Table 2.

Effects of the polymorphisms on the bulls' breeding values for the quantitative traits with each marker analyzed separately

			Quantitative traits
Marker	Number of bulls	Frequency of the more common allele	Milk	Fat	Protein	% Fat	% Protein
BM143^a	346	55.1	-34	0.7	-3.5^**	0.019	-0.022^*
MLR1	298	50.5	-67	-2.8	0.7	-0.005	0.025^*
MED28	316	57.2	80	6.0^***	4.4^***	0.031	0.018^*
LAP3	341	57.3	13	6.1^**	4.7^***	0.053^**	0.039^****
IBSP	336	61.3	-35	1.1	0.6	0.021	0.015
SPP1(1)	366	57.0	-123^**	-0.1	0.8	0.039^*	0.043^****
SPP1(2)	309	72.9	-171^**	-0.7	1.4	0.048^*	0.061^****
PKD2	326	67.1	-141^**	0.6	0.9	0.046^*	0.048^****
ABCG2(2)^b	335	80.5	-341^****	5.3^*	4.1^**	0.159^****	0.135^****
ABCG2(1)	282	55.4	-67	0.8	2.4	0.029	0.042^****
PPMIK	369	73.6	-58	-1.7	1.8	0.001	0.033^**
HERC6	328	67.9	-14	4.9^**	5.6^****	0.049^**	0.056^****
FAM13A1(1)	381	81.8	-64	0.3	1.1	0.023	0.028^*
FAM13A1(2)	370	41.1	-107^*	2.0	1.2	0.053^**	0.042^****

Significance: ^*, p < 0.05; ^**, p < 0.01; ^***, p < 0.001; ^****, p < 0.0001.

For all the other markers, the effects were computed relative to the allele in LD association with the + allele for ABCG2(2).

This microsatellite was analyzed as a diallelic marker as described in the Supplemental data

For ABCG2(2) effects were computed relative to the Y581 allele. This allele, denoted the + allele, was associated with increased protein concentration