Genome-wide association study and functional analysis of carcase and meat quality traits in double-muscled Piemontese cattle

Meat quality traits are important drivers of consumer acceptance and purchase intention. Recently, Piemontese meat was awarded the EU Protected Geographical Indication (PGI) status ‘Vitelloni Piemontesi della coscia’ which has increased the interest in improving the meat quality attributes for this breed. Therefore, aim of this study was to investigate the genomic regions and biological pathways controlling the variation in carcase and meat quality traits in double-muscled Piemontese cattle breed. We carried out genome-wide associations (GWAS) and pathway enrichment analyses for carcase traits (age at slaughtering [AS], carcase weight [CW], carcase daily gain [CDG], conformation score [EUS] and ribeye muscle area [REMA]) and meat quality traits (pH, Warner-Bratzler shear force [WBSF], purge loss [PL], cooking loss [CL] and colour parameters [lightness, L*; redness, a*; yellowness, b*; chroma, C*; hue, H*]) in a cohort of 1166 Piemontese young bulls. Animals were slaughtered at 539 days on average. Genotype data from the ‘GeneSeek Genomic Profiler Bovine LD’ array was used. A single marker regression model was applied for GWAS using the GenABEL R package and the GRAMMAR-GC approach. The functional enrichment analysis was conducted using the Cytoscape plugin ClueGo to identify signifi-cantly overrepresented pathways and ontologies (right-sided hypergeometric test with false discovery rate correction). In total, we identified 37 significant single nucleotide polymorphisms (SNPs), which were associated with 12 traits (p < 5 × 10−5). Notably, 14 SNPs associated with CW, CDG and AS were detected in the region at ~38.57–38.94 Mb on Bos taurus autosome (BTA) 6 and mapped within four genes, i.e. Leucine Aminopeptidase 3 (LAP3), Family with Sequence Similarity 184 Member B (FAM184B), Non-SMC Condensin I Complex Subunit G (NCAPG) and Ligand-Dependent Nuclear Receptor Corepressor-Like (LCORL). Significantly enriched GO terms and KEGG pathways were found for four meat quality parameters, i.e. a*, b*, C* and CL, and for two carcase traits, i.e. CW and EUS. In particular, pathways related to transmembrane transport (i.e. oxygen, cal-cium, ion and cation) were overrepresented for meat colour parameters. The information acquired might be useful for genomic selection programmes aimed at improving beef production and meat quality in the Piemontese breed.