A Breed-Specific SNP Panel With Higher Theoretical Exclusion Power and Practical Equivalence to International...

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^-8), with the PRE-specific panel achieving the lowest NEP (1.7 × 10^-54). 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.