Horsemeat, known for its high nutritional value and lower environmental impact compared to beef, faces cultural and ethical challenges. Despite its potential, genetic research on horsemeat quality remains limited and no Quantitative Trait Loci (QTLs) have been identified. The aim of this study was to identify and prioritize Single Nucleotide Polymorphism (SNP) markers on the GeneSeek^® GenomicProfiler™ Equine chip for traits related to meat quality. Genes associated with meat quality were identified through a PubMEd search. These were analyzed for SNPs with potential regulatory or functional effects based on Genomic Evolutionary Rate Profiling (GERP) scores, constrained element locations, orthologous regulatory regions in mice and humans, and effects on polyadenylation, miRNA, and transcription factor binding. Further prioritization focused on genes whose orthologs are within QTLs for meat quality traits in other species. Including SNPs in linkage disequilibrium with chip markers from the Animal-SNPAtlas, we identified 27 SNP markers associated with 19 genes. Notable candidates include ALDOA, CS, GOT1, PLIN1, PYGM, and SDHB, linked to metabolic pathways, and MYL11, MYOM1, PDLIM5, RYR3, and TNNT3, associated with muscle structure and development. This research provides genetic insights to improve horsemeat quality and help breeders and smallholder farmers. Integrating these results with larger datasets can improve breeding value predictions and support effective breeding programs.

In small, closed populations such as the Lipizzan horse, maintaining genetic diversity while limiting inbreeding is a key challenge in conservation breeding. The Lipizzan is an indigenous Slovenian breed with a small population and restricted gene flow from other subpopulations. Inbreeding is traditionally monitored with pedigree-based coefficients, but these often underestimate realised autozygosity, particularly when pedigree depth is limited. This study compared pedigree-based inbreeding (F_PED) with four genomic estimators (F_HOM, F_ROH, F_HBD, F_GRM) in 329 Slovenian Lipizzan horses genotyped with a 70K SNP array. Data were processed in PLINK and R. Segment-based estimators (F_ROH, F_HBD) revealed higher inbreeding than F_PED and partitioned autozygosity into recent and distant components. F_ROH identified long homozygous segments reflecting recent inbreeding, whereas HBD classification showed that most autozygosity came from distant ancestors. Correlations between pedigree- and genomic-based coefficients were moderate (ρ = −0.18–0.56), while genomic estimators showed strong agreement. These results demonstrate that genomic measures complement pedigree-based metrics by providing a fuller picture of inbreeding and its temporal origin. Incorporating genomic estimators into routine monitoring can improve mate selection, reduce inbreeding depression, and support sustainable management of genetic diversity in the Lipizzan horse, while offering a case study for other small populations with conservation goals.