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The Journal of heredity2021; 113(3); 238-247; doi: 10.1093/jhered/esab070

Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms.

Abstract: American Standardbreds were developed as a harness racing horse breed. The United States Trotting Association closed the studbook in 1973 and implemented a book size cap in 2009. This study aimed to investigate genetic diversity in the American Standardbred after the studbook cap was introduced using short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). Sixteen STRs from horses foaled from 2010 to 2015 and their sires and dams (n = 50 621) were utilized to examine allelic richness (Ar), expected heterozygosity (HE), observed heterozygosity (HO), unbiased heterozygosity (HU), inbreeding coefficient (FIS), and fixation index (FST). These analyses found that trotting and pacing sires were less genetically diverse than dams (HEPBonferroni = 0.029 and 6.3 × 10-5, respectively) and their offspring (ArPBonferroni = 0.034 and 6.9 × 10-6, respectively), and pacing offspring were significantly less diverse than their dams (HEPBonferroni = 2 × 10-3). Inbreeding coefficients for trotters (FIS = -0.014) and pacers (FIS = -0.012) suggest that breeding practices have maintained diversity. Moderate levels of genetic differentiation (0.066 < FST < 0.11) were found between pacing and trotting groups. Additionally, 10 of the most prolific trotting sires and their male offspring (n = 84) were genotyped on the 670K Axiom Equine HD Array. HO values higher than HE (P < 0.001), low inbreeding coefficients (mean F = -0.064), and mean FROH = 21% indicate relatively high levels of diversity in this cohort, further supporting the STR data. However, in contrast, HO values were higher for trotting sires (0.41) than their offspring (0.36). This observation warrants further monitoring of diversity over time. These data provide an updated foundation of diversity indices for further, long-term analysis in the breed.
© The American Genetic Association. 2021.
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Publication Date: 2021-12-12 PubMed ID: 34893836PubMed Central: PMC9270868DOI: 10.1093/jhered/esab070Google Scholar: Lookup
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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 explores the genetic diversity in the American Standardbred horse breed after a cap was introduced on the studbook in 2009. The results of the study suggest that breeding practices have maintained diversity in the breed, despite variations between the genetic diversity of pacing and trotting horses.

Research Purpose and Methodology

  • The study sought to gain further insight into the genetic diversity of the American Standardbred horse following 2009’s cap on the size of the studbook. In particular, the researchers wanted to see whether the genetic diversity of the breed has been maintained under these new restrictions.
  • The researchers had two primary genetic tools to study this: short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). They used these tools to investigate various parameters related to genetic diversity, including allelic richness, expected heterozygosity, observed heterozygosity, unbiased heterozygosity, inbreeding coefficient, and fixation index.
  • A sizeable sample of horses born from 2010 to 2015, along with their sires and dams, were studied. In total, the researchers used data from 50,621 specimens.

Research Findings

  • The study revealed that there are differences in genetic diversity between trotting and pacing sires, as well as their offspring. Trotting and pacing sires were found to be less genetically diverse compared to the dams and their offspring.
  • In terms of inbreeding coefficients – which give an indication of whether inbreeding occurred – the researchers noted values of -0.014 and -0.012 for trotters and pacers, respectively. These negative values suggest that the breeding practices have preserved diversity within this breed.
  • The study also discovered moderate levels of genetic differentiation between pacing and trotting groups, which adds further depth to the understanding of genetic diversity within the breed.
  • Examining the most prolific trotting sires and their male offspring provided further support for the general maintenance of genetic diversity in this breed. The observed heterozygosity (HO) values were found to be higher than the expected heterozygosity (HE) values, suggesting a high level of genetic diversity. However, the fact that the HO values for the trotting sires were higher than for their offspring may warrant further investigation to understand any developing trends in genetic diversity.

Implications of the Research

  • This research provides valuable insights into the genetic diversity and breeding practices of the American Standardbred horse. It suggests that the capping of the studbook, which can sometimes lead to a decrease in diversity over time, has managed to maintain genetic diversity within the breed.
  • From a practical perspective, this research serves as an updated foundation for understanding the genetic diversity of the breed. It may guide breeding strategies in the future to ensure that diversity is maintained and aid in long-term conservation of the breed.
  • The findings from this study could also be applicable to other horse breeds or potentially other animal species which have undergone similar breeding restrictions.

Cite This Article

APA
Esdaile E, Avila F, Bellone RR. (2021). Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms. J Hered, 113(3), 238-247. https://doi.org/10.1093/jhered/esab070

Publication

The Journal of heredity
ISSN: 1465-7333
NlmUniqueID: 0375373
Country: United States
Language: English
Volume: 113
Issue: 3
Pages: 238-247

Researcher Affiliations

Esdaile, Elizabeth
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
Avila, Felipe
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
Bellone, Rebecca R
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.

MeSH Terms

  • Alleles
  • Animals
  • Breeding
  • Genetic Variation
  • Horses / genetics
  • Inbreeding
  • Male
  • Microsatellite Repeats
  • Polymorphism, Single Nucleotide
  • United States

Grant Funding

  • United States Trotting Association

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Citations

This article has been cited 5 times.
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  4. Avila F, Esdaile E, Bellone RR. Using STR Data to Investigate the Impact of the Studbook Cap on Genetic Diversity in the American Standardbred Horse from 1998 to 2021. Genes (Basel) 2025 Jun 27;16(7).
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