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Home / Equine Research Bank / J Hered / Analysis of Genetic Diversity in the American Standardbred H...
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

References

This article includes 34 references
  1. Adams HA, Sonstegard TS, VanRaden PM, Null DJ, Van Tassell CP, Larkin DM, Lewin HA. Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle.. J Dairy Sci 2016 Aug;99(8):6693-6701.
    pubmed: 27289157doi: 10.3168/jds.2015-10517google scholar: lookup
  2. Adelman ML. The first modern sport in America: harness racing in New York City, 1825–1870.. J Sport Hist 8(1):5–32.
  3. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets.. Gigascience 2015;4:7.
    pmc: PMC4342193pubmed: 25722852doi: 10.1186/s13742-015-0047-8google scholar: lookup
  4. Cothran EG, MacCluer JW, Weitkamp LR, Guttormsen SA. Genetic variability, inbreeding, and reproductive performance in standardbred horses.. Zoo Biol 5(2): 191–201.
  5. Cothran EG, MacCluer JW, Weitkamp LR, Pfennig DW, Boyce AJ. Inbreeding and reproductive performance in standardbred horses.. J Hered 1984 May-Jun;75(3):220-4.
    pubmed: 6736603doi: 10.1093/oxfordjournals.jhered.a109916google scholar: lookup
  6. Cothran EG, MacCluer JW, Weitkamp LR, Bailey E. Genetic differentiation associated with gait within American standardbred horses.. Anim Genet 1987;18(4):285-96.
    pubmed: 3481678doi: 10.1111/j.1365-2052.1987.tb00772.xgoogle scholar: lookup
  7. Dieringer D, Schlötterer C. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets.. Mol Ecol Notes 3(1): 167–169.
  8. Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis.. Evol Bioinform Online 2007 Feb 23;1:47-50.
    pmc: PMC2658868pubmed: 19325852
  9. Fischer MC, Rellstab C, Leuzinger M, Roumet M, Gugerli F, Shimizu KK, Holderegger R, Widmer A. Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri.. BMC Genomics 2017 Jan 11;18(1):69.
    pmc: PMC5225627pubmed: 28077077doi: 10.1186/s12864-016-3459-7google scholar: lookup
  10. Khanshour A, Conant E, Juras R, Cothran EG. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.. J Hered 2013 May-Jun;104(3):386-98.
    pubmed: 23450090doi: 10.1093/jhered/est003google scholar: lookup
  11. King JA. Changes in heterozygosity through time in American Standardbred and American Saddlebred Horses (1960–1990) (Master thesis). Denton (TX): University of North Texas.
  12. Kraus M, Physick-Sheard P, Brito LF, Sargolzaei M, Schenkel FS. Marginal ancestral contributions to atrial fibrillation in the Standardbred racehorse: Comparison of cases and controls.. PLoS One 2018;13(5):e0197137.
    pmc: PMC5953485pubmed: 29763439doi: 10.1371/journal.pone.0197137google scholar: lookup
  13. Kraus M, Physick-Sheard PW, Brito LF, Schenkel FS. Estimates of heritability of atrial fibrillation in the Standardbred racehorse.. Equine Vet J 2017 Nov;49(6):718-722.
    pubmed: 28391631doi: 10.1111/evj.12687google scholar: lookup
  14. Lischer HE, Excoffier L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.. Bioinformatics 2012 Jan 15;28(2):298-9.
    pubmed: 22110245doi: 10.1093/bioinformatics/btr642google scholar: lookup
  15. Lykkjen S, Olsen HF, Dolvik NI, Grøndahl AM, Røed KH, Klemetsdal G. Heritability estimates of tarsocrural osteochondrosis and palmar/plantar first phalanx osteochondral fragments in Standardbred trotters.. Equine Vet J 2014 Jan;46(1):32-7.
    pubmed: 23448227doi: 10.1111/evj.12058google scholar: lookup
  16. MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfenning DW, Parsons CJ. Inbreeding and pedigree structure in Standardbred horses.. J Hered 74(6):394–399.
  17. Mack M, Kowalski E, Grahn R, Bras D, Penedo MCT, Bellone R. Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino Horses.. G3 (Bethesda) 2017 Aug 7;7(8):2799-2806.
    pmc: PMC5555483pubmed: 28655738doi: 10.1534/g3.117.043786google scholar: lookup
  18. 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 Jan 12;17:41.
    pmc: PMC4709891pubmed: 26753841doi: 10.1186/s12864-016-2385-zgoogle scholar: lookup
  19. McCoy AM, Norton EM, Kemper AM, Beeson SK, Mickelson JR, McCue ME. SNP-based heritability and genetic architecture of tarsal osteochondrosis in North American Standardbred horses.. Anim Genet 2019 Feb;50(1):78-81.
    pubmed: 30353927doi: 10.1111/age.12738google scholar: lookup
  20. McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population.. Sci Rep 2020 Jan 16;10(1):466.
    pmc: PMC6965197pubmed: 31949252doi: 10.1038/s41598-019-57389-5google scholar: lookup
  21. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF. Runs of homozygosity in European populations.. Am J Hum Genet 2008 Sep;83(3):359-72.
    pmc: PMC2556426pubmed: 18760389doi: 10.1016/j.ajhg.2008.08.007google scholar: lookup
  22. Meyermans R, Gorssen W, Buys N, Janssens S. How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species.. BMC Genomics 2020 Jan 29;21(1):94.
    pmc: PMC6990544pubmed: 31996125doi: 10.1186/s12864-020-6463-xgoogle scholar: lookup
  23. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals.. Genetics 1978 Jul;89(3):583-90.
    pmc: PMC1213855pubmed: 17248844doi: 10.1093/genetics/89.3.583google scholar: lookup
  24. Norton EM, Mickelson JR, Binns MM, Blott SC, Caputo P, Isgren CM, McCoy AM, Moore A, Piercy RJ, Swinburne JE, Vaudin M, McCue ME. Heritability of Recurrent Exertional Rhabdomyolysis in Standardbred and Thoroughbred Racehorses Derived From SNP Genotyping Data.. J Hered 2016 Nov;107(6):537-43.
    pmc: PMC5006745pubmed: 27489252doi: 10.1093/jhered/esw042google scholar: lookup
  25. Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data.. PLoS One 2013;8(1):e54997.
    pmc: PMC3559798pubmed: 23383025doi: 10.1371/journal.pone.0054997google scholar: lookup
  26. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses.. Am J Hum Genet 2007 Sep;81(3):559-75.
    pmc: PMC1950838pubmed: 17701901doi: 10.1086/519795google scholar: lookup
  27. R Core Team. R: a language and environment for statistical computing.. Vienna, Austria: R Foundation for Statistical Computing.
  28. Sereno FTP de S, Sereno JRB, Vega-Pla JL, Kelly L, Bermejo JVD. Genetic diversity of Brazilian Pantaneiro horse and relationships among horse breeds.. Pesqui Agropecu Brasil 43(5):595–604.
  29. Sevinga M, Vrijenhoek T, Hesselinks JW, Barkema HW, Groen AF. Effect of inbreeding on the incidence of retained placenta in Friesian horses.. J Anim Sci 2004 Apr;82(4):982-6.
    pubmed: 15080317doi: 10.2527/2004.824982xgoogle scholar: lookup
  30. van de Goor LH, van Haeringen WA, Lenstra JA. Population studies of 17 equine STR for forensic and phylogenetic analysis.. Anim Genet 2011 Dec;42(6):627-33.
    pubmed: 22035004doi: 10.1111/j.1365-2052.2011.02194.xgoogle scholar: lookup
  31. Wallace JH. Wallace’s American Trotting Register. Vol. 1.. New York: Geo. E. Woodward, Orange Judd & Co..
  32. Weir BS, Cockerham CC. ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE.. Evolution 1984 Nov;38(6):1358-1370.
    pubmed: 28563791doi: 10.1111/j.1558-5646.1984.tb05657.xgoogle scholar: lookup
  33. Wickham H. ggplot2—Elegant Graphics for Data Analysis. 2nd ed.. Cham (Switzerland): Springer International Publishing.
  34. Wright S. Evolution and the Genetics of Populations. Vol. 4.. Chicago: University of Chicago Press.

Citations

This article has been cited 2 times.
  1. Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A. The Genetic Diversity of Stallions of Different Breeds in Russia.. Genes (Basel) 2023 Jul 24;14(7).
    doi: 10.3390/genes14071511pubmed: 37510415google scholar: lookup
  2. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity.. Genes (Basel) 2022 Dec 2;13(12).
    doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
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