Exploring Genetic Influences on Equine Meat Quality: A Bioinformatics Approach

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 <i>ALDOA</i>, <i>CS</i>, <i>GOT1</i>, <i>PLIN1</i>, <i>PYGM</i>, and <i>SDHB</i>, linked to metabolic pathways, and <i>MYL11</i>, <i>MYOM1</i>, <i>PDLIM5</i>, <i>RYR3</i>, and <i>TNNT3</i>, 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.