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Home / Equine Research Bank / BMC Genomics / Identification and validation of risk loci for osteochondros...
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
  • N.I.H.
  • Extramural
  • Research Support
  • 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

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Citations

This article has been cited 14 times.
  1. Zimmermann E, Distl O. SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses. Animals (Basel) 2023 Apr 25;13(9).
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