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

Table 3 Impact of reference population size on the SNP effect estimates for milk yield

Phenotypic data of milk yield from conventional evaluations	Nb of reference bulls	Variance of SNP effect estimates^§	Estimate of largest SNP effect^$	Correlation of SNP effect estimates between evaluations
				B	C	D	E	F	G	H
January 2009	735 (A)	1	1	0.81	0.56	0.50	0.46	0.43	0.41	0.41
April 2009	1088 (B)	1.49	1.46		0.69	0.61	0.55	0.53	0.50	0.50
	1939 (C)	2.61	2.45			0.83	0.72	0.69	0.65	0.65
	3081 (D)	3.71	3.10				0.86	0.84	0.79	0.78
August 2009	3684 (E)	4.38	3.63					0.95	0.88	0.87
	4339 (F)	4.78	3.90						0.92	0.92
January 2010	4896 (G)	5.12	4.10							0.98
February 2010	5025 (H)	5.22	4.13

^§Variance of SNP effect estimates of reference population A is set to 1; ^$the largest (same) SNP effect estimate for the first reference population A is set to 1

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