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Animal genetics2024; doi: 10.1111/age.13408

Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses.

Abstract: The International Society for Animal Genetics (ISAG) currently advocates for a transition towards single nucleotide polymorphism (SNP) markers as a potential alternative for equine parentage verification. To ascertain the efficacy of this transition, it is imperative to evaluate the performance of parentage testing using SNPs in juxtaposition with short tandem repeats (STRs). As per ISAG's recommendation, we used an equine genotyping-by-sequencing panel with 144 SNPs for this purpose. Equine parentage is currently realized using 16 microsatellites (STRs) excluding the LEX3 marker. In this study, 1074 horses were genotyped using the 144 SNPs panel, including 432 foals, 414 mares, and 228 stallions, from five different breeds: 293 Arabians, 167 Barbs, 189 Thoroughbreds, 73 Anglo-Arabians, and 352 Arabian-Barbs. As a result, two SNPs markers were eliminated from the panel system due to inconsistent amplification across all examined individuals leaving 142 SNPs markers for analysis. A comparative analysis between SNPs and STRs markers revealed that the mean expected heterozygosity was 0.457 for SNPs and 0.76 for STRs, while the mean observed heterozygosity stood at 0.472 for SNPs and 0.72 for STRs. Furthermore, the probability of identity was calculated to be 5.722 × 10 for SNPs and 1.25 × 10 for STRs markers. In alignment with the Hardy-Weinberg equilibrium in polyploids test, 110 out of the total SNPs were consistent with the Hardy-Weinberg equilibrium in polyploids test (p > 0.05). Employing both SNPs and STRs markers, the mean polymorphic information content was discerned to be 0.351 for SNPs and 0.72 for STRs. The cumulative exclusion probabilities for SNP markers exceeded 99.99%, indicating that the 142 SNPs panel might be adequate for parentage testing. In contrast, when utilizing STRs markers, the combined average exclusion probabilities for one and both parents were determined to be 99.8% and 99.9%, respectively. Our comprehensive study underscores the potential of SNPs in equine parentage verification, especially when compared to STRs in terms of exclusion probabilities. As a corollary, the application of SNPs for parentage verification and identification can significantly contribute to the conservation initiative for the five Moroccan horse breeds. Nonetheless, further research is required to address and replace the deficient SNPs within the panel.
© 2024 Stichting International Foundation for Animal Genetics.
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Publication Date: 2024-02-21 PubMed ID: 38383954DOI: 10.1111/age.13408Google 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.

This study explores the efficiency of single nucleotide polymorphisms (SNPs) as an alternative to microsatellite markers for verifying parentage in Moroccan horses, finding that the cumulative exclusion probabilities for SNP markers exceeded 99.99%, indicating that the SNPs might be adequate for parentage testing.

Introduction and Context

  • The study is aimed at examining the effectiveness of single nucleotide polymorphisms (SNPs) for parentage verification in horses, as compared to microsatellite markers or short tandem repeats (STRs).
  • The International Society for Animal Genetics (ISAG) has suggested a shift towards the use of SNP markers for this purpose. To evaluate the efficiency of this proposed change, this study compared the results of parentage tests using SNPs versus STRs.

Methods

  • The researchers used an equine genotyping-by-sequencing panel consisting of 144 SNPs for the study, following ISAG’s recommendation. Currently, equine parentage is verified using 16 STRs.
  • A total of 1074 horses comprising of 432 foals, 414 mares, and 228 stallions from five different breeds were genotyped using this SNP panel.
  • In the course of the study, two SNP markers were discarded due to inconsistent amplification across examined individuals, leaving 142 remaining SNP markers for analyses.

Results

  • The comparative analysis revealed varying values between SNPs and STRs regarding mean expected heterozygosity, mean observed heterozygosity, and the probability of identity.
  • Out of the total SNPs, 110 were found to be consistent with the Hardy-Weinberg equilibrium in polyploids test (a principle critical for the study of population genetics).
  • The mean polymorphic information content for SNPs and STRs was also determined, with the results favoring STRs.
  • Notably, cumulative exclusion probabilities for SNP markers exceeded 99.9%, suggesting SNP utility for parentage testing. In comparison, the mean exclusion probabilities for STRs were 99.8% for one parent and 99.9% for both parents.

Conclusion

  • The findings underscore the potential of SNPs for equine parentage verification, particularly concerning exclusion probabilities.
  • The study suggests that using SNPs for parentage verification and identification could significantly benefit conservation initiatives for the five Moroccan horse breeds tested.
  • However, it also highlights that additional research is necessary to address and replace the deficient SNPs within the panel.

Cite This Article

APA
Aminou O, Badaoui B, Machmoum M, Piro M. (2024). Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses. Anim Genet. https://doi.org/10.1111/age.13408

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English

Researcher Affiliations

Aminou, O
  • Veterinary Genetic Analysis Laboratory, Hassan II Agronomic and Veterinary Institute, Rabat, Morocco.
Badaoui, B
  • Biodiversity, Ecology and Genome Laboratory, Mohammed V University, Faculty of Sciences, Rabat, Morocco.
  • African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco.
Machmoum, M
  • Veterinary Genetic Analysis Laboratory, Hassan II Agronomic and Veterinary Institute, Rabat, Morocco.
Piro, M
  • Veterinary Genetic Analysis Laboratory, Hassan II Agronomic and Veterinary Institute, Rabat, Morocco.

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Citations

This article has been cited 5 times.
  1. Yin D, Zhang H, Tang M, Que J, Lin D, Ying C, Zhang J, Yu J, Liu K. Genome-Wide Development and Validation of KASP-Based SNP Markers in Neophocaena asiaeorientalis asiaeorientalis. Animals (Basel) 2026 Feb 3;16(3).
    doi: 10.3390/ani16030475pubmed: 41681456google scholar: lookup
  2. Kim D, Lee S, Oyungerel B, Cho G. Evaluation of the Effectiveness of Single-Nucleotide Polymorphisms Versus Microsatellites for Parentage Verification in Horse Breeds. Vet Sci 2025 Sep 15;12(9).
    doi: 10.3390/vetsci12090890pubmed: 41012816google scholar: lookup
  3. Tang M, Yin D, Que J, Lin D, Ying C, Liu J, Liu F, Wang P, Li W, Yu J, Liu K. Development and Validation of Tetranucleotide Repeat Microsatellite Markers at the Whole-Genome Level in the Yangtze Finless Porpoise. Animals (Basel) 2025 Sep 4;15(17).
    doi: 10.3390/ani15172603pubmed: 40941398google scholar: lookup
  4. Wang Y, Tang C, Xue P, Yang N, Sun X, Serik K, Assanbayer T, Shamekova M, Kozhanov Z, Sapakhova Z, Khurramovich JK, Zhou X, Kairat I, Muhatai G. Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses. Genes (Basel) 2025 Feb 27;16(3).
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  5. Valera M, Karlau A, Anaya G, Bugno-Poniewierska M, Molina A, Encina A, Azor PJ, Demyda-Peyrás S. The Use of Genomic Screening for the Detection of Chromosomal Abnormalities in the Domestic Horse: Five New Cases of 65,XXY Syndrome in the Pura Raza Español Breed. Animals (Basel) 2024 Sep 3;14(17).
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