Detecting Pleiotropic Loci for Weight, Conformation, Precocity and Muscling Traits in Nellore Cattle (Bos indicus) Via Multi-Trait Meta-Analysis

Weight measurements and visual evaluations of conformation, precocity and muscling (CPM) are routinely employed in beef cattle selection for carcass yield in Brazil. The present study aimed at mapping pleiotropic loci affecting weight and CPM traits in Nellore cattle (Bos indicus). A dataset of 788 influential Nellore sires genotyped with the Illumina® BovineHD assay was used in the present study. These animals had deregressed breeding values available for the following traits: birth weight, pre-weaning gain, post-weaning gain, conformation at weaning, conformation at yearling, precocity at weaning, precocity at yearling, muscling at weaning, and muscling at yearling. The same model was fitted across traits: y ~ mean + SNP + animal + error. The animal and error terms were modeled as random effects, whereas markers were fitted as fixed effects. Three different approaches were applied in order to combine the results across traits: (1) the meta-analysis approach described by Bolormaa et al. (2014); (2) the classical Stouffer method for meta-analysis; (3) and use of the first principal component from an eigendecomposition of the phenotypic matrix as pseudo-phenotype in the regression analysis. The Stouffer method presented the lowest false discovery rate among all approaches (4.46%, p < 1 x 10^-5). The strongest association signal (p = 2.27 x 10^-10) was found on autosome 14, mapping to the PLAG1 region, which has been previously described to be associated with stature, weight gain and insulin-like growth factors in cattle. The enrichment analysis of 44 significant loci also points to pathways related to growth and the somatotropin hormone.