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Sánchez-Molano E, Kapsona VV, Oikonomou S, McLaren A, Lambe N, Conington J, Banos G. Breeding strategies for animal resilience to weather variation in meat sheep. BMC Genet 2020; 21:116. [PMID: 33028212 PMCID: PMC7542729 DOI: 10.1186/s12863-020-00924-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The alteration in weather patterns expected due to climate change will affect farm animal performance, probably resulting in lower quantity and quality of available products. A potential mitigation strategy would be to breed selected animals for enhanced resilience to climate change. In this context, resilience would reflect stable animal performance in spite of weather variation. The objectives of this study were to (i) derive and characterise novel animal resilience phenotypes, (ii) investigate their genetic profiles and (iii) assess the impact of integrating them in breeding strategies for genetic improvement in meat sheep. RESULTS Random regression models were used to jointly analyse live body weight measured in different time points throughout the growth phases of 4469 Scottish Blackface sheep and weather variables during the same period to derive novel resilience phenotypes. The genetic analysis of these phenotypes revealed significant genetic variance and heritability, and an antagonistic genetic correlation with some animal performance traits. Simulated breeding strategies demonstrated that a relative emphasis of 10% on resilience compared to other traits would enhance performance stability against weather volatility without compromising animal growth. CONCLUSIONS Novel resilience traits exhibited sufficient genetic variation to be amenable to genetic improvement with selective breeding and are recommended to be included in future breeding goals.
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Affiliation(s)
- Enrique Sánchez-Molano
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Vanessa V Kapsona
- Scotland's Rural College, The Roslin Institute Building, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Stavroula Oikonomou
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloniki, Greece
| | - Ann McLaren
- Scotland's Rural College, The Roslin Institute Building, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Nicola Lambe
- Scotland's Rural College, The Roslin Institute Building, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Joanne Conington
- Scotland's Rural College, The Roslin Institute Building, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Georgios Banos
- Scotland's Rural College, The Roslin Institute Building, Easter Bush, Edinburgh, EH25 9RG, UK.
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2
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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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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: 12] [Impact Index Per Article: 2.4] [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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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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Ilska JJ, Meuwissen THE, Kranis A, Woolliams JA. Use and optimization of different sources of information for genomic prediction. Genet Sel Evol 2017; 49:90. [PMID: 29228899 PMCID: PMC5725675 DOI: 10.1186/s12711-017-0365-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 11/30/2017] [Indexed: 11/26/2022] Open
Abstract
Background Molecular data is now commonly used to predict breeding values (BV). Various methods to calculate genomic relationship matrices (GRM) have been developed, with some studies proposing regression of coefficients back to the reference matrix of pedigree-based relationship coefficients (A). The objective was to compare the utility of two GRM: a matrix based on linkage analysis (LA) and anchored to the pedigree, i.e. \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}} ,$$\end{document}GLA, and a matrix based on linkage disequilibrium (LD), i.e. \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LD}}}}$$\end{document}GLD, using genomic and phenotypic data collected on 5416 broiler chickens. Furthermore, the effects of regressing the coefficients of \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LD}}}}$$\end{document}GLD back to A (LDA) and to \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}}$$\end{document}GLA (LDLA) were evaluated, using a range of weighting factors. The performance of the matrices and their composite products was assessed by the fit of the models to the data, and the empirical accuracy and bias of the BV that they predicted. The sensitivity to marker choice was examined by using two chips of equal density but including different single nucleotide polymorphisms (SNPs). Results The likelihood of models using GRM and composite matrices exceeded the likelihood of models based on pedigree alone and was highest with intermediate weighting factors for both the LDA and LDLA approaches. For these data, empirical accuracies were not strongly affected by the weighting factors, although they were highest when different sources of information were combined. The optimum weighting factors depended on the type of matrices used, as well as on the choice of SNPs from which the GRM were constructed. Prediction bias was strongly affected by the chip used and less by the form of the GRM. Conclusions Our findings provide an empirical comparison of the efficacy of pedigree and genomic predictions in broiler chickens and examine the effects of fitting GRM with coefficients regressed back to a reference anchored to the pedigree, either A or \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}}$$\end{document}GLA. For the analysed dataset, the best results were obtained when \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LD}}}}$$\end{document}GLD was combined with relationships in A or \documentclass[12pt]{minimal}
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\begin{document}$${\mathbf{G}}_{{{\mathbf{LA}}}}$$\end{document}GLA, with optimum weighting factors that depended on the choice of SNPs used. The optimum weighting factor for broiler body weight differed from weighting factors that were based on the density of SNPs and theoretically derived using generalised assumptions.
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Affiliation(s)
- Joanna J Ilska
- Roslin Institute (Edinburgh), Easter Bush, Midlothian, EH25 9RG, UK.
| | - Theo H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Andreas Kranis
- Roslin Institute (Edinburgh), Easter Bush, Midlothian, EH25 9RG, UK.,Aviagen Ltd., 11 Lochend Road Newbridge, Edinburgh, UK
| | - John A Woolliams
- Roslin Institute (Edinburgh), Easter Bush, Midlothian, EH25 9RG, UK
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6
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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: 27] [Impact Index Per Article: 3.9] [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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7
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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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8
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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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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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10
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Farrell LL, Schoenebeck JJ, Wiener P, Clements DN, Summers KM. The challenges of pedigree dog health: approaches to combating inherited disease. Canine Genet Epidemiol 2015; 2:3. [PMID: 26401331 PMCID: PMC4579364 DOI: 10.1186/s40575-015-0014-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/13/2015] [Indexed: 01/29/2023] Open
Abstract
The issue of inherited disorders and poor health in pedigree dogs has been widely discussed in recent years. With the advent of genome-wide sequencing technologies and the increasing development of new diagnostic DNA disease tests, the full extent and prevalence of inherited disorders in pedigree dogs is now being realized. In this review we discuss the challenges facing pedigree dog breeds: the common pitfalls and problems associated with combating single gene mediated disorders, phenotypic selection on complex disorders, and ways of managing genetic diversity. Breeding strategies incorporating screening schemes have been shown to be successful in significantly reducing the prevalence of an inherited disorder and improving the overall health in certain breeds. However, with 215 breeds officially recognized by the Kennel Club in the United Kingdom and 396 inherited disorders currently identified, many breeds have reached the point at which successfully breeding away from susceptible individuals at a population-wide scale will require new genomic selection strategies in combination with currently available breeding schemes. Whilst DNA-based tests identifying disease causing mutation(s) remain the most informative and effective approach for single gene disorder disease management, they must be used along with current screening schemes, genomic selection, and pedigree information in breeding programs in the effort to maintain genetic diversity while also significantly reducing the number of inherited disorders in pedigree dogs.
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Affiliation(s)
- Lindsay L Farrell
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Jeffrey J Schoenebeck
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Pamela Wiener
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Dylan N Clements
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Kim M Summers
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
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Soo M, Sneddon NW, Lopez-Villalobos N, Worth AJ. Genetic evaluation of the total hip score of four populous breeds of dog, as recorded by the New Zealand Veterinary Association Hip Dysplasia Scheme (1991–2011). N Z Vet J 2015; 63:79-85. [DOI: 10.1080/00480169.2014.961581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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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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13
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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: 31] [Impact Index Per Article: 3.1] [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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