patient responses in all but two of the trials. In conclusion, companion animals with naturally occurring diseases analogous to human conditions can be recruited into clinical trials and provide realistic insight into feasibility, safety, and biologic activity of novel stem cell therapies. However, improvements in the rigor of manufacturing, study design, and regulatory compliance will be needed to better utilize these models. Stem Cells 2016;34:1709-1729.
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Affiliation(s)
- Andrew M Hoffman
- Regenerative Medicine Laboratory, Department of Clinical Sciences, Cummings School of Veterinary Medicine, Tufts University, Grafton, Massachusetts, USA
| | - Steven W Dow
- Center for Immune and Regenerative Medicine, Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
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30
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Ginja M, Gaspar AR, Ginja C. Emerging insights into the genetic basis of canine hip dysplasia. VETERINARY MEDICINE-RESEARCH AND REPORTS 2015; 6:193-202. [PMID: 30101106 PMCID: PMC6070022 DOI: 10.2147/vmrr.s63536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Canine hip dysplasia (CHD) is the most common inherited polygenic orthopedic trait in dogs with the phenotype influenced also by environmental factors. This trait was described in the dog in 1935 and leads to a debilitating secondary hip osteoarthritis. The diagnosis is confirmed radiographically by evaluating signs of degenerative joint disease, incongruence, and/or passive hip joint laxity. There is no ideal medical or surgical treatment so prevention based on controlled breeding is the optimal approach. The definitive CHD diagnosis based on radiographic examination involves the exposure to ionizing radiation under general anesthesia or heavy sedation but the image does not reveal the underlying genetic quality of the dog. Phenotypic expression of CHD is modified by environmental factors and dogs with a normal phenotype can be carriers of some mutations and transmit these genes to their offspring. Programs based on selection of dogs with better individual phenotypes for breeding are effective when strictly applied but remain inferior to the selection of dogs based on estimation of breeding values. Molecular studies for dissecting the genetic basis of CHD are ongoing, but progress has been slow. In the future, the recommended method to improve hip quality in controlled breeding schemes, which will allow higher selection pressure, would be based on the estimation of the genomic breeding value. Since 2012, a commercial DNA test has been available for Labrador Retrievers using a blood sample and provides a probability for development of CHD but we await evidence that this test reduces the incidence or severity of CHD.
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Affiliation(s)
- Mário Ginja
- Department of Veterinary Sciences-CITAB, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal,
| | - Ana Rita Gaspar
- Department of Veterinary Sciences-CITAB, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal,
| | - Catarina Ginja
- Ce3C - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,CIBIO-InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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31
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Sánchez-Molano E, Pong-Wong R, Clements DN, Blott SC, Wiener P, Woolliams JA. Genomic prediction of traits related to canine hip dysplasia. Front Genet 2015; 6:97. [PMID: 25821457 PMCID: PMC4358223 DOI: 10.3389/fgene.2015.00097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/23/2015] [Indexed: 11/29/2022] Open
Abstract
Increased concern for the welfare of pedigree dogs has led to development of selection programs against inherited diseases. An example is canine hip dysplasia (CHD), which has a moderate heritability and a high prevalence in some large-sized breeds. To date, selection using phenotypes has led to only modest improvement, and alternative strategies such as genomic selection (GS) may prove more effective. The primary aims of this study were to compare the performance of pedigree- and genomic-based breeding against CHD in the UK Labrador retriever population and to evaluate the performance of different GS methods. A sample of 1179 Labrador Retrievers evaluated for CHD according to the UK scoring method (hip score, HS) was genotyped with the Illumina CanineHD BeadChip. Twelve functions of HS and its component traits were analyzed using different statistical methods (GBLUP, Bayes C and Single-Step methods), and results were compared with a pedigree-based approach (BLUP) using cross-validation. Genomic methods resulted in similar or higher accuracies than pedigree-based methods with training sets of 944 individuals for all but the untransformed HS, suggesting that GS is an effective strategy. GBLUP and Bayes C gave similar prediction accuracies for HS and related traits, indicating a polygenic architecture. This conclusion was also supported by the low accuracies obtained in additional GBLUP analyses performed using only the SNPs with highest test statistics, also indicating that marker-assisted selection (MAS) would not be as effective as GS. A Single-Step method that combines genomic and pedigree information also showed higher accuracy than GBLUP and Bayes C for the log-transformed HS, which is currently used for pedigree based evaluations in UK. In conclusion, GS is a promising alternative to pedigree-based selection against CHD, requiring more phenotypes with genomic data to improve further the accuracy of prediction.
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Affiliation(s)
- Enrique Sánchez-Molano
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Ricardo Pong-Wong
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Dylan N Clements
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Sarah C Blott
- Kennel Club Genetics Centre at the Animal Health Trust Newmarket, UK ; School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - John A Woolliams
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
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