Accounting for dominance genetic variation in carcass quality traits of Canadian crossbred beef cattle

The objectives of this study were to evaluate the contribution of additive and dominance genetic effects to the phenotypic variation of carcass quality traits and to identify the underlying genetic variants associated with these traits. A total of 3958 Canadian crossbred beef cattle with phenotype and genotype data were used in two models: (1) additive and (2) joint additive and dominance genomic models that included fixed contemporary group, and covariates of slaughter age, and the eigenvectors of five principal components to account for population structure. Variance components and genome-wide association analyses were performed, and a 10% genome-wide false discovery rate (FDR) was applied to declare associations as significant. Genomic heritability ranged from 0.31 + 0.03 for ultrasound rib eye area to 0.46 + 0.05 for marbling score. Up to 10% dominance genetic variation was observed for ultrasound rib eye area and marbling score, indicating the contribution of dominance genetic effects to these trait variations. Eleven overlapping significant single-nucleotide polymorphism associations were identified across the studied traits and models. The identified candidate genes (e.g., BTC, SPP1, and SEPSECS) have biological functions related to tissue growth and skeletal muscle development and can be further validated in other cattle populations to determine their usefulness for beef cattle genetic improvement.