Animal genetics2026; 57(3); e70147; doi: 10.1002/age.70147

A Breed-Specific SNP Panel With Higher Theoretical Exclusion Power and Practical Equivalence to International Standards for Parentage Testing in Pura Raza Española Horses.

Laseca, N
·
Molina, A
·
Marshall, T
·
González, I
·
Poyato-Bonilla, J
·
Valera, M

Abstract: Accurate parentage assignment is essential for managing livestock breeding and genetic improvement. This study evaluated a breed-specific SNP panel (375 SNPs) for the Pura Raza Española (PRE) horse, comparing its performance against the traditional STR reference panel (18 microsatellite) and the international ISAG SNP core panel (378 SNPs) across population scenarios differing in levels of inbreeding and kinship. The PRE-specific SNPs were selected from the Axiom EQUIGENE array based on high genotyping reliability (call-rate > 99%), Mendelian error minimization, Hardy-Weinberg equilibrium (p > 0.05), minor allele frequency (MAF > 0.495) and linkage disequilibrium pruning. Using genomic data from 1000 individuals and random mating simulations via CERVUS software, we assessed non-exclusion probabilities (NEP) and assignment accuracy under idealized, current, and highly inbred population models using varying proportions of sampled candidate parents. Both SNP panels showed markedly higher theoretical power than the STR panel (3 × 10), with the PRE-specific panel achieving the lowest NEP (1.7 × 10). Simulation results confirmed that the PRE-specific and ISAG SNP core panels showed similar parentage assignment accuracy. In both cases, assignment rates approached the theoretical maxima imposed by candidate parent sampling proportions, regardless of inbreeding level. While the PRE-specific panel exhibited slightly lower theoretical non-exclusion probabilities, both panels provide a robust framework for parentage assignment in PRE horses. These results support transitioning to SNP-based technologies to enhance the integrity of genealogical records.

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Publication Date: 2026-06-12 PubMed ID: 42281386DOI: 10.1002/age.70147Google 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.

Accurate genetic parentage testing is crucial for breeding management in Pura Raza Española horses. This study developed and assessed a breed-specific SNP panel for parentage testing, demonstrating it performs equivalently or better than current international SNP and STR standards.

Introduction and Objective

Parentage assignment accuracy is vital for breeding management and genetic improvement in livestock.
The study focuses on the Pura Raza Española (PRE) horse breed.
Goal: develop a breed-specific single nucleotide polymorphism (SNP) panel and compare its performance to traditional microsatellite (STR) and international SNP panels for parentage testing.

Design and Methods

A breed-specific panel containing 375 SNPs was created from a larger SNP array called Axiom EQUIGENE.
SNPs were selected based on several quality criteria:
- High genotyping reliability with call rates above 99%.
- Minimal Mendelian inheritance errors.
- Conformance to Hardy-Weinberg equilibrium (p > 0.05).
- High minor allele frequency (MAF > 0.495) ensuring informative markers.
- Linkage disequilibrium pruning to reduce redundancy and ensure independence among markers.
Performance comparisons were made to:
- Traditional STR panel with 18 microsatellites.
- International Society for Animal Genetics (ISAG) core SNP panel with 378 SNPs.
Population scenarios simulated using genomic data from 1,000 PRE horses included:
- Idealized population with random mating.
- Current population with existing kinship levels.
- Highly inbred population model.
CERVUS software simulated different proportions of candidate parents sampled to assess assignment power.

Metrics Evaluated

Non-exclusion probability (NEP): the chance that a non-parent cannot be excluded as a parent, lower values indicate higher power.
Assignment accuracy: proportion of correct parentage assignments in simulations.

Key Findings

Both SNP panels (breed-specific and ISAG core) showed approximately 30-fold higher theoretical exclusion power than the STR panel.
The breed-specific PRE SNP panel had the lowest NEP (1.7 × 10^(-x), indicating very high exclusion power), slightly better than the ISAG SNP panel.
Simulation results showed that both SNP panels achieved nearly the theoretical maximum parentage assignment rates allowed by candidate parent sampling rates.
Assignment accuracy was consistent across all population inbreeding and kinship scenarios with either SNP panel.
The traditional STR panel underperformed compared to SNP panels in both theoretical and practical assignment metrics.

Implications and Conclusions

The breed-specific SNP panel is robust and at least equivalent to international SNP standards for parentage testing in PRE horses.
Higher exclusion power and reliability of SNP-based testing supports transitioning away from microsatellite STR methods.
Using this SNP panel can improve the integrity and accuracy of genealogical records, which benefits breeding decisions and genetic improvement programs.
Implementation of SNP technology enhances parentage verification under different population genetic scenarios, including high inbreeding.

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APA

Laseca N, Molina A, Marshall T, González I, Poyato-Bonilla J, Valera M. (2026). A Breed-Specific SNP Panel With Higher Theoretical Exclusion Power and Practical Equivalence to International Standards for Parentage Testing in Pura Raza Española Horses. Anim Genet, 57(3), e70147. https://doi.org/10.1002/age.70147

Publication

Animal genetics

ISSN: 1365-2052

NlmUniqueID: 8605704

Country: England

Language: English

Volume: 57

Issue: 3

Pages: e70147

Researcher Affiliations

Laseca, Nora

Department of Agronomy, Higher Technical School of Agronomic Engineering (ETSIA), University of Seville, Seville, Spain.

Molina, Antonio

Department of Genetics, University of Cordoba, Cordoba, Spain.

Marshall, Tristan

Field Genetics Ltd, London, UK.

González, Ismael

Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Sevilla, Spain.

Poyato-Bonilla, Julia

Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Sevilla, Spain.

Valera, Mercedes

Department of Agronomy, Higher Technical School of Agronomic Engineering (ETSIA), University of Seville, Seville, Spain.

Grant Funding

JDC2023-051241-I / Juan de la Cierva 2023 postdoctoral fellowship, AEI/10.13039/501100011033 and the European Social Fund Plus (FSE+)
PR202304988 / Research Foundation of the University of Seville (FIUS) and the Real Asociación Nacional de Criadores de Caballos de Pura Raza Española

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