Comparative accuracies of genetic values predicted for economically important milk traits, genome-wide association, and linkage disequilibrium patterns of Canadian Holstein cows

Genomic selection methodologies and genome-wide association studies use powerful statistical procedures that correlate large amounts of high-density SNP genotypes phenotypic data. Actual 305-d milk (MY), fat (FY), protein (PY) yield data on 695 cows 76,355 genotyping-by-sequencing-generated marker from Canadian Holstein dairy were used to characterize linkage disequilibrium (LD) structure cows. Also, the comparison pedigree-based BLUP, genomic BLUP (GBLUP), Bayesian (BayesB) methods in ridge regression BayesB carried out for MY, FY, PY. Results LD analysis revealed as distance decreases, increases through chromosomes. However, unexpected high peaks observed between pairs with larger distances all The GBLUP models resulted similar heritability estimates 10-fold cross-validation MY PY; however, model higher than FY. predictive ability was significantly lower Association analyses indicated 28 high-effect markers Bos taurus autosome 14 located within 6 genes (DOP1B, TONSL, CPSF1, ADCK5, PARP10, GRINA) associated