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Additional file 3: Table S2. Posterior mean number of SNPs in each distribution [0, 0.0001, 0.001 or 0.01 of the pedigree estimated genetic variance], data from Kemper et al. [1]

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Additional file 8: Figure S3. Genetic relationship between nine dairy and beef cattle breeds

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Additional file 1: Table S1. Phenotypic and genetic correlation between milk yield traits, with trait heritability from the pedigree-based multi-trait model

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Additional file 5: Table S4. This file contains highly significant SNPs (P < 1 × 10−6) from the mixed model analysis of the milk minerals and proteins

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Additional file 4: Table S3. Top 100 SNPs with the highest mean posterior probability (PP) for inclusion in the model from the Holstein/Jersey reference population using BayesMV [39–41]

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Additional file 7: Table S5. Genomic prediction accuracy and bias from the univariate GBLUP model, data from Kemper et al. [1]

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Additional file 2: Figure S1. Mean power and false-discovery rate for QTL discovery in simulated data for a single trait

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Additional file 6: Figure S2. Mean posterior probability for BayesMV and BayesR, and the −log10(P) association test statistic between SNP and potassium concentration on bovine chromosome 19 near KCNJ2