BMC Genomics | |
Quantitative trait loci mapping for canine hip dysplasia and its related traits in UK Labrador Retrievers | |
Pamela Wiener2  Sarah C Blott1  Dylan N Clements3  Ricardo Pong-Wong2  John A Woolliams2  Enrique Sánchez-Molano2  | |
[1] School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK;The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK;Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG Scotland, UK | |
关键词: Genomic selection; GWAS; QTL; Norberg Angle; Labrador Retriever; Canine hip dysplasia; | |
Others : 1139350 DOI : 10.1186/1471-2164-15-833 |
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received in 2014-04-10, accepted in 2014-09-23, 发布年份 2014 | |
【 摘 要 】
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.
【 授权许可】
2014 Sánchez-Molano et al.; licensee BioMed Central Ltd.
【 预 览 】
Files | Size | Format | View |
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20150321095424613.pdf | 880KB | download | |
Figure 3. | 50KB | Image | download |
Figure 2. | 51KB | Image | download |
Figure 1. | 84KB | Image | download |
【 图 表 】
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【 参考文献 】
- [1]Coopman F, Verhoeven G, Saunders J, Duchateau L, van Bree H: Prevalence of hip dysplasia, elbow dysplasia and humeral head osteochondrosis in dog breeds in Belgium. Vet Rec 2008, 163(22):654-658.
- [2]Hip Dysplasia [http://www.akcchf.org/canine-health/your-dogs-health/disease-information/hip-dysplasia.html webcite]
- [3]Fries CL, Remedios AM: The pathogenesis and diagnosis of canine hip dysplasia: A review. Can Vet J 1995, 36:494-502.
- [4]Lewis TW, Blott SC, Woolliams JA: Genetic evaluation of Hip Score in UK Labrador Retrievers. PLoS One 2010, 5(10):e12797.
- [5]Willis MB: A review of the progress in canine hip-dysplasia control in Britain. J Am Vet Med Assoc 1997, 210:1480-1482.
- [6]Lewis TW, Woolliams JA, Blott SC: Genetic Evaluation of the Nine Component Features of Hip Score in UK Labrador Retrievers. PLoS One 2010, 5(10):e13610.
- [7]Malm S, Fikse WF, Danell B, Strandberg E: Genetic variation and genetic trends in hip and elbow dysplasia in Swedish Rottweiler and Bernese mountain dog. J Anim Breed Genet 2008, 125:403-412.
- [8]Leppanen M, Saloniemi H: Controlling canine hip dysplasia in Finland. Prev Vet Med 1999, 42:121-131.
- [9]Hou Y, Wang Y, Xuemei Lu X, Zhang X, Zhao Q, Todhunter RJ, Zhang Z: Monitoring Hip and Elbow Dysplasia Achieved Modest Genetic Improvement of 74 Dog Breeds over 40 Years in USA. PLoS One 2013, 8(10):e76390.
- [10]Wilson BJ, Nicholas FW, James JW, Wade CM, Thomson PC: Estimated Breeding Values for Canine Hip Dysplasia Radiographic Traits in a Cohort of Australian German Shepherd Dogs. Plos One 2013, 8(10):e77470.
- [11]Lewis TW, Blott SC, Woolliams JA: Comparative analyses of genetic trends and prospects for selection against hip and elbow dysplasia in 15 UK dog breeds. BMC Genet 2013, 14:16.
- [12]Lande R, Thompson R: Efficiency of Marker-Assisted Selection in the improvement of quantitative traits. Genetics 1990, 124:743-756.
- [13]Meuwissen THE, Hayes BJ, Goddard ME: Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. Genetics 2001, 157:1819-1829.
- [14]Chase K, Lawler DF, Adler FR, Ostrander EA, Lark KG: Bilaterally asymmetric effects of quantitative trait loci (QTLs): QTLs that affect laxity in the right versus left coxofemoral (hip) joints of the dog (Canis familiaris). Am J Med Genet A 2004, 124:239-247.
- [15]Todhunter RJ, Mateescu R, Lust G, Burton-Wurster NI, Dykes NL, Bliss SP, Williams AJ, Vernier-Singer M, Corey E, Harjes C, Quaas RL, Zhang Z, Gilbert RO, Volkman D, Casella G, Wu R, Acland GM: Quantitative trait loci for hip dysplasia in a crossbreed canine pedigree. Mamm Genome 2005, 16:720-730.
- [16]Marschall Y, Distl O: Mapping quantitative trait loci for canine hip dysplasia in German Shepherd dogs. Mamm Genome 2007, 18:861-870.
- [17]Zhu L, Chen S, Jiang Z, Zhang Z, Ku H, 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 analysis. J Appl Stat 2012, 39:1719-1731.
- [18]Zhu L, Zhang Z, Feng F, Schweitzer P, Phavaphutanon J, Vernier-Singer M, Corey E, Friedenberg S, Mateescu R, Williams A, Lust G, Acland G, Todhunter R: Single nucleotide polymorphisms refine QTL intervals for hip joint laxity in dogs. Anim Genet 2008, 39:141-146.
- [19]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, 7(11):e49782.
- [20]Friedenberg SG, Zhu L, Zhang Z, Foels W, 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(4):530-540.
- [21]Qiagen: QIAamp DNA Blood Midi/Maxi Handbook. 2012.
- [22]Illumina I: Canine HD BeadChip. Data Sheet: DNA Genotyping 2010.
- [23]Turner S, Armstrong LL, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes G, Jarvik G, Jiang L, Kullo IJ, Li R, Ling H, Manolio T, Matsumoto M, McCarty CA, McDavid AN, Mirel DB, Paschall JE, Pugh EW, Rasmussen LV, Wilke RA, Zuvich RL, Ritchie MD: Quality Control Procedures for Genome Wide Association Studies. Curr Protoc Hum Genet 2011, 68:1.19.
- [24]Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC: PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 2007, 81:559-575.
- [25]Zhou X, Stephens M: Genome-wide Efficient Mixed Model Analysis for Association Studies. Nat Genet 2012, 44:821-824.
- [26]Seren U, Vilhjalmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M: GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis. Plant Cell 2012, 24:4793-4805.
- [27]Amin N, van Duijn CM, Aulchenko YS: A Genomic Background Based Method for Association Analysis in Related Individuals. PLoS One 2007, 2(12):e1274.
- [28]Nagamine Y, Pong-Wong R, Navarro P, Vitart V, Hayward C, Rudan I, Campbell H, Wilson J, Wild S, Hicks A, Pramstaller PP, Hastie N, Wright AF, Haley CS: Localising Loci underlying Complex Trait Variation Using Regional Genomic Relationship Mapping. PLoS One 2012, 7(10):e46501.
- [29]Gray A, Stewart I, Tenesa A: Advanced Complex Trait Analysis. Bioinformatics 2012, 28:3134-3136.
- [30]Cebamanos L, Gray A, Stewart I, Tenesa A: Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures. Bioinformatics 2014. doi:10.1093/bioinformatics/btt754
- [31]Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21:263-265.
- [32]Xu S: Theoretical Basis of the Beavis Effect. Genetics 2003, 165:2259-2268.
- [33]Uemoto Y, Pong-Wong R, Navarro P, Vitart V, Hayward C, Wilson JF, Rudan I, Campbell H, Hastie ND, Wright AF, Haley CS: The power of regional heritability analysis for rare and common variant detection: simulations and application to eye biometrical traits. Front Genet 2013, 4:232.
- [34]Falconer DS, Mackay TFC: Introduction to Quantitative Genetics. Addison Wesley Longman: Harlow; 1996.
- [35]Riser WH, Rhodes WH, Newton CD: Hip Dysplasia. In Texbook of Small Animal Orthopaedics. Edited by Newton CD, Nunamaker DM. Philadelphia (U.S.A): J. B. Lippincott Company; 1985.
- [36]Todhunter RJ, Zachos TA, Gilbert RO, Erb HN, Williams AJ, Burton-Wurster NI, Lust G: Onset of epiphyseal mineralization and growth plate closure in radiographically normal and dysplastic Labrador retrievers. J Am Vet Med Assoc 1997, 210:1458-1462.
- [37]Wilson BJ, Nicholas FW, James JW, Wade CM, Tammen I, Raadsma HW, Castle K, Thomson PC: Symmetry of hip dysplasia traits in the German Sheperd Dog in Australia. J Anim Breed Genet 2011, 128:230-243.
- [38]Colborne GR, Good L, Cozens LE, Kirk LS: Symmetry of limb mechanics in orthopedically normal trotting Labrador Retrievers. Am J Vet Res 2011, 72(3):336-344.
- [39]Hayes BJ, Pryce J, Chamberlain AJ, Bowman PJ, Goddard ME: Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits. PLoS Genet 2010, 6:e1001139.
- [40]Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA: The Impact of Genetic Architecture on Genome-Wide Evaluation Methods. Genetics 2010, 185(3):1021-1031.
- [41]Lavrijsen IC, Leegwater PA, Martin AJ, Harris SJ, Tryfonidou MA, Heuven HC, Hazewinkel HA: 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. doi:87710.81371/journal.pone.0087735
- [42]Sutter NB, Eberle MA, Parker HG, Pullar BJ, Kirkness EF, Kruglyak L, Ostrander EA: Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res 2004, 14:2388-2396.
- [43]McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Neto ED, Gill CA, Gao C, Mannen H, Stothard P, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS: Whole genome linkage disequilibrium maps in cattle. BMC Genet 2007, 8:74-85.
- [44]Sánchez-Molano E, Woolliams JA, Blott SC, Wiener P: Assessing the impact of genomic selection against hip dysplasia in the Labrador Retriever dog. J Anim Breed Genet 2013. doi:10.1111/jbg.12056