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

Table 5 Impact of assumed variance of the residual polygenic effect on SNP effect estimates for milk yield based on the EuroGenomics reference population

Scenario regarding residual polygenic variance	Variance of SNP effect estimates^$	Estimate of the largest SNP effect^†	Correlation of SNP effect estimates between scenarios
			A (5%)	B (10%)	C (20%)
M (0.02%)^!	1	1	0.942	0.910	0.860
A (5%)	0.65	0.84		0.993	0.964
B (10%)	0.50	0.75			0.987
C (20%)	0.34	0.62

^$ variance of SNP effect estimates of the scenario with the lowest residual polygenic variance (0.2%) was set to 1; ^† estimate of the largest SNP effect when the lowest residual polygenic variance (0.2%) was set to 1; ^! M: the scenario with the lowest residual polygenic variance 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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