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Scientific reports2020; 10(1); 466; doi: 10.1038/s41598-019-57389-5

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population.

Abstract: The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (F R = 0.942, P = 2.19 × 10; F R = 0.88, P = 1.81 × 10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.
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Publication Date: 2020-01-16 PubMed ID: 31949252PubMed Central: PMC6965197DOI: 10.1038/s41598-019-57389-5Google Scholar: Lookup
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  • Journal Article

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 explores the impact of using a limited number of popular sire lines in breeding Thoroughbred horses, indicating that this practice negatively affects global genetic diversity in this horse breed over time. These scientific findings suggest a need for using genomics-based methods for stallion selection to maintain genetic diversity and counter inbreeding trends.

Objectives and Methodology

  • The researchers aimed to better understand the genetic trends in Thoroughbred horses. Specifically, they were interested in the potential losses in genetic diversity, possibly caused by the repeated use of a few popular sire lines in breeding.
  • To do this, they took a globally representative sample of Thoroughbreds (10,118 in total), which includes many significant stallions (305) from major bloodstock regions.
  • Genomic diversity and inbreeding were then assessed using SNP genotypes, which are a highly accurate type of genetic marker. These assessments, together with estimates of population size, allowed researchers to look at the possible effects of narrowed sire line usage on Thoroughbred diversity.

Results

  • The study found a significant decrease in global genetic diversity of Thoroughbreds over the past fifty years. This decline is likely due to the extensive use of popular sire lines in breeding.
  • Inbreeding, which tends to be a consequence of selection for specific aesthetic, cultural, or economically advantageous traits, was evident in Thoroughbred populations.
  • The researchers found that this selective breeding affected genes associated with behavior, physical conformation, and metabolism, many of which contribute to the Thoroughbred’s athletic performance. Areas of adaptation included cardiovascular signaling, growth and developmental functions, cellular stress and injury responses, metabolic processes, and neurotransmitter signaling.

Implications and Recommendations

  • A key implication of this research is the urgent need for enhanced genetic diversity within the Thoroughbred breed to counter the inbreeding trend.
  • The results also suggest that some regional variation exists, which could potentially be exploited to improve global genetic diversity of Thoroughbreds.
  • The researchers emphasize that genomics-based approaches could provide invaluable objectivity in stallion selection, enhancing traditional selection methods and protecting against future inbreeding.
  • Such methods could actively monitor Thoroughbred populations, helping to preserve their genetic health, diversity, and breed characteristics.

Cite This Article

APA
McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW. (2020). Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population. Sci Rep, 10(1), 466. https://doi.org/10.1038/s41598-019-57389-5

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 10
Issue: 1
Pages: 466
PII: 466

Researcher Affiliations

McGivney, Beatrice A
  • Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland.
Han, Haige
  • Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland.
  • UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
Corduff, Leanne R
  • Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland.
Katz, Lisa M
  • UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
Tozaki, Teruaki
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan.
MacHugh, David E
  • UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
  • UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
Hill, Emmeline W
  • Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland. Emmeline.Hill@ucd.ie.
  • UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland. Emmeline.Hill@ucd.ie.

MeSH Terms

  • Animals
  • Genetics, Population
  • Genome
  • Genomics
  • Genotype
  • Horses / genetics
  • Inbreeding
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Selection, Genetic

Grant Funding

  • 11/PI/1166 / Science Foundation Ireland (SFI)

Conflict of Interest Statement

This research was conducted with the financial support of Plusvital Ltd. (www.plusvital.com) and a grant to EWH from Science Foundation Ireland (www.sfi.ie) (SFI/11/PI/1166). EWH is Chief Science Officer for Plusvital Ltd. BAM, HH and LRC are employees of Plusvital Ltd. EWH and DEM are shareholders in Plusvital Ltd. LMK and DEM are consultants of Plusvital Ltd. Other than the authors, the funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Plusvital Ltd. has been engaged by the American Jockey Club (The Jockey Club) to provide expert advice and services, which may relate to data/results included in the manuscript.

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