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Genes2025; 16(7); 748; doi: 10.3390/genes16070748

Using STR Data to Investigate the Impact of the Studbook Cap on Genetic Diversity in the American Standardbred Horse from 1998 to 2021.

Abstract: Standardbreds, a breed of horses used in harness racing at either the trot or the pace, established a closed studbook in 1973. Concerns about genetic diversity within the breed led the United States Trotting Association (USTA) to establish a limit of mares bred per stallion (i.e., a studbook cap) in 2009. Here, we aimed to evaluate the impact of the breeding restrictions on genetic diversity between and among subpopulations. : Sixteen short tandem repeats (STRs) were analyzed across a dataset of 176,424 Standardbreds foaled in the United States between 1998 and 2021. We examined allelic richness (), number of effective alleles (), expected heterozygosity (), observed heterozygosity (), inbreeding coefficient (), and fixation index () across 24 years, differentiating by gate type, and comparing pre-(1998-2009) and post-(2010-2021) studbook cap periods using regression analysis. : Our results support decreased genetic diversity for both trotters and pacers over time. However, pacing Standardbreds exhibited significantly slower rates of decrease in genetic diversity after the 2009 studbook cap, as evidenced by , , and ( < 0.01). Additionally, moderate levels of genetic differentiation were found between trotters and pacers (0.05 < < 0.09), which increased over time. : Given that the rate of loss of diversity does not appear to differ pre and post studbook cap in trotters and that there is an increase in genetic differentiation between the groups over time, developing additional breeding tools and strategies is necessary to help the subpopulation mitigate further decline.
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Publication Date: 2025-06-27 PubMed ID: 40725405PubMed Central: PMC12294264DOI: 10.3390/genes16070748Google 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.

This research studied the impact of restricted breeding practices on the genetic diversity of American Standardbred horses over a period of 24 years. The results showed that despite placing a limit on the number of mares bred per stallion, the rate of loss in genetic diversity did not change significantly, implicating a need for improved breeding strategies.

Objective of the Research

  • The primary objective of this study was to analyze the impact of the United States Trotting Association’s (USTA) studbook cap on the genetic diversity of American Standardbred horses, a breed mainly used in harness racing.

Methodology

  • The study analyzed sixteen short tandem repeats (STRs), which are sequences of DNA that repeat back-to-back, across a dataset of 176,424 horses born between 1998 and 2021.
  • Various genetic metrics like the number of effective alleles, observed and expected heterozygosity, inbreeding coefficient, and fixation index were observed over this 24-year period.
  • The researchers conducted a regression analysis to compare the genetic diversity pre-(1998-2009) and post-(2010-2021) the implementation of the studbook cap.

Findings

  • Results revealed a continued decrease in genetic diversity for both trotting and pacing Standardbreds over time, indicating that the restriction on the number of mares bred per stallion did not significantly halt the rate of loss in genetic diversity.
  • While pacing Standardbreds showed a slower rate of decrease in genetic diversity post-studbook cap, the difference was not significant enough to suggest a superior genetic diversity in this subpopulation.
  • Moreover, the study found moderate levels of genetic differentiation between trotters and pacers, which increased over time.

Implications

  • The findings suggest that setting a limit on the number of mares bred per stallion as a measure to protect genetic diversity within the breed is insufficient.
  • Breeding programs need to adopt additional tools and strategies to help subpopulations mitigate further genetic decline and maintain a healthy gene pool.

Cite This Article

APA
Avila F, Esdaile E, Bellone RR. (2025). 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), 16(7), 748. https://doi.org/10.3390/genes16070748

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 16
Issue: 7
PII: 748

Researcher Affiliations

Avila, Felipe
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Esdaile, Elizabeth
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
Bellone, Rebecca R
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.

MeSH Terms

  • Animals
  • Horses / genetics
  • Genetic Variation
  • Microsatellite Repeats / genetics
  • Breeding
  • United States
  • Female
  • Inbreeding
  • Alleles

Grant Funding

  • N/A / United States Trotting Association

Conflict of Interest Statement

F.A., E.E., and R.R.B. are affiliated with the Veterinary Genetics Laboratory, a laboratory offering parentage and diagnostic DNA tests in horses and other species.

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