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Table 5 The accuracy and bias of with-breed prediction of GBLUP, BayesR(BR), emBayesR (EM), and HyB_BR (HB)

From: A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping

  Milk yield Protein yield Fat% Fertility
Acc. Bias Acc. Bias Acc. Bias Acc. Bias
  Holstein reference to predict Holstein validation
GBLUP +Polya 0.57 0.96 0.63 0.98 0.73 0.96 0.43 1.26
-Polyb 0.56 0.86 0.59 0.87 0.71 1.15 0.42 1.27
BR +Polya 0.63 0.91 0.64 1.01 0.79 1.06 0.43 1.19
-Polyb 0.61 1.00 0.63 1.06 0.77 1.13 0.41 1.19
EM +Polya 0.62 0.79 0.63 0.85 0.77 0.98 0.42 1.15
-Polyb 0.62 0.92 0.62 0.94 0.74 1.06 0.41 1.15
HB +Polya 0.63 0.93 0.63 0.97 0.79 1.09 0.43 1.19
-Polyb 0.63 1.03 0.62 1.06 0.76 1.17 0.42 1.19
  Jersey reference to predict Jersey validation
GBLUP +Polya 0.59 0.93 0.65 0.91 0.54 0.71 0.15 1.05
-Polyb 0.58 1.05 0.64 1.09 0.54 0.77 0.14 1.08
BR +Polya 0.64 0.94 0.68 0.93 0.71 0.87 0.15 1.02
-Polyb 0.63 0.98 0.68 1.01 0.69 0.93 0.14 1.04
EM +Polya 0.64 0.87 0.68 0.92 0.69 0.75 0.15 1.09
-Polyb 0.64 0.98 0.66 1.01 0.67 0.79 0.15 1.09
HB +Polya 0.64 0.97 0.68 0.90 0.71 0.89 0.15 1.02
-Polyb 0.64 1.06 0.66 0.96 0.69 0.87 0.15 1.02
  1. ameans polygenic effects are included in the predictions; while bmeans the predictions do not include polygenic effects into the model