1
|
Genome-wide association analyses of osteochondrosis in Belgian Warmbloods reveal candidate genes associated with chondrocyte development. J Equine Vet Sci 2022; 111:103870. [DOI: 10.1016/j.jevs.2022.103870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/09/2021] [Accepted: 01/17/2022] [Indexed: 01/22/2023]
|
2
|
Simulation Study on the Integration of Health Traits in Horse Breeding Programs. Animals (Basel) 2020; 10:ani10071153. [PMID: 32645982 PMCID: PMC7401664 DOI: 10.3390/ani10071153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The disease osteochondrosis dissecans (OCD) is an important health-related trait in horse breeding. This study aimed at finding a breeding strategy to reduce the occurrence of OCD without affecting the riding horse performance traits substantially. Therefore, a lifelike simulation of different possible ways to include this trait in a horse breeding program was performed. Effective strategies can be the exclusion of affected animals from breeding as well as the selection based on a breeding value estimation which considered OCD susceptibility together with riding horse performance traits in an index. A reduction in the frequency of occurrence of OCD was found to be linked with a slight decrease in the breeding values for the riding horse characteristics. Abstract Osteochondrosis dissecans (OCD) is a degenerative disease of the cartilage leading to osseous fragments in the joints. It is important in horse breeding both from an animal welfare and an economic perspective. To study adequate breeding strategies to reduce OCD prevalence, a lifelike simulation of the breeding program of German Warmblood horses was performed with the R package MoBPS. We simulated complex breeding schemes of riding horses with different selection steps and realistic age structure, mimicking the German situation. As an example, osseous fragments in fetlock and hock joints were considered. Different scenarios, either using threshold selection, index selection or genomic index selection, respectively, were compared regarding their impact on health and performance traits. A rigorous threshold selection as well as the integration of OCD in a selection index at the stage of stallion licensing and chosen frequency of use in breeding cases on a selection index that includes breeding values for OCD traits performed best on a comparable level. Simply integrating OCD in this breeding value was less effective in terms of OCD reduction. Scenarios with a higher reduction of OCD also showed a slightly reduced improvement in the riding horse performance traits.
Collapse
|
3
|
Abstract
Orthopedic diseases are a common cause for limited exercise capacity in the horse. They often underlie genetic risk factors, which can affect bone, articular cartilage, tendons, ligaments, and adnexal structures among others. The genetic effects can directly interfere with tissue development and skeletal growth or can trigger degenerative or inflammatory processes. Many of these diseases of the locomotor system like osteochondrosis are complex and can be affected by multifactorial influences. For this reason, it is important for those performing diagnostic procedures to have a comprehensive knowledge of orthopedic diseases, their prevalence within breeds, and genetic background.
Collapse
Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, Hannover 30559, Germany.
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, Hannover 30559, Germany
| |
Collapse
|
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; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
Collapse
Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
| |
Collapse
|
5
|
Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits. Genet Sel Evol 2019; 51:22. [PMID: 31132983 PMCID: PMC6537210 DOI: 10.1186/s12711-019-0465-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/14/2019] [Indexed: 12/04/2022] Open
Abstract
Background Since the 1950s, the Norwegian–Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequently, the aims of the current study were to estimate genomic-based inbreeding coefficients, i.e. the proportion of runs of homozygosity (ROH), for a sample of NSCT individuals using high-density genotyping array data, and subsequently to compare the resulting rate of genomic-based F (FROH) to that of pedigree-based F (FPED) coefficients within the breed. Results A total of 566 raced NSCT were available for analyses. Average FROH ranged from 1.78 to 13.95%. Correlations between FROH and FPED were significant (P < 0.001) and ranged from 0.27 to 0.56, with FPED and FROH from 2000 to 2009 increasing by 1.48 and 3.15%, respectively. Comparisons of ROH between individuals yielded 1403 regions that were present in at least 95% of the sampled horses. The average percentage of a single chromosome covered in ROH ranged from 9.84 to 18.82% with chromosome 31 and 18 showing, respectively, the largest and smallest amount of homozygosity. Conclusions Genomic inbreeding coefficients were higher than pedigree inbreeding coefficients with both methods showing a gradual increase in inbreeding level in the NSCT breed between 2000 and 2009. Opportunities exist for the NSCT industry to develop programs that provide breeders with easily interpretable feedback on regions of the genome that are suboptimal from the perspective of genetic merit or that are sensitive to inbreeding within the population. The use of molecular data to identify genomic regions that may contribute to inbreeding depression in the NSCT will likely prove to be a valuable tool for the preservation of its genetic diversity in the long term. Electronic supplementary material The online version of this article (10.1186/s12711-019-0465-7) contains supplementary material, which is available to authorized users.
Collapse
|
6
|
Wypchło M, Korwin-Kossakowska A, Bereznowski A, Hecold M, Lewczuk D. Polymorphisms in selected genes and analysis of their relationship with osteochondrosis in Polish sport horse breeds. Anim Genet 2018; 49:623-627. [DOI: 10.1111/age.12715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2018] [Indexed: 12/22/2022]
Affiliation(s)
- M. Wypchło
- Institute of Genetics and Animal Breeding of the Polish Academy of Science in Jastrzebiec; Postepu Street 36A 05-552 Magdalenka Poland
| | - A. Korwin-Kossakowska
- Institute of Genetics and Animal Breeding of the Polish Academy of Science in Jastrzebiec; Postepu Street 36A 05-552 Magdalenka Poland
| | - A. Bereznowski
- Warsaw University of Life Sciences-SGGW; Nowoursynowska Street 166 02-787 Warsaw Poland
| | - M. Hecold
- Warsaw University of Life Sciences-SGGW; Nowoursynowska Street 166 02-787 Warsaw Poland
| | - D. Lewczuk
- Institute of Genetics and Animal Breeding of the Polish Academy of Science in Jastrzebiec; Postepu Street 36A 05-552 Magdalenka Poland
| |
Collapse
|
7
|
Naccache F, Metzger J, Distl O. Genetic risk factors for osteochondrosis in various horse breeds. Equine Vet J 2018; 50:556-563. [DOI: 10.1111/evj.12824] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022]
Affiliation(s)
- F. Naccache
- University of Veterinary Medicine Hannover, Foundation Institute for Animal Breeding and Genetics Hannover Germany
| | - J. Metzger
- University of Veterinary Medicine Hannover, Foundation Institute for Animal Breeding and Genetics Hannover Germany
| | - O. Distl
- University of Veterinary Medicine Hannover, Foundation Institute for Animal Breeding and Genetics Hannover Germany
| |
Collapse
|
8
|
|
9
|
Sevane N, Dunner S, Boado A, Cañon J. Candidate gene analysis of osteochondrosis in Spanish Purebred horses. Anim Genet 2016; 47:570-8. [DOI: 10.1111/age.12453] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 01/05/2023]
Affiliation(s)
- N. Sevane
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
| | - S. Dunner
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
| | - A. Boado
- Traumatología Equina; El Boalo Madrid 28413 Spain
| | - J. Cañon
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
| |
Collapse
|
10
|
McCoy AM, Beeson SK, Splan RK, Lykkjen S, Ralston SL, Mickelson JR, McCue ME. Identification and validation of risk loci for osteochondrosis in standardbreds. BMC Genomics 2016; 17:41. [PMID: 26753841 PMCID: PMC4709891 DOI: 10.1186/s12864-016-2385-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 01/07/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND 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.
Collapse
Affiliation(s)
- Annette M McCoy
- Veterinary Population Medicine Department, University of Minnesota, 1365 Gortner Ave., St. Paul, MN, USA. .,Department of Veterinary Clinical Medicine, University of Illinois, 1008 Hazelwood Dr., Urbana, IL, USA.
| | - Samantha K Beeson
- Veterinary Population Medicine Department, University of Minnesota, 1365 Gortner Ave., St. Paul, MN, USA.
| | - Rebecca K Splan
- Department of Animal and Poultry Sciences, Virginia Tech, 3470 Litton Reaves Hall, Blacksburg, VA, USA.
| | - Sigrid Lykkjen
- Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, NMBU-School of Veterinary Science, P.O. Box 8146 Dep., Oslo, Norway.
| | - Sarah L Ralston
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 84 Lipman Dr., New Brunswick, NJ, USA.
| | - James R Mickelson
- Veterinary Biological Sciences Department, University of Minnesota, 1988 Fitch Ave., St. Paul, MN, USA.
| | - Molly E McCue
- Veterinary Population Medicine Department, University of Minnesota, 1365 Gortner Ave., St. Paul, MN, USA.
| |
Collapse
|
11
|
Bates JT, Jacobs JC, Shea KG, Oxford JT. Emerging genetic basis of osteochondritis dissecans. Clin Sports Med 2014; 33:199-220. [PMID: 24698039 DOI: 10.1016/j.csm.2013.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWAS) provide an unbiased approach in the identification of genes that increase the risk for osteochondritis dissecans (OCD). Recent GWAS in humans, horses, and pigs are reviewed and genes identified. The identified genes tended to cluster with respect to function and biologic processes. GWAS in humans are a critical next step in the effort to provide a better understanding of the causes of OCD, which will, in turn, allow preventive strategies for treatment of adolescents and young adults who are at risk for the development of degenerative joint disease due to the effects of OCD.
Collapse
Affiliation(s)
- J Tyler Bates
- Department of Biological Sciences, Biomolecular Research Center, Musculoskeletal Research Institute, Boise State University, 1910 University Drive, Boise, ID 83725, USA
| | - John C Jacobs
- University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, UT 84132, USA
| | - Kevin G Shea
- St. Luke's Sports Medicine, St. Luke's Health System, St. Luke's Children's Hospital, 600 North Robbins Road, Suite 400, Boise, ID 83702, USA; Department of Orthopedics, University of Utah, 590 Wakara Way, Salt Lake City, UT 84108, USA
| | - Julia Thom Oxford
- Department of Biological Sciences, Biomolecular Research Center, Musculoskeletal Research Institute, Boise State University, 1910 University Drive, Boise, ID 83725, USA.
| |
Collapse
|
12
|
Abstract
Osteochondrosis (OC) develops in growing horses due to disturbed differentiation and maturation of cartilage, particularly at the predilection sites of the fetlock, hock and stifle joints. Horses with osteochondrotic lesions are at a high risk of developing orthopaedic problems later in life. This article briefly reviews the published heritability estimates for OC and offers perspectives for selection in the horse industry. Heritabilities for OC in Warmblood and Standardbred horses have been estimated at 0.1-0.4 in animal threshold models. Whole genome scans using microsatellites have identified 14 quantitative trait loci (QTL) and the eight most important QTL have been refined using dense marker maps. Genome-wide association studies with single nucleotide polymorphisms revealed further QTL in Thoroughbred, Standardbred and Hanoverian horses. Only a few QTL have corresponding locations among the different breeds. Comparative genomics using positional candidate genes and next-generation-sequencing may lead to new insights into the genetic determination of equine OC and might help in understanding the molecular mechanisms of its pathogenesis. Implementation of selection schemes based on breeding values, or even genomic selection against OC, should be considered as an option for improving equine musculoskeletal health.
Collapse
Affiliation(s)
- Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany.
| |
Collapse
|