FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Genes (Basel) / Using STR Data to Investigate the Impact of the Studbook Cap...
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.
Get Full Text
Publication Date: 2025-06-27 PubMed ID: 40725405PubMed Central: PMC12294264DOI: 10.3390/genes16070748Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • 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.

References

This article includes 25 references
  1. MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfenning DW, Parsons CJ. Inbreeding and pedigree structure in Standardbred horses.. J. Hered. 1983;74:394–399.
    doi: 10.1093/oxfordjournals.jhered.a109824google scholar: lookup
  2. Cothran EG, MacCluer JW, Weitkamp LR, Guttormsen SA. Genetic variability, inbreeding, and reproductive performance in Standardbred horses.. Zoo Biol. 1986;5:191–201.
    doi: 10.1002/zoo.1430050213google scholar: lookup
  3. Cothran EG, MacCluer JW, Weitkamp LR, Pfennig DW, Boyce AJ. Inbreeding and reproductive performance in Standardbred horses.. J. Hered. 1984;75:220–224.
    doi: 10.1093/oxfordjournals.jhered.a109916pubmed: 6736603google scholar: lookup
  4. Cothran EG, MacCluer JW, Weitkamp LR, Bailey E. Genetic differentiation associated with gait within American Standardbred horses.. Anim. Genet. 1987;18:285–296.
    doi: 10.1111/j.1365-2052.1987.tb00772.xpubmed: 3481678google scholar: lookup
  5. King JA. Changes in Heterozygosity Through Time in American Standardbred and American Saddlebred Horses (1960–1990). .
  6. Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P. Genetic diversity in the modern horse illustrated from genome-wide SNP data.. PLoS ONE 2013;8:e54997.
    doi: 10.1371/journal.pone.0054997pmc: PMC3559798pubmed: 23383025google scholar: lookup
  7. Esdaile E, Avila F, Bellone RR. Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms.. J. Hered. 2022;113:238–247.
    doi: 10.1093/jhered/esab070pmc: PMC9270868pubmed: 34893836google scholar: lookup
  8. Cho GJ, Cho BW. Microsatellite DNA Typing Using 16 Markers for Parentage Verification of the Korean Native Horse.. Asian-Aust. J. Anim. Sci. 2004;17:750–754.
    doi: 10.5713/ajas.2004.750google scholar: lookup
  9. Kwon DY, Cho GJ. Standardization and Usefulness of ISAG Microsatellite Markers for Individual Identification and Parentage Verification in Horse Breeds.. J. Vet. Clin. 2009;26:220–225.
  10. Peakall R, Smouse PE. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update.. Bioinformatics 2012;28:2537–2539.
    pmc: PMC3463245pubmed: 22820204
  11. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure.. Evolution 1984;38:1358–1370.
    doi: 10.2307/2408641pubmed: 28563791google scholar: lookup
  12. Goudet J. Hierfstat, a package for R to compute and test variance components and F-statistics.. Mol. Ecol. Notes 2005;5:184–186.
    doi: 10.1111/j.1471-8286.2004.00828.xgoogle scholar: lookup
  13. R Core Team. R: A Language and Environment for Statistical Computing.. 2020.
  14. Lenth R. Emmeans: Estimated Marginal Means, Aka Least-Squares Means. R Package Version 1.8.4-1.. 2023.
  15. Wright S. Evolution and the Genetics of Populations. Volume 4. 1978.
  16. Ellegren H, Johansson M, Sandberg K, Andersson L. Cloning of highly polymorphic microsatellites in the horse.. Anim. Genet. 1992;23:133–142.
    doi: 10.1111/j.1365-2052.1992.tb00032.xpubmed: 1443772google scholar: lookup
  17. Bowling AT, Penedo MCT, Stott ML, Malyj W. Introduction of DNA Testing for Horse and Cattle Parentage Verification, Proceedings of the 5th International Symposium on Human Identification, Scottsdale, AZ, USA, 27–29 October 1993.. 1994;pp. 75–80.
  18. Binns MM, Holmes NG, Holliman A, Scott AM. The identification of polymorphic microsatellite loci in the horse and their use in Thoroughbred parentage testing.. Br. Vet. J. 1995;151:9–15.
    doi: 10.1016/S0007-1935(05)80057-0pubmed: 7735875google scholar: lookup
  19. Bowling AT, Eggleston-Stott ML, Byrns G, Clark RS, Dileanis S, Wictum E. Validation of microsatellite markers for routine horse parentage testing.. Anim. Genet. 1997;28:247–252.
    doi: 10.1111/j.1365-2052.1997.00123.xpubmed: 9345720google scholar: lookup
  20. Nakamura M, Tozaki T, Kakoi H, Nakamura K, Rajabi-Toustani R, Ohba Y, Matsubara T, Takasu M. Decreased genetic diversity in Kiso horses revealed through annual microsatellite genotyping.. J. Vet. Med. Sci. 2020;82:503–505.
    doi: 10.1292/jvms.19-0535pmc: PMC7192717pubmed: 32147602google scholar: lookup
  21. Yun J, Oyungerel B, Kong HS. Genetic diversity and population structure of Mongolian regional horses with 14 microsatellite markers.. Anim. Biosci. 2022;35:1121–1128.
    doi: 10.5713/ab.21.0497pmc: PMC9262727pubmed: 35240022google scholar: lookup
  22. Orazymbetova Z, Ualiyeva D, Dossybayev K, Torekhanov A, Sydykov D, Mussayeva A, Baktybayev G. Genetic diversity of Kazakhstani Equus caballus (Linnaeus, 1758) horse breeds inferred from microsatellite markers.. Vet. Sci. 2023;10:598.
    doi: 10.3390/vetsci10100598pmc: PMC10611244pubmed: 37888550google scholar: lookup
  23. Yordanov G, Mehandjyiski I, Palova N, Atsenova N, Neov B, Radoslavov G, Hristov P. Genetic diversity and structure of the main Danubian horse paternal genealogical lineages based on microsatellite genotyping.. Vet. Sci. 2022;9:333.
    doi: 10.3390/vetsci9070333pmc: PMC9322366pubmed: 35878350google scholar: lookup
  24. Fornal A, Kowalska K, Zabek T, Piestrzynska-Kajtoch A, Musiał AD, Ropka-Molik K. Genetic diversity and population structure of Polish Konik horse based on individuals from all the male founder lines and microsatellite markers.. Animals 2020;10:1569.
    doi: 10.3390/ani10091569pmc: PMC7552212pubmed: 32899310google scholar: lookup
  25. Khanshour A, Conant E, Juras R, Cothran EG. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.. J. Hered. 2013;104:386–398.
    doi: 10.1093/jhered/est003pubmed: 23450090google scholar: lookup

Citations

This article has been cited 0 times.
Subscribe to our newsletter
Join 99,357 horse owners like you who receive our email updates on horse health and nutrition.