Table 3.

The multi-breed prediction accuracy and bias of GBLUP, BayesR, and HyB_BR on SEQ data related to Fat Yield, Milk Yield, Protein Yield, Fat%, Protein% and Fertility

		Holstein and Jersey reference to predict Holstein validation
		Fat Yield		Milk Yield		Protein Yield		Fat%		Protein%		Fertility
		Acc.	Bias	Acc.	Bias	Acc.	Bias	Acc.	Bias	Acc.	Bias	Acc.	Bias
GBLUP	+Polya	0.64	1.07	0.66	0.92	0.63	0.95	0.76	0.95	0.83	0.98	0.42	1.70
	-Polyb	0.62	1.32	0.60	0.83	0.58	1.15	0.75	1.01	0.81	1.09	0.42	1.70
BayesR	+Polya	0.65	1.27	0.69	0.91	0.68	1.04	0.81	1.01	0.83	0.99	0.42	1.32
	-Polyb	0.63	1.17	0.67	0.85	0.65	0.91	0.80	1.01	0.82	0.96	0.42	1.32
HyB_BR	+Polya	0.66	1.04	0.69	0.89	0.68	0.96	0.81	0.99	0.83	0.96	0.42	1.32
	-Polyb	0.63	0.96	0.69	0.89	0.66	0.88	0.81	0.99	0.81	0.94	0.42	1.32
		Holstein and Jersey reference to predict Jersey validation
		Fat Yield		Milk Yield		Protein Yield		Fat%		Protein%		Fertility
		Acc.	Bias	Acc.	Bias	Acc.	Bias	Acc.	Bias	Acc.	Bias	Acc.	Bias
GBLUP	+Polya	0.54	0.76	0.65	0.88	0.69	0.94	0.67	0.86	0.77	0.94	0.23	1.13
	-Polyb	0.52	0.93	0.65	1.03	0.68	1.24	0.66	0.93	0.75	1.02	0.23	1.13
BayesR	+Polya	0.57	0.88	0.70	0.96	0.72	1.22	0.77	0.97	0.77	0.89	0.23	1.03
	-Polyb	0.52	0.73	0.68	0.87	0.67	1.02	0.76	0.95	0.77	0.87	0.23	1.02
HyB_BR	+Polya	0.58	0.87	0.69	0.95	0.73	0.91	0.77	0.93	0.79	0.87	0.23	0.97
	-Polyb	0.57	0.74	0.69	0.85	0.73	0.91	0.76	0.93	0.78	0.85	0.23	0.97

The bulls and cows from two breeds of Holstein and Jersey are used as the reference set to predict Holstein bulls and Jersey bulls separately. ^aThe prediction accuracy when adding the polygenic term in the model; while^bis the prediction accuracy when leaving out the polygenic term from the model