Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction

Table 6 Impact of the assumed variance of residual polygenic effects on DGV estimates for milk yield of reference bulls in the EuroGenomics reference population

Scenario regarding residual polygenic variance	Correlation of conventional EBV with		Variance of DGV/DGVt divided by variance of EBV
	DGV	DGVt^$	DGV	DGVt
M (0.02%)^!	0.95	0.95	0.95	0.96
A (5%)	0.90	0.96	0.57	0.94
B (10%)	0.87	0.97	0.47	0.95
C (20%)	0.84	0.98	0.36	0.96

^$ DGVt represents the sum of the estimate based on SNP effects (DGV) and the residual polygenic effect estimate; ^!M: the genomic model assumes a residual polygenic heritability of 0.0001 which is equivalent to a 0.02% residual polygenic variance for milk yield

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