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Silva C, Requicha J, Dias I, Bastos E, Viegas C. Genomic Medicine in Canine Periodontal Disease: A Systematic Review. Animals (Basel) 2023; 13:2463. [PMID: 37570272 PMCID: PMC10417655 DOI: 10.3390/ani13152463] [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: 06/19/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Genomic medicine has become a growing reality; however, it is still taking its first steps in veterinary medicine. Through this approach, it will be possible to trace the genetic profile of a given individual and thus know their susceptibility to certain diseases, namely periodontal disease. This condition is one of the most frequently diagnosed in companion animal clinics, especially in dogs. Due to the limited existing information and the lack of comprehensive studies, the objective of the present study was to systematically review the existing scientific literature regarding genomic medicine in canine periodontal disease and determine which genes have already been studied and their probable potential. This study followed the recommendations of the PRISMA 2020 methodology. Canine periodontal disease allied to genomic medicine were the subjects of this systematic review. Only six articles met all of the inclusion criteria, and these were analyzed in detail. These studies described genetic variations in the following genes: interleukin-6, interleukin-10, interleukin-1, lactotransferrin, toll-like receptor 9, and receptor activator of nuclear factor-kappa B. Only in two of them, namely interleukin-1 and toll-like receptor 9 genes, may the identified genetic variations explain the susceptibility that certain individuals have to the development of periodontal disease. It is necessary to expand the studies on the existing polymorphic variations in genes and their relationship with the development of periodontal disease. Only then will it be possible to fully understand the biological mechanisms that are involved in this disease and that determine the susceptibility to its development.
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Affiliation(s)
- Carolina Silva
- Department of Veterinary Sciences, School of Agricultural and Veterinary Sciences (ECAV), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal; (C.S.); (J.R.); (I.D.)
- CECAV—Centre for Animal Sciences and Veterinary Studies, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - João Requicha
- Department of Veterinary Sciences, School of Agricultural and Veterinary Sciences (ECAV), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal; (C.S.); (J.R.); (I.D.)
- CECAV—Centre for Animal Sciences and Veterinary Studies, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
| | - Isabel Dias
- Department of Veterinary Sciences, School of Agricultural and Veterinary Sciences (ECAV), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal; (C.S.); (J.R.); (I.D.)
- CECAV—Centre for Animal Sciences and Veterinary Studies, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
- CITAB—Center for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Inov4Agro-Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production, 5000-801 Vila Real, Portugal
| | - Estela Bastos
- CITAB—Center for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Inov4Agro-Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production, 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, School of Life and Environmental Sciences, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Carlos Viegas
- Department of Veterinary Sciences, School of Agricultural and Veterinary Sciences (ECAV), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal; (C.S.); (J.R.); (I.D.)
- CECAV—Centre for Animal Sciences and Veterinary Studies, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
- CITAB—Center for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Inov4Agro-Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production, 5000-801 Vila Real, Portugal
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Meuwissen T, van den Berg I, Goddard M. On the use of whole-genome sequence data for across-breed genomic prediction and fine-scale mapping of QTL. Genet Sel Evol 2021; 53:19. [PMID: 33637049 PMCID: PMC7908738 DOI: 10.1186/s12711-021-00607-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Whole-genome sequence (WGS) data are increasingly available on large numbers of individuals in animal and plant breeding and in human genetics through second-generation resequencing technologies, 1000 genomes projects, and large-scale genotype imputation from lower marker densities. Here, we present a computationally fast implementation of a variable selection genomic prediction method, that could handle WGS data on more than 35,000 individuals, test its accuracy for across-breed predictions and assess its quantitative trait locus (QTL) mapping precision. Methods The Monte Carlo Markov chain (MCMC) variable selection model (Bayes GC) fits simultaneously a genomic best linear unbiased prediction (GBLUP) term, i.e. a polygenic effect whose correlations are described by a genomic relationship matrix (G), and a Bayes C term, i.e. a set of single nucleotide polymorphisms (SNPs) with large effects selected by the model. Computational speed is improved by a Metropolis–Hastings sampling that directs computations to the SNPs, which are, a priori, most likely to be included into the model. Speed is also improved by running many relatively short MCMC chains. Memory requirements are reduced by storing the genotype matrix in binary form. The model was tested on a WGS dataset containing Holstein, Jersey and Australian Red cattle. The data contained 4,809,520 genotypes on 35,549 individuals together with their milk, fat and protein yields, and fat and protein percentage traits. Results The prediction accuracies of the Jersey individuals improved by 1.5% when using across-breed GBLUP compared to within-breed predictions. Using WGS instead of 600 k SNP-chip data yielded on average a 3% accuracy improvement for Australian Red cows. QTL were fine-mapped by locating the SNP with the highest posterior probability of being included in the model. Various QTL known from the literature were rediscovered, and a new SNP affecting milk production was discovered on chromosome 20 at 34.501126 Mb. Due to the high mapping precision, it was clear that many of the discovered QTL were the same across the five dairy traits. Conclusions Across-breed Bayes GC genomic prediction improved prediction accuracies compared to GBLUP. The combination of across-breed WGS data and Bayesian genomic prediction proved remarkably effective for the fine-mapping of QTL.
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Affiliation(s)
- Theo Meuwissen
- Norwegian University of Life Sciences, Box 5003, 1432, Ås, Norway.
| | | | - Mike Goddard
- Agriculture Victoria, Bundoora, Australia.,Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
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Todhunter RJ, Garrison SJ, Jordan J, Hunter L, Castelhano MG, Ash K, Meyers-Wallen V, Krotscheck U, Hayward JJ, Grenier J. Gene expression in hip soft tissues in incipient canine hip dysplasia and osteoarthritis. J Orthop Res 2019; 37:313-324. [PMID: 30450639 DOI: 10.1002/jor.24178] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/30/2018] [Indexed: 02/04/2023]
Abstract
Canine hip dysplasia and developmental dysplasia of the human hip share demographic, phenotypic, and clinical features including the predisposition to develop osteoarthritis in affected joints. To support the results of genetic mapping studies for CHD and its concomitant osteoarthritis with functional information, we performed RNA-seq on hip capsule and teres ligament of affected and unaffected dogs. RNA seq showed that expressed genes segregated according age, capsule or ligament, and hip phenotype. Expression of HHIP, DACT2, and WIF1 was significantly higher in capsule from control hips than dysplastic hips indicating a disruption of the hedgehog signaling pathway. Expression of SPON 1, a key component of the WNT pathway, was increased significantly in both dysplastic capsule and ligament while FBN2 and EMILIN3 were significantly increased in dysplastic capsule. Of genes associated with human hip osteoarthritis, expression of ACAN, IGF1, CILP2, COL11A1, COL8A1, and HAPLN was increased significantly in dysplastic capsule. The significant increase in expression of PLA2F, TNFRSF, TMEM, and IGFBP in dysplastic capsule indicated an injury response. Gene set enrichment analysis revealed that genes involved in extracellular matrix structure, epithelial to mesenchymal transition, myogenesis, growth factor signaling, cancer and immune pathways were enriched in dysplastic capsule. For teres ligament from dysplastic joints, genes in retinoic signaling pathways and those encoding extracellular matrix molecules, but not proteoglycans, were enriched. Hip tissues respond to abnormal mechanics early in dysplastic hip development and these pathways present targets for intervention in the early synovitis and capsulitis secondary to canine and human hip dysplasia. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:313-324, 2019.
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Affiliation(s)
- Rory J Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853.,Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Susan J Garrison
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853.,Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Julie Jordan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853.,Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Linda Hunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Marta G Castelhano
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853.,Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Kristian Ash
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Vicki Meyers-Wallen
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Ursula Krotscheck
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Jessica J Hayward
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853.,Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Jennifer Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
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Bartolomé N, Segarra S, Artieda M, Francino O, Sánchez E, Szczypiorska M, Casellas J, Tejedor D, Cerdeira J, Martínez A, Velasco A, Sánchez A. A genetic predictive model for canine hip dysplasia: integration of Genome Wide Association Study (GWAS) and candidate gene approaches. PLoS One 2015; 10:e0122558. [PMID: 25874693 PMCID: PMC4395148 DOI: 10.1371/journal.pone.0122558] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/22/2015] [Indexed: 01/18/2023] Open
Abstract
Canine hip dysplasia is one of the most prevalent developmental orthopedic diseases in dogs worldwide. Unfortunately, the success of eradication programs against this disease based on radiographic diagnosis is low. Adding the use of diagnostic genetic tools to the current phenotype-based approach might be beneficial. The aim of this study was to develop a genetic prognostic test for early diagnosis of hip dysplasia in Labrador Retrievers. To develop our DNA test, 775 Labrador Retrievers were recruited. For each dog, a blood sample and a ventrodorsal hip radiograph were taken. Dogs were divided into two groups according to their FCI hip score: control (A/B) and case (D/E). C dogs were not included in the sample. Genetic characterization combining a GWAS and a candidate gene strategy using SNPs allowed a case-control population association study. A mathematical model which included 7 SNPs was developed using logistic regression. The model showed a good accuracy (Area under the ROC curve = 0.85) and was validated in an independent population of 114 dogs. This prognostic genetic test represents a useful tool for choosing the most appropriate therapeutic approach once genetic predisposition to hip dysplasia is known. Therefore, it allows a more individualized management of the disease. It is also applicable during genetic selection processes, since breeders can benefit from the information given by this test as soon as a blood sample can be collected, and act accordingly. In the authors' opinion, a shift towards genomic screening might importantly contribute to reducing canine hip dysplasia in the future. In conclusion, based on genetic and radiographic information from Labrador Retrievers with hip dysplasia, we developed an accurate predictive genetic test for early diagnosis of hip dysplasia in Labrador Retrievers. However, further research is warranted in order to evaluate the validity of this genetic test in other dog breeds.
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Affiliation(s)
- Nerea Bartolomé
- Progenika Biopharma SA, a Grifols Company, Derio, Bizkaia, Spain
- * E-mail:
| | | | - Marta Artieda
- Progenika Biopharma SA, a Grifols Company, Derio, Bizkaia, Spain
| | - Olga Francino
- Servei Veterinari de Genètica Molecular, Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisenda Sánchez
- Servei Veterinari de Genètica Molecular, Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Joaquim Casellas
- Servei Veterinari de Genètica Molecular, Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Diego Tejedor
- Progenika Biopharma SA, a Grifols Company, Derio, Bizkaia, Spain
| | | | - Antonio Martínez
- Progenika Biopharma SA, a Grifols Company, Derio, Bizkaia, Spain
| | | | - Armand Sánchez
- Servei Veterinari de Genètica Molecular, Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
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Soo M, Worth AJ. Canine hip dysplasia: phenotypic scoring and the role of estimated breeding value analysis. N Z Vet J 2014; 63:69-78. [DOI: 10.1080/00480169.2014.949893] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Sánchez-Molano E, Woolliams JA, Pong-Wong R, Clements DN, Blott SC, Wiener P. Quantitative trait loci mapping for canine hip dysplasia and its related traits in UK Labrador Retrievers. BMC Genomics 2014; 15:833. [PMID: 25270232 PMCID: PMC4190382 DOI: 10.1186/1471-2164-15-833] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/23/2014] [Indexed: 01/03/2023] Open
Abstract
Background Canine hip dysplasia (CHD) is characterised by a malformation of the hip joint, leading to osteoarthritis and lameness. Current breeding schemes against CHD have resulted in measurable but moderate responses. The application of marker-assisted selection, incorporating specific markers associated with the disease, or genomic selection, incorporating genome-wide markers, has the potential to dramatically improve results of breeding schemes. Our aims were to identify regions associated with hip dysplasia or its related traits using genome and chromosome-wide analysis, study the linkage disequilibrium (LD) in these regions and provide plausible gene candidates. This study is focused on the UK Labrador Retriever population, which has a high prevalence of the disease and participates in a recording program led by the British Veterinary Association (BVA) and The Kennel Club (KC). Results Two genome-wide and several chromosome-wide QTLs affecting CHD and its related traits were identified, indicating regions related to hip dysplasia. Conclusion Consistent with previous studies, the genetic architecture of CHD appears to be based on many genes with small or moderate effect, suggesting that genomic selection rather than marker-assisted selection may be an appropriate strategy for reducing this disease. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-833) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK.
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Lavrijsen ICM, Leegwater PAJ, Martin AJ, Harris SJ, Tryfonidou MA, Heuven HCM, Hazewinkel HAW. Genome wide analysis indicates genes for basement membrane and cartilage matrix proteins as candidates for hip dysplasia in Labrador Retrievers. PLoS One 2014; 9:e87735. [PMID: 24498183 PMCID: PMC3907504 DOI: 10.1371/journal.pone.0087735] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/29/2013] [Indexed: 12/22/2022] Open
Abstract
Hip dysplasia, an abnormal laxity of the hip joint, is seen in humans as well as dogs and is one of the most common skeletal disorders in dogs. Canine hip dysplasia is considered multifactorial and polygenic, and a variety of chromosomal regions have been associated with the disorder. We performed a genome-wide association study in Dutch Labrador Retrievers, comparing data of nearly 18,000 single nucleotide polymorphisms (SNPs) in 48 cases and 30 controls using two different statistical methods. An individual SNP analysis based on comparison of allele frequencies with a χ(2) statistic was used, as well as a simultaneous SNP analysis based on Bayesian variable selection. Significant association with canine hip dysplasia was observed on chromosome 8, as well as suggestive association on chromosomes 1, 5, 15, 20, 25 and 32. Next-generation DNA sequencing of the exons of genes of seven regions identified multiple associated alleles on chromosome 1, 5, 8, 20, 25 and 32 (p<0.001). Candidate genes located in the associated regions on chromosomes 1, 8 and 25 included LAMA2, LRR1 and COL6A3, respectively. The associated region on CFA20 contained candidate genes GDF15, COMP and CILP2. In conclusion, our study identified candidate genes that might affect susceptibility to canine hip dysplasia. These genes are involved in hypertrophic differentiation of chondrocytes and extracellular matrix integrity of basement membrane and cartilage. The functions of the genes are in agreement with the notion that disruptions in endochondral bone formation in combination with soft tissue defects are involved in the etiology of hip dysplasia.
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Affiliation(s)
- Ineke C. M. Lavrijsen
- Department of Clinical Sciences of Companion Animal, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter A. J. Leegwater
- Department of Clinical Sciences of Companion Animal, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Alan J. Martin
- Waltham Centre for Pet Nutrition, Leicestershire, United Kingdom
| | | | - Marianna A. Tryfonidou
- Department of Clinical Sciences of Companion Animal, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Henri C. M. Heuven
- Department of Clinical Sciences of Companion Animal, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Herman A. W. Hazewinkel
- Department of Clinical Sciences of Companion Animal, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Wilson BJ, Nicholas FW, James JW, Wade CM, Raadsma HW, Thomson PC. Genetic correlations among canine hip dysplasia radiographic traits in a cohort of Australian German Shepherd Dogs, and implications for the design of a more effective genetic control program. PLoS One 2013; 8:e78929. [PMID: 24244386 PMCID: PMC3820674 DOI: 10.1371/journal.pone.0078929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/17/2013] [Indexed: 12/19/2022] Open
Abstract
Canine hip dysplasia (CHD) is a common musculoskeletal disease in pedigree dog populations. It can cause severe pain and dysfunction which may require extensive medication and/or surgical treatment and often ultimately requires humane euthanasia. CHD has been found to be moderately heritable and, given its impact on welfare, should be considered an imperative breeding priority. The British Veterinary Association/Kennel Club scoring method is one of several measures used to assess the genetic propensity of potential breeding stock for dysplastic changes to the hips based on radiographic examination. It is a complex measure composed of nine ordinal traits, intended to evaluate both early and late dysplastic changes. It would be highly desirable if estimated breeding values (EBVs) for these nine traits were consolidated into a simpler, EBV-based, selection index more easily usable by breeders. A multivariate analysis on the phenotype scores from an Australian cohort of 13,124 German Shepherd Dogs (GSDs) returned genetic correlations between 0.48–0.97 for the nine traits which fell into two trait groups, Group 1 reflecting early changes (“laxity”) and Group 2 reflecting late changes (“osteoarthritis”). Principal components analysis of the ordinal EBVs suggested the same pattern, with strong differentiation between “laxity” and “osteoarthritis” traits in the second component. Taking account of all results, we recommend interim use of two selection indexes: the first being the average of ordinal EBVs for “laxity” traits and the second being the average of ordinal EBVs for “osteoarthritis” traits. The correlation between these two selection indexes (0.771–0.774) is sufficiently less than unity enabling the selection of dogs with different genetic propensity for laxity and for osteoarthritic CHD changes in GSDs; this may also be applicable in other breeds. Dogs with low propensity for severe osteoarthritic change in the presence of laxity may be of interest both in molecular research and breeding programs.
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Affiliation(s)
- Bethany J. Wilson
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
| | - Frank W. Nicholas
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - John W. James
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Claire M. Wade
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Herman W. Raadsma
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter C. Thomson
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
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Duan F, Ogden D, Xu L, Liu K, Lust G, Sandler J, Dykes NL, Zhu L, Harris S, Jones P, Todhunter RJ, Zhang Z. Principal component analysis of canine hip dysplasia phenotypes and their statistical power for genome-wide association mapping. J Appl Stat 2013. [DOI: 10.1080/02664763.2012.740617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Pfahler S, Distl O. Identification of quantitative trait loci (QTL) for canine hip dysplasia and canine elbow dysplasia in Bernese mountain dogs. PLoS One 2012. [PMID: 23189162 PMCID: PMC3506637 DOI: 10.1371/journal.pone.0049782] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A genome-wide association study for canine hip dysplasia (CHD) and canine elbow dysplasia (CED) using the Illumina canine high density bead chip had been performed for 174 Bernese mountain dogs. General and mixed linear model analysis identified two different regions with single nucleotide polymorphisms (SNPs) on dog chromosome (CFA) 14 significantly associated with CHD and a further significantly CHD-associated region on CFA37. For CED, four SNPs on CFA11 and 27 were significantly associated. The identified SNPs of four associated regions included nearby candidate genes. These possible positional candidates were the genes PON2 on CFA14 and FN1 on CFA37 for CHD and the genes LMNB1 on CFA11 and WNT10B on CFA27 for CED.
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Affiliation(s)
- Sophia Pfahler
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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Zhu L, Chen S, Jiang Z, Zhang Z, Ku HC, Li X, McCann M, Harris S, Lust G, Jones P, Todhunter R. Identification of quantitative trait loci for canine hip dysplasia by two sequential multipoint linkage analyses. J Appl Stat 2012. [DOI: 10.1080/02664763.2012.673121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Abstract
Canine hip dysplasia (CHD) is a multifactorial skeletal disorder which is very common in pedigree dogs and represents a huge concern for canine welfare. Control schemes based on selective breeding have been in operation for decades. The aim of these schemes is to reduce the impact of CHD on canine welfare by selecting for reduced radiographic evidence of CHD pathology as assessed by a variety of phenotypes. There is less information regarding the genotypic correlation between these phenotypes and the impact of CHD on canine welfare. Although the phenotypes chosen as the basis for these control schemes have displayed heritable phenotypic variation in many studies, success in achieving improvement in the phenotypes has been mixed. There is significant room for improvement in the current schemes through the use of estimated breeding values (EBVs), which can combine a dog's CHD phenotype with CHD phenotypes of relatives, other phenotypes as they are proven to be genetically correlated with CHD (especially elbow dysplasia phenotypes), and information from genetic tests for population-relevant DNA markers, as such tests become available. Additionally, breed clubs should be encouraged and assisted to formulate rational, evidenced-based breeding recommendations for CHD which suit their individual circumstances and dynamically to adjust the breeding recommendations based on continuous tracking of CHD genetic trends. These improvements can assist in safely and effectively reducing the impact of CHD on pedigree dog welfare.
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Affiliation(s)
- Bethany Wilson
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia.
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Friedenberg SG, Zhu L, Zhang Z, Foels WVDB, Schweitzer PA, Wang W, Fisher PJ, Dykes NL, Corey E, Vernier-Singer M, Jung SW, Sheng X, Hunter LS, McDonough SP, Lust G, Bliss SP, Krotscheck U, Gunn TM, Todhunter RJ. Evaluation of a fibrillin 2 gene haplotype associated with hip dysplasia and incipient osteoarthritis in dogs. Am J Vet Res 2011; 72:530-40. [PMID: 21453155 DOI: 10.2460/ajvr.72.4.530] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether a mutation in the fibrillin 2 gene (FBN2) is associated with canine hip dysplasia (CHD) and osteoarthritis in dogs. ANIMALS 1,551 dogs. Procedures-Hip conformation was measured radiographically. The FBN2 was sequenced from genomic DNA of 21 Labrador Retrievers and 2 Greyhounds, and a haplotype in intron 30 of FBN2 was sequenced in 90 additional Labrador Retrievers and 143 dogs of 6 other breeds. Steady-state values of FBN2 mRNA and control genes were measured in hip joint tissues of fourteen 8-month-old Labrador Retriever-Greyhound crossbreeds. RESULTS The Labrador Retrievers homozygous for a 10-bp deletion haplotype in intron 30 of FBN2 had significantly worse CHD as measured via higher distraction index and extended-hip joint radiograph score and a lower Norberg angle and dorsolateral subluxation score. Among 143 dogs of 6 other breeds, those homozygous for the same deletion haplotype also had significantly worse radiographic CHD. Among the 14 crossbred dogs, as the dorsolateral subluxation score decreased, the capsular FBN2 mRNA increased significantly. Those dogs with incipient hip joint osteoarthritis had significantly increased capsular FBN2 mRNA, compared with those dogs without osteoarthritis. Dogs homozygous for the FBN2 deletion haplotype had significantly less FBN2 mRNA in their femoral head articular cartilage. CONCLUSIONS AND CLINICAL RELEVANCE The FBN2 deletion haplotype was associated with CHD. Capsular gene expression of FBN2 was confounded by incipient secondary osteoarthritis in dysplastic hip joints. Genes influencing complex traits in dogs can be identified by genome-wide screening, fine mapping, and candidate gene screening.
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Affiliation(s)
- Steven G Friedenberg
- Department of Clinical Sciences, College of Arts and Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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14
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Zhou Z, Sheng X, Zhang Z, Zhao K, Zhu L, Guo G, Friedenberg SG, Hunter LS, Vandenberg-Foels WS, Hornbuckle WE, Krotscheck U, Corey E, Moise NS, Dykes NL, Li J, Xu S, Du L, Wang Y, Sandler J, Acland GM, Lust G, Todhunter RJ. Differential genetic regulation of canine hip dysplasia and osteoarthritis. PLoS One 2010; 5:e13219. [PMID: 20949002 PMCID: PMC2952589 DOI: 10.1371/journal.pone.0013219] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/12/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Canine hip dysplasia (HD) is a common polygenic trait characterized by hip malformation that results in osteoarthritis (OA). The condition in dogs is very similar to developmental dysplasia of the human hip which also leads to OA. METHODOLOGY/PRINCIPAL FINDINGS A total of 721 dogs, including both an association and linkage population, were genotyped. The association population included 8 pure breeds (Labrador retriever, Greyhounds, German Shepherd, Newfoundland, Golden retriever, Rottweiler, Border Collie and Bernese Mountain Dog). The linkage population included Labrador retrievers, Greyhounds, and their crosses. Of these, 366 dogs were genotyped at ∼22,000 single nucleotide polymorphism (SNP) loci and a targeted screen across 8 chromosomes with ∼3,300 SNPs was performed on 551 dogs (196 dogs were common to both sets). A mixed linear model approach was used to perform an association study on this combined association and linkage population. The study identified 4 susceptibility SNPs associated with HD and 2 SNPs associated with hip OA. CONCLUSION/SIGNIFICANCE The identified SNPs included those near known genes (PTPRD, PARD3B, and COL15A1) reported to be associated with, or expressed in, OA in humans. This suggested that the canine model could provide a unique opportunity to identify genes underlying natural HD and hip OA, which are common and debilitating conditions in both dogs and humans.
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Affiliation(s)
- Zhengkui Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Xihui Sheng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- Department of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Keyan Zhao
- Department of Computational Biology and Statistics, Cornell University, Ithaca, New York, United States of America
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Gang Guo
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Steve G. Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Linda S. Hunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Wendy S. Vandenberg-Foels
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - William E. Hornbuckle
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ursula Krotscheck
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Elizabeth Corey
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Nancy S. Moise
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Nathan L. Dykes
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shangzhong Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixin Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yachun Wang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Jody Sandler
- Guiding Eyes for the Blind, Yorktown Heights, New York, United States of America
| | - Gregory M. Acland
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - George Lust
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - Rory J. Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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15
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Phavaphutanon J, Mateescu RG, Tsai KL, Schweitzer PA, Corey EE, Vernier-Singer MA, Williams AJ, Dykes NL, Murphy KE, Lust G, Todhunter RJ. Evaluation of quantitative trait loci for hip dysplasia in Labrador Retrievers. Am J Vet Res 2009; 70:1094-101. [DOI: 10.2460/ajvr.70.9.1094] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Zhu L, Zhang Z, Friedenberg S, Jung SW, Phavaphutanon J, Vernier-Singer M, Corey E, Mateescu R, Dykes N, Sandler J, Acland G, Lust G, Todhunter R. The long (and winding) road to gene discovery for canine hip dysplasia. Vet J 2009; 181:97-110. [PMID: 19297220 PMCID: PMC2679856 DOI: 10.1016/j.tvjl.2009.02.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 11/21/2008] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
Hip dysplasia is a common inherited trait of dogs that results in secondary osteoarthritis. In this article the methods used to uncover the mutations contributing to this condition are reviewed, beginning with hip phenotyping. Coarse, genome-wide, microsatellite-based screens of pedigrees of greyhounds and dysplastic Labrador retrievers were used to identify linked quantitative trait loci (QTL). Fine-mapping across two chromosomes (CFA11 and 29) was employed using single nucleotide polymorphism (SNP) genotyping. Power analyses and preferential selection of dogs for ongoing SNP-based genotyping is described with the aim of refining the QTL intervals to 1-2 megabases on these and several additional chromosomes prior to candidate gene screening. The review considers how a mutation or a genetic marker such as a SNP or haplotype of SNPs might be combined with pedigree and phenotype information to create a 'breeding value' that could improve the accuracy of predicting a dog's hip conformation.
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Affiliation(s)
- Lan Zhu
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Zhiwu Zhang
- Institute for Genomic Diversity, 175 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Steven Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Seung-Woo Jung
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Janjira Phavaphutanon
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Margaret Vernier-Singer
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth Corey
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Raluca Mateescu
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Nathan Dykes
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jody Sandler
- Guiding Eyes for the Blind, Yorktown Heights, NY 10598, USA
| | - Gregory Acland
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - George Lust
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rory Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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17
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Zhang Z, Zhu L, Sandler J, Friedenberg SS, Egelhoff J, Williams AJ, Dykes NL, Hornbuckle W, Krotscheck U, Moise NS, Lust G, Todhunter RJ. Estimation of heritabilities, genetic correlations, and breeding values of four traits that collectively define hip dysplasia in dogs. Am J Vet Res 2009; 70:483-92. [DOI: 10.2460/ajvr.70.4.483] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Castelhano MGP, Acland GM, Ciccone PA, Corey EE, Mezey JG, Schimenti JC, Todhunter RJ. Development and use of DNA archives at veterinary teaching hospitals to investigate the genetic basis of disease in dogs. J Am Vet Med Assoc 2009; 234:75-80. [PMID: 19119968 DOI: 10.2460/javma.234.1.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The DNA archives developed at veterinary medical teaching hospitals will be important resources for mapping disease loci and identifying underlying genes. The most important feature of a DNA archive is accurate identification or exclusion of diseases in each animal. Such archives will be complimentary resources to tissue banks that are currently available.
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Affiliation(s)
- Marta G P Castelhano
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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