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BMC genomics2016; 17; 41; doi: 10.1186/s12864-016-2385-z

Identification and validation of risk loci for osteochondrosis in standardbreds.

Abstract: Osteochondrosis (OC), simply defined as a failure of endochondral ossification, is a complex disease with both genetic and environmental risk factors that is commonly diagnosed in young horses, as well as other domestic species. Although up to 50 % of the risk for developing OC is reportedly inherited, specific genes and alleles underlying risk are thus far completely unknown. Regions of the genome identified as associated with OC vary across studies in different populations of horses. In this study, we used a cohort of Standardbred horses from the U.S. (n = 182) specifically selected for a shared early environment (to reduce confounding factors) to identify regions of the genome associated with tarsal OC. Subsequently, putative risk variants within these regions were evaluated in both the discovery population and an independently sampled validation population of Norwegian Standardbreds (n = 139) with tarsal OC. Results: After genome-wide association analysis of imputed data with information from >200,000 single nucleotide polymorphisms, two regions on equine chromosome 14 were associated with OC in the discovery cohort. Variant discovery in these and 30 additional regions of interest (including 11 from other published studies) was performed via whole-genome sequencing. 240 putative risk variants from 10 chromosomes were subsequently genotyped in both the discovery and validation cohorts. After correction for population structure, gait (trot or pace) and sex, the variants most highly associated with OC status in both populations were located within the chromosome 14 regions of association. Conclusions: The association of putative risk alleles from within the same regions with disease status in two independent populations of Standardbreds suggest that these are true risk loci in this breed, although population-specific risk factors may still exist. Evaluation of these loci in other populations will help determine if they are specific to the Standardbred breed, or to tarsal OC or are universal risk loci for OC. Further work is needed to identify the specific variants underlying OC risk within these loci. This is the first step towards the long-term goal of constructing a genetic risk model for OC that allows for genetic testing and quantification of risk in individuals.
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Publication Date: 2016-01-12 PubMed ID: 26753841PubMed Central: PMC4709891DOI: 10.1186/s12864-016-2385-zGoogle Scholar: Lookup
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  • Journal Article
  • Research Support
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  • Extramural
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  • Non-U.S. Gov't
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article discusses a study that aims to identify and validate potential genetic risk factors for osteochondrosis (OC) – a joint-condition commonly diagnosed in young horses, particularly in Standardbreds. The research primarily utilizes genome sequencing to pinpoint loci associated with the disease.

Objective

The research aims to identify specific regions of the genome associated with osteochondrosis (OC), a disease prevalent in young Standardbred horses. Significantly, the research focuses on clarifying the genetic nature of the disease, potentially contributing to the development of genetic testing and quantification of risk in individual horses.

Method

  • The study utilized a cohort of US Standardbred horses (n=182) diagnosed with tarsal OC. The selection was primarily based on the horses’ common early environment to minimize confounding factors during the study.
  • A genome-wide association analysis was undertaken using over 200,000 single nucleotide polymorphism information.
  • The study consequently identified two regions on equine chromosome 14 correlated with the incidence of OC. Additional regions of interest were also taken into account.
  • Subsequent whole-genome sequencing identified 240 putative risk variants on ten chromosomes.
  • These variants were then genotyped in the discovery cohort and an independent validation cohort of Norwegian Standardbreds (n=139) with tarsal OC. Population structure, gait, and sex were all controlled for during this analysis.

Results

  • The study found that the variants most related to OC status within both populations were located within the two identified regions of chromosome 14.
  • This finding suggests that these indeed were genuine risk loci for OC within the breed, as implied by their simultaneous incidence in two independent Standardbred populations.

Conclusion

  • The research concludes that the identified loci could either be breed-specific, common to tarsal OC or universal risk factors for OC.
  • However, further investigation is necessary to identify the precise variants responsible for the risk of OC within the identified loci.
  • The study represents a crucial step toward forming a genetic risk model that can facilitate genetic testing and quantifying individual risk for OC.

Cite This Article

APA
McCoy AM, Beeson SK, Splan RK, Lykkjen S, Ralston SL, Mickelson JR, McCue ME. (2016). Identification and validation of risk loci for osteochondrosis in standardbreds. BMC Genomics, 17, 41. https://doi.org/10.1186/s12864-016-2385-z

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 17
Pages: 41

Researcher Affiliations

McCoy, Annette M
  • Veterinary Population Medicine Department, University of Minnesota, 1365 Gortner Ave., St. Paul, MN, USA. mccoya@illinois.edu.
  • Department of Veterinary Clinical Medicine, University of Illinois, 1008 Hazelwood Dr., Urbana, IL, USA. mccoya@illinois.edu.
Beeson, Samantha K
  • Veterinary Population Medicine Department, University of Minnesota, 1365 Gortner Ave., St. Paul, MN, USA. beeso018@umn.edu.
Splan, Rebecca K
  • Department of Animal and Poultry Sciences, Virginia Tech, 3470 Litton Reaves Hall, Blacksburg, VA, USA. rsplan@vt.edu.
Lykkjen, Sigrid
  • Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, NMBU-School of Veterinary Science, P.O. Box 8146 Dep., Oslo, Norway. sigrid.lykkjen@nmbu.no.
Ralston, Sarah L
  • School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 84 Lipman Dr., New Brunswick, NJ, USA. ralstonvmd@msn.com.
Mickelson, James R
  • Veterinary Biological Sciences Department, University of Minnesota, 1988 Fitch Ave., St. Paul, MN, USA. micke001@umn.edu.
McCue, Molly E
  • Veterinary Population Medicine Department, University of Minnesota, 1365 Gortner Ave., St. Paul, MN, USA. mccų@umn.edu.

MeSH Terms

  • Animals
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Genotype
  • Horse Diseases / genetics
  • Horse Diseases / pathology
  • Horses
  • Osteochondrosis / genetics
  • Osteochondrosis / pathology
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci / genetics
  • Risk Factors

Grant Funding

  • T32 AR007612 / NIAMS NIH HHS
  • T32 OD010993 / NIH HHS
  • F30 OD023369 / NIH HHS
  • K08 AR055713 / NIAMS NIH HHS
  • 1K08AR055713-01A2 / NIAMS NIH HHS

References

This article includes 64 references
  1. Denoix JM, Jeffcott LB, McIlwraith CW, van Weeren PR. A review of terminology for equine juvenile osteochondral conditions (JOCC) based on anatomical and functional considerations.. Vet J 2013 Jul;197(1):29-35.
    doi: 10.1016/j.tvjl.2013.03.038pubmed: 23683533google scholar: lookup
  2. Hurtig MB, Pool RR. Pathogenesis of equine osteochondrosis. In: McIlwraith CW, Trotter GW, editors. Joint disease in the horse. Philadelphia: W.B. Saunders Company; 1996. pp. 335–58.
  3. Pool RR. Pathogenesis of developmental lesions. In: McIlwraith CW, editor. Proceedings panel on developmental orthopedic disease. Dallas: American Quarter Horse Association; 1986. pp. 22–5.
  4. Olstad K, Ytrehus B, Ekman S, Carlson CS, Dolvik NI. Epiphyseal cartilage canal blood supply to the tarsus of foals and relationship to osteochondrosis.. Equine Vet J 2008 Jan;40(1):30-9.
    doi: 10.2746/042516407X239836pubmed: 18083657google scholar: lookup
  5. Olstad K, Ytrehus B, Ekman S, Carlson CS, Dolvik NI. Early lesions of articular osteochondrosis in the distal femur of foals.. Vet Pathol 2011 Nov;48(6):1165-75.
    doi: 10.1177/0300985811398250pubmed: 21321104google scholar: lookup
  6. Olstad K, Hendrickson EH, Carlson CS, Ekman S, Dolvik NI. Transection of vessels in epiphyseal cartilage canals leads to osteochondrosis and osteochondrosis dissecans in the femoro-patellar joint of foals; a potential model of juvenile osteochondritis dissecans.. Osteoarthritis Cartilage 2013 May;21(5):730-8.
    doi: 10.1016/j.joca.2013.02.005pubmed: 23428601google scholar: lookup
  7. Skagen PS, Horn T, Kruse HA, Staergaard B, Rapport MM, Nicolaisen T. Osteochondritis dissecans (OCD), an endoplasmic reticulum storage disease?: a morphological and molecular study of OCD fragments.. Scand J Med Sci Sports 2011 Dec;21(6):e17-33.
    doi: 10.1111/j.1600-0838.2010.01128.xpubmed: 20561273google scholar: lookup
  8. van de Lest CH, Brama PA, van El B, DeGroot J, van Weeren PR. Extracellular matrix changes in early osteochondrotic defects in foals: a key role for collagen?. Biochim Biophys Acta 2004 Sep 6;1690(1):54-62.
    doi: 10.1016/j.bbadis.2004.05.002pubmed: 15337170google scholar: lookup
  9. Desjardin C, Chat S, Gilles M, Legendre R, Riviere J, Mata X, Balliau T, Esquerré D, Cribiu EP, Betch JM, Schibler L. Involvement of mitochondrial dysfunction and ER-stress in the physiopathology of equine osteochondritis dissecans (OCD).. Exp Mol Pathol 2014 Jun;96(3):328-38.
    doi: 10.1016/j.yexmp.2014.03.004pubmed: 24657499google scholar: lookup
  10. McIlwraith CW, Association AQH. Summary of panel findings. In: McIlwraith CW, editor. Proceedings panel on developmental orthopedic disease, AQHA developmental orthopedic symposium. Amarillo: American Quarter Horse Association; 1986. pp. 55–61.
  11. Hintz HF. Factors which influence developmental orthopedic disease. Am Assoc Equine Practr Proc. 1987;33:159–62.
  12. Ralston SLPL, Pelczer I, Spears PF. NMR-bsed metabonomic analyses of horse serum: detection of metabolic markers of disease. Recent Adv Anim Nutr 2011;18:197–205.
  13. Gabel AA, Knight DA, Reed SM. Comparison of incidence and severity of developmental orthopedic disease on 17 farms before and after adjustment of ration. Am Assoc Equine Practr Proc 1987;33:163–70.
  14. van Weeren PR, Barneveld A. The effect of exercise on the distribution and manifestation of osteochondrotic lesions in the Warmblood foal.. Equine Vet J Suppl 1999 Nov;(31):16-25.
    doi: 10.1111/j.2042-3306.1999.tb05309.xpubmed: 10999656google scholar: lookup
  15. Lepeule J, Bareille N, Robert C, Ezanno P, Valette JP, Jacquet S, Blanchard G, Denoix JM, Seegers H. Association of growth, feeding practices and exercise conditions with the prevalence of Developmental Orthopaedic Disease in limbs of French foals at weaning.. Prev Vet Med 2009 Jun 1;89(3-4):167-77.
    doi: 10.1016/j.prevetmed.2009.02.018pubmed: 19329202google scholar: lookup
  16. Lepeule J, Bareille N, Robert C, Valette JP, Jacquet S, Blanchard G, Denoix JM, Seegers H. Association of growth, feeding practices and exercise conditions with the severity of the osteoarticular status of limbs in French foals.. Vet J 2013 Jul;197(1):65-71.
    doi: 10.1016/j.tvjl.2013.03.043pubmed: 23664071google scholar: lookup
  17. Grøndahl AM, Dolvik NI. Heritability estimations of osteochondrosis in the tibiotarsal joint and of bony fragments in the palmar/plantar portion of the metacarpo- and metatarsophalangeal joints of horses.. J Am Vet Med Assoc 1993 Jul 1;203(1):101-4.
    pubmed: 8407439
  18. Philipsson J, Andreasson E, Sandgren B, Dalin G, Carlsten J. Osteochondrosis in the tarsocrural joint and osteochondral fragments in the fetlock joints in Standardbred trotters. II Heritability. Equine Vet J Suppl 1993;16:38–41.
  19. Lykkjen S, Olsen HF, Dolvik NI, Grøndahl AM, Røed KH, Klemetsdal G. Heritability estimates of tarsocrural osteochondrosis and palmar/plantar first phalanx osteochondral fragments in Standardbred trotters.. Equine Vet J 2014 Jan;46(1):32-7.
    doi: 10.1111/evj.12058pubmed: 23448227google scholar: lookup
  20. Ricard A, Perrocheau M, Couroucé-Malblanc A, Valette JP, Tourtoulou G, Dufosset JM, Robert C, Chaffaux S, Denoix JM, Guérin G. Genetic parameters of juvenile osteochondral conditions (JOCC) in French Trotters.. Vet J 2013 Jul;197(1):77-82.
    doi: 10.1016/j.tvjl.2013.03.045pubmed: 23639370google scholar: lookup
  21. van Grevenhof EM, Schurink A, Ducro BJ, van Weeren PR, van Tartwijk JM, Bijma P, van Arendonk JA. Genetic variables of various manifestations of osteochondrosis and their correlations between and within joints in Dutch warmblood horses.. J Anim Sci 2009 Jun;87(6):1906-12.
    doi: 10.2527/jas.2008-1199pubmed: 19213707google scholar: lookup
  22. Hilla D, Distl O. Heritabilities and genetic correlations between fetlock, hock and stifle osteochondrosis and fetlock osteochondral fragments in Hanoverian Warmblood horses.. J Anim Breed Genet 2014 Feb;131(1):71-81.
    doi: 10.1111/jbg.12062pubmed: 24236645google scholar: lookup
  23. Orr N, Hill EW, Gu J, Govindarajan P, Conroy J, van Grevenhof EM, Ducro BJ, van Arendonk JA, Knaap JH, van Weeren PR, Machugh DE, Ennis S, Brama PA. Genome-wide association study of osteochondrosis in the tarsocrural joint of Dutch Warmblood horses identifies susceptibility loci on chromosomes 3 and 10.. Anim Genet 2013 Aug;44(4):408-12.
    doi: 10.1111/age.12016pubmed: 23278111google scholar: lookup
  24. Wittwer C, Hamann H, Rosenberger E, Distl O. Genetic parameters for the prevalence of osteochondrosis in the limb joints of South German Coldblood horses.. J Anim Breed Genet 2007 Oct;124(5):302-7.
    doi: 10.1111/j.1439-0388.2007.00670.xpubmed: 17868083google scholar: lookup
  25. Falconer DS, Mackay TFC. Introduction to quantitative genetics. 4. Pearson Education Limited: Essex, England; 1996.
  26. Valentino LW, Lillich JD, Gaughan EM, Biller DR, Raub RH. Radiographic prevalence of osteochondrosis in yearling feral horses. Vet Comp Orthop Traumatol 1999;12:151–5.
  27. McCoy AM, Toth F, Dolvik NI, Ekman S, Ellermann J, Olstad K, Ytrehus B, Carlson CS. Articular osteochondrosis: a comparison of naturally-occurring human and animal disease.. Osteoarthritis Cartilage 2013 Nov;21(11):1638-47.
    doi: 10.1016/j.joca.2013.08.011pmc: PMC3815567pubmed: 23954774google scholar: lookup
  28. Distl O. The genetics of equine osteochondrosis.. Vet J 2013 Jul;197(1):13-8.
    doi: 10.1016/j.tvjl.2013.03.036pubmed: 23809989google scholar: lookup
  29. Dierks C, Komm K, Lampe V, Distl O. Fine mapping of a quantitative trait locus for osteochondrosis on horse chromosome 2.. Anim Genet 2010 Dec;41 Suppl 2:87-90.
    doi: 10.1111/j.1365-2052.2010.02113.xpubmed: 21070281google scholar: lookup
  30. Lampe V, Dierks C, Distl O. Refinement of a quantitative gene locus on equine chromosome 16 responsible for osteochondrosis in Hanoverian warmblood horses.. Animal 2009 Sep;3(9):1224-31.
    doi: 10.1017/S1751731109004765pubmed: 22444898google scholar: lookup
  31. Corbin LJ, Blott SC, Swinburne JE, Sibbons C, Fox-Clipsham LY, Helwegen M, Parkin TD, Newton JR, Bramlage LR, McIlwraith CW, Bishop SC, Woolliams JA, Vaudin M. A genome-wide association study of osteochondritis dissecans in the Thoroughbred.. Mamm Genome 2012 Apr;23(3-4):294-303.
    doi: 10.1007/s00335-011-9363-1pubmed: 22052004google scholar: lookup
  32. Wittwer C, Hamann H, Distl O. The candidate gene XIRP2 at a quantitative gene locus on equine chromosome 18 associated with osteochondrosis in fetlock and hock joints of South German Coldblood horses.. J Hered 2009 Jul-Aug;100(4):481-6.
    doi: 10.1093/jhered/esp006pubmed: 19304740google scholar: lookup
  33. McCoy AM, McCue ME. Validation of imputation between equine genotyping arrays.. Anim Genet 2014 Feb;45(1):153.
    doi: 10.1111/age.12093pmc: PMC4000747pubmed: 24164665google scholar: lookup
  34. Petersen JLR, A.K., Mickelson JR, Equine Genetic Diversity Consortium, McCue ME. Identification of ancestry informative markers in the domestic horse. Proceedings, Plant and Animal Genome Conference XX January 14–18, 2012 2012; San Diego, CA.
  35. Robertson A, Lerner IM. The Heritability of All-or-None Traits: Viability of Poultry.. Genetics 1949 Jul;34(4):395-411.
    pmc: PMC1209454pubmed: 17247323doi: 10.1093/genetics/34.4.395google scholar: lookup
  36. Lykkjen S, Dolvik NI, McCue ME, Rendahl AK, Mickelson JR, Roed KH. Genome-wide association analysis of osteochondrosis of the tibiotarsal joint in Norwegian Standardbred trotters.. Anim Genet 2010 Dec;41 Suppl 2:111-20.
    doi: 10.1111/j.1365-2052.2010.02117.xpubmed: 21070284google scholar: lookup
  37. Teyssèdre S, Dupuis MC, Guérin G, Schibler L, Denoix JM, Elsen JM, Ricard A. Genome-wide association studies for osteochondrosis in French Trotter horses.. J Anim Sci 2012 Jan;90(1):45-53.
    doi: 10.2527/jas.2011-4031pubmed: 21841084google scholar: lookup
  38. Li M, Boehnke M, Abecasis GR. Efficient study designs for test of genetic association using sibship data and unrelated cases and controls.. Am J Hum Genet 2006 May;78(5):778-792.
    doi: 10.1086/503711pmc: PMC1474028pubmed: 16642434google scholar: lookup
  39. Jiang D, McPeek MS. Robust rare variant association testing for quantitative traits in samples with related individuals.. Genet Epidemiol 2014 Jan;38(1):10-20.
    doi: 10.1002/gepi.21775pmc: PMC4510991pubmed: 24248908google scholar: lookup
  40. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. Genome-wide association studies for complex traits: consensus, uncertainty and challenges.. Nat Rev Genet 2008 May;9(5):356-69.
    doi: 10.1038/nrg2344pubmed: 18398418google scholar: lookup
  41. Zhang Z, Todhunter RJ, Buckler ES, Van Vleck LD. Technical note: Use of marker-based relationships with multiple-trait derivative-free restricted maximal likelihood.. J Anim Sci 2007 Apr;85(4):881-5.
    doi: 10.2527/jas.2006-656pubmed: 17085728google scholar: lookup
  42. McCoy AM, Ralston SL, McCue ME. Short- and long-term racing performance of Standardbred pacers and trotters after early surgical intervention for tarsal osteochondrosis.. Equine Vet J 2015 Jul;47(4):438-44.
    doi: 10.1111/evj.12297pmc: PMC4229490pubmed: 24819047google scholar: lookup
  43. Spencer CC, Su Z, Donnelly P, Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip.. PLoS Genet 2009 May;5(5):e1000477.
    doi: 10.1371/journal.pgen.1000477pmc: PMC2688469pubmed: 19492015google scholar: lookup
  44. Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome.. Nat Rev Genet 2003 Aug;4(8):587-97.
    doi: 10.1038/nrg1123pubmed: 12897771google scholar: lookup
  45. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.. PLoS Genet 2012 Jan;8(1):e1002451.
    doi: 10.1371/journal.pgen.1002451pmc: PMC3257288pubmed: 22253606google scholar: lookup
  46. Römer P, Weingärtner J, Desaga B, Kubein-Meesenburg D, Reicheneder C, Proff P. Effect of excessive methionine on the development of the cranial growth plate in newborn rats.. Arch Oral Biol 2012 Sep;57(9):1225-30.
    doi: 10.1016/j.archoralbio.2012.02.007pubmed: 22386249google scholar: lookup
  47. Hosea Blewett HJ. Exploring the mechanisms behind S-adenosylmethionine (SAMe) in the treatment of osteoarthritis.. Crit Rev Food Sci Nutr 2008 May;48(5):458-63.
    doi: 10.1080/10408390701429526pubmed: 18464034google scholar: lookup
  48. Dowthwaite GP, Edwards JC, Pitsillides AA. An essential role for the interaction between hyaluronan and hyaluronan binding proteins during joint development.. J Histochem Cytochem 1998 May;46(5):641-51.
    doi: 10.1177/002215549804600509pubmed: 9562572google scholar: lookup
  49. Aikawa T, Segre GV, Lee K. Fibroblast growth factor inhibits chondrocytic growth through induction of p21 and subsequent inactivation of cyclin E-Cdk2.. J Biol Chem 2001 Aug 3;276(31):29347-52.
    doi: 10.1074/jbc.M101859200pubmed: 11384971google scholar: lookup
  50. Wu G, Chen W, Fan H, Zheng C, Chu J, Lin R, Ye J, Xu H, Li X, Huang Y, Ye H, Liu X, Wu M. Duhuo Jisheng Decoction promotes chondrocyte proliferation through accelerated G1/S transition in osteoarthritis.. Int J Mol Med 2013 Nov;32(5):1001-10.
    pubmed: 24009074doi: 10.3892/ijmm.2013.1481google scholar: lookup
  51. Löwenheim H, Reichl J, Winter H, Hahn H, Simon C, Gültig K, Müller A, Zenner HP, Zimmermann U, Knipper M. In vitro expansion of human nasoseptal chondrocytes reveals distinct expression profiles of G1 cell cycle inhibitors for replicative, quiescent, and senescent culture stages.. Tissue Eng 2005 Jan-Feb;11(1-2):64-75.
    doi: 10.1089/ten.2005.11.64pubmed: 15738662google scholar: lookup
  52. Beier F, Loeser RF. Biology and pathology of Rho GTPase, PI-3 kinase-Akt, and MAP kinase signaling pathways in chondrocytes.. J Cell Biochem 2010 Jun 1;110(3):573-80.
    doi: 10.1002/jcb.22604pmc: PMC2883292pubmed: 20512918google scholar: lookup
  53. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer.. N Engl J Med 2004 Dec 30;351(27):2817-26.
    doi: 10.1056/NEJMoa041588pubmed: 15591335google scholar: lookup
  54. Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering.. Am J Hum Genet 2007 Nov;81(5):1084-97.
    doi: 10.1086/521987pmc: PMC2265661pubmed: 17924348google scholar: lookup
  55. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses.. Am J Hum Genet 2007 Sep;81(3):559-75.
    doi: 10.1086/519795pmc: PMC1950838pubmed: 17701901google scholar: lookup
  56. Schaefer R. Selection of tagging SNPs and imputation efficiency of the 670 K commercial SNP chip. Proceedings, Plant & Animal Genome XXIII January 10–14, 2015; San Diego, CA. 2015.
  57. Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies.. Nat Genet 2012 Jun 17;44(7):821-4.
    doi: 10.1038/ng.2310pmc: PMC3386377pubmed: 22706312google scholar: lookup
  58. Li MX, Yeung JM, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets.. Hum Genet 2012 May;131(5):747-56.
    doi: 10.1007/s00439-011-1118-2pmc: PMC3325408pubmed: 22143225google scholar: lookup
  59. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps.. Bioinformatics 2005 Jan 15;21(2):263-5.
    doi: 10.1093/bioinformatics/bth457pubmed: 15297300google scholar: lookup
  60. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. The structure of haplotype blocks in the human genome.. Science 2002 Jun 21;296(5576):2225-9.
    doi: 10.1126/science.1069424pubmed: 12029063google scholar: lookup
  61. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data.. Nat Genet 2011 May;43(5):491-8.
    doi: 10.1038/ng.806pmc: PMC3083463pubmed: 21478889google scholar: lookup
  62. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.. Fly (Austin) 2012 Apr-Jun;6(2):80-92.
    doi: 10.4161/fly.19695pmc: PMC3679285pubmed: 22728672google scholar: lookup
  63. Cingolani P, Patel VM, Coon M, Nguyen T, Land SJ, Ruden DM, Lu X. Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift.. Front Genet 2012;3:35.
    doi: 10.3389/fgene.2012.00035pmc: PMC3304048pubmed: 22435069google scholar: lookup
  64. VanRaden PM. Efficient methods to compute genomic predictions.. J Dairy Sci 2008 Nov;91(11):4414-23.
    doi: 10.3168/jds.2007-0980pubmed: 18946147google scholar: lookup

Citations

This article has been cited 14 times.
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    doi: 10.3390/ani13091462pubmed: 37174498google scholar: lookup
  2. Durward-Akhurst SA, Schaefer RJ, Grantham B, Carey WK, Mickelson JR, McCue ME. Genetic Variation and the Distribution of Variant Types in the Horse. Front Genet 2021;12:758366.
    doi: 10.3389/fgene.2021.758366pubmed: 34925451google scholar: lookup
  3. Esdaile E, Avila F, Bellone RR. Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms. J Hered 2022 Jul 9;113(3):238-247.
    doi: 10.1093/jhered/esab070pubmed: 34893836google scholar: lookup
  4. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019 Dec;50(6):569-597.
    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
  5. Lewczuk D, Metera-Zarzycka E. Horse phenotyping based on video image analysis of jumping performance for conservation breeding. PeerJ 2019;7:e7450.
    doi: 10.7717/peerj.7450pubmed: 31413931google scholar: lookup
  6. McCoy AM, Beeson SK, Rubin CJ, Andersson L, Caputo P, Lykkjen S, Moore A, Piercy RJ, Mickelson JR, McCue ME. Identification and validation of genetic variants predictive of gait in standardbred horses. PLoS Genet 2019 May;15(5):e1008146.
    doi: 10.1371/journal.pgen.1008146pubmed: 31136578google scholar: lookup
  7. Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, Müller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Anim Genet 2018 Dec;49(6):564-570.
    doi: 10.1111/age.12717pubmed: 30311254google scholar: lookup
  8. Velie BD, Fegraeus KJ, Solé M, Rosengren MK, Røed KH, Ihler CF, Strand E, Lindgren G. A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism. BMC Genet 2018 Aug 29;19(1):80.
    doi: 10.1186/s12863-018-0670-3pubmed: 30157760google scholar: lookup
  9. Lewczuk D, Bereznowski A, Hecold M, Frąszczak M, Ruść A, Korwin-Kossakowska A, Szyda J, Kamiński S. Differences between horse selection based on two forms of osteochondrosis in fetlock. J Appl Genet 2018 May;59(2):225-230.
    doi: 10.1007/s13353-018-0437-6pubmed: 29524049google scholar: lookup
  10. Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 2017 Jul 27;18(1):565.
    doi: 10.1186/s12864-017-3943-8pubmed: 28750625google scholar: lookup
  11. Chessari G, Reich P, Criscione A, Falker-Gieske C, Mastrangelo S, Tumino S, Bordonaro S, Marletta D, Tetens J. Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds. BMC Genomics 2025 Nov 29;26(1):1086.
    doi: 10.1186/s12864-025-12256-8pubmed: 41318401google scholar: lookup
  12. Nazari-Ghadikolaei A, Fikse WF, Viklund ÅG, Mikko S, Eriksson S. Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses. J Anim Breed Genet 2025 Sep;142(5):499-512.
    doi: 10.1111/jbg.12923pubmed: 39754479google scholar: lookup
  13. De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024 Jan 23;14(1):2003.
    doi: 10.1038/s41598-023-48103-7pubmed: 38263320google scholar: lookup
  14. Becker GM, Shira KA, Woods JL, Khilji SF, Schauer CS, Webb BT, Stewart WC, Murdoch BM. Angular limb deformity associated with TSPAN18, NRG3 and NOVA2 in Rambouillet rams. Sci Rep 2023 Sep 25;13(1):16059.
    doi: 10.1038/s41598-023-43320-6pubmed: 37749158google scholar: lookup
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