Genomic Prediction and Association Analysis with Models Including Dominance Effects for Important Traits in Chinese Simmental Beef Cattle

SIMPLE SUMMARY: Dominance effects play important roles in determining genetic changes with regard to complex traits. We conducted genomic predictions and genome-wide association studies in order to investigate the effects of dominance on carcass weight, dressing percentage, meat percentage, average daily gain, and chuck roll in 1233 Simmental beef cattle. Using dominance models, we improved the predictive abilities and found several candidate single-nucleotide polymorphisms (SNPs) and genes associated with these traits. Our studies helped us to understand causal mutation mapping and genomic selection models with dominance effects in Chinese Simmental beef cattle. ABSTRACT: Non-additive effects play important roles in determining genetic changes with regard to complex traits; however, such effects are usually ignored in genetic evaluation and quantitative trait locus (QTL) mapping analysis. In this study, a two-component genome-based restricted maximum likelihood (GREML) was applied to obtain the additive genetic variance and dominance variance for carcass weight (CW), dressing percentage (DP), meat percentage (MP), average daily gain (ADG), and chuck roll (CR) in 1233 Simmental beef cattle. We estimated predictive abilities using additive models (genomic best linear unbiased prediction (GBLUP) and BayesA) and dominance models (GBLUP-D and BayesAD). Moreover, genome-wide association studies (GWAS) considering both additive and dominance effects were performed using a multi-locus mixed-model (MLMM) approach. We found that the estimated dominance variances accounted for 15.8%, 16.1%, 5.1%, 4.2%, and 9.7% of the total phenotypic variance for CW, DP, MP, ADG, and CR, respectively. Compared with BayesA and GBLUP, we observed 0.5–1.1% increases in predictive abilities of BayesAD and 0.5–0.9% increases in predictive abilities of GBLUP-D, respectively. Notably, we identified a dominance association signal for carcass weight within RIMS2, a candidate gene that has been associated with carcass weight in beef cattle. Our results suggest that dominance effects yield variable degrees of contribution to the total genetic variance of the studied traits in Simmental beef cattle. BayesAD and GBLUP-D are convenient models for the improvement of genomic prediction, and the detection of QTLs using a dominance model shows promise for use in GWAS in cattle.