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Veterinary sciences2025; 12(9); 890; doi: 10.3390/vetsci12090890

Evaluation of the Effectiveness of Single-Nucleotide Polymorphisms Versus Microsatellites for Parentage Verification in Horse Breeds.

Abstract: This study aimed to generate information for parentage testing in horse breeds using microsatellites (STRs) and single-nucleotide polymorphisms (SNPs). Genotype data were obtained from 189 horse hair root samples, including 38 Thoroughbreds (TBs), 17 Jeju horses (JHs), 20 Quarter horses (QHs), 21 American Miniatures (AMs), and 93 Mongolian horses (MHs), using 15 STR markers and 71 SNP markers. Comparative analysis revealed that the mean expected heterozygosity ranged from 0.468 (AM) to 0.491 (JH) for SNPs and from 0.695 (TB) to 0.791 (MH) for STRs. The mean observed heterozygosity ranged from 0.415 (AM) to 0.487 (MH) for SNPs and from 0.706 (JH) to 0.776 (MH) for STRs. The mean polymorphic information content ranged from 0.349 (AM) to 0.364 (MH) for SNPs and from 0.635 (TB) to 0.761 (MH) for STRs. The inbreeding coefficient ranged from -0.009 (MH) to 0.113 (AM) for SNPs and from -0.058 (TB) to 0.043 (AM) for STRs. The cumulative exclusion probability (PE) for the 71-SNP panel exceeded 0.9999, indicating that SNP markers may be sufficient for parentage testing. In comparison, the STR markers yielded a combined PE of 0.9988 when one parent was known and 0.9999 when both parents were known. These findings highlight the potential of SNPs as alternatives to STRs for routine paternity verification in horses.
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Publication Date: 2025-09-15 PubMed ID: 41012816PubMed Central: PMC12474383DOI: 10.3390/vetsci12090890Google 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.

Overview

  • This study compared the effectiveness of two genetic marker types—single-nucleotide polymorphisms (SNPs) and microsatellites (STRs)—for verifying parentage in various horse breeds.
  • The research analyzed genetic data from 189 horses across five breeds to assess which marker type is more reliable and informative for parentage testing.

Background and Objective

  • Parentage verification in horses is essential for breed registries, pedigree verification, and breeding management.
  • Microsatellites (STRs) have traditionally been used for this purpose due to their high variability.
  • Single-nucleotide polymorphisms (SNPs) are newer genetic markers that offer the advantages of being more abundant, stable, and easier to automate in genotyping assays.
  • The study’s goal was to compare the effectiveness of SNPs versus STRs in verifying parentage across multiple horse breeds, to see if SNPs could serve as reliable alternatives in routine testing.

Materials and Methods

  • Collected hair root samples from 189 horses representing five breeds:
    • 38 Thoroughbreds (TB)
    • 17 Jeju horses (JH)
    • 20 Quarter horses (QH)
    • 21 American Miniature horses (AM)
    • 93 Mongolian horses (MH)
  • Genotyping was performed using:
    • 15 microsatellite (STR) markers
    • 71 SNP markers
  • Several genetic diversity and informativeness parameters were calculated for each breed and marker type, including:
    • Expected heterozygosity (He) – the likelihood of finding different alleles at a locus in the population
    • Observed heterozygosity (Ho) – actual proportion of heterozygous individuals
    • Polymorphic information content (PIC) – a measure of marker informativeness for parentage testing
    • Inbreeding coefficient (F) – estimate of inbreeding level within the population
    • Cumulative exclusion probability (PE) – probability that a marker set excludes a non-parent in parentage testing

Results: Genetic Diversity and Marker Informativeness

  • Expected Heterozygosity (He):
    • SNP markers: ranged from 0.468 (AM) to 0.491 (JH), indicating moderate genetic variability.
    • STR markers: higher variability ranging from 0.695 (TB) to 0.791 (MH), consistent with STRs’ known high polymorphism.
  • Observed Heterozygosity (Ho):
    • SNP markers: ranged from 0.415 (AM) to 0.487 (MH).
    • STR markers: higher values from 0.706 (JH) to 0.776 (MH), showing more actual genetic variation observed in the samples.
  • Polymorphic Information Content (PIC):
    • SNP markers: relatively low PIC ranging from 0.349 (AM) to 0.364 (MH), reflecting lower individual marker informativeness.
    • STR markers: higher PIC values from 0.635 (TB) to 0.761 (MH), indicating greater usefulness per locus for discrimination.
  • Inbreeding Coefficient (F):
    • SNPs: Values ranged from -0.009 (MH) suggesting slight outbreeding to 0.113 (AM) suggesting some inbreeding.
    • STRs: Values were between -0.058 (TB) and 0.043 (AM), similarly indicating populations mostly at or slightly above Hardy-Weinberg equilibrium.

Results: Parentage Verification Power

  • Cumulative Exclusion Probability (PE):
    • The 71-SNP panel showed a cumulative PE greater than 0.9999, meaning it can exclude incorrect parents with very high confidence.
    • The 15 STR markers had a combined PE of 0.9988 when only one parent’s genotype was known and reached 0.9999 when both parents were available.
    • This indicates that the large SNP panel is at least as powerful as the STR panel for parentage verification, especially when one parent is unknown.

Conclusions and Implications

  • Despite STR markers exhibiting higher genetic diversity and informativeness per locus, the large SNP panel compensates with the sheer number of markers.
  • SNP markers provide extremely high exclusion probabilities, making them reliable for parentage testing in horses.
  • SNPs have practical benefits such as easier standardization, reproducibility, and potential for automation, which support their use as alternatives to STRs.
  • The study supports adopting SNP-based parentage verification methods in horse breeding and registry applications to improve efficiency and accuracy.

Cite This Article

APA
Kim D, Lee S, Oyungerel B, Cho G. (2025). Evaluation of the Effectiveness of Single-Nucleotide Polymorphisms Versus Microsatellites for Parentage Verification in Horse Breeds. Vet Sci, 12(9), 890. https://doi.org/10.3390/vetsci12090890

Publication

Veterinary sciences
ISSN: 2306-7381
NlmUniqueID: 101680127
Country: Switzerland
Language: English
Volume: 12
Issue: 9
PII: 890

Researcher Affiliations

Kim, Dongsoo
  • College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea.
Lee, Sunyoung
  • Racing Laboratory, Korea Racing Authority, Gwacheon 13822, Republic of Korea.
Oyungerel, Baatartsogt
  • School of Animal Science and Biotechnology, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia.
Cho, Giljae
  • College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea.

Conflict of Interest Statement

The authors declare no conflicts of interest.

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