Table 2.

Estimates of two haplotype effects fitted individually or jointly in the model

Trait	M1 = breed + HAP1 + Animal		M2 = breed + HAP2 + Animal		M3 = breed + HAP1 + HAP2 + Animal
	Eff. HAP1	SE. HAP1	Eff. HAP2	SE. HAP2	Eff. HAP1	SE. HAP1	Eff. HAP2	SE. HAP2
Stature	5.09	0.40	3.84	0.22	5.89	0.39	4.10	0.22
Body depth	2.69	0.49	2.84	0.29	3.20	0.49	3.00	0.29
Chest width	3.64	0.51	3.36	0.31	4.32	0.51	3.59	0.31
Dairy form	0.61	0.43	0.48	0.26	0.69	0.43	0.52	0.26
Rump width	2.88	0.45	3.52	0.28	3.49	0.45	3.72	0.28
Rump angle	−0.23	0.44	−0.62	0.27	−0.26	0.45	−0.64	0.27
SCEF	−5.97	0.32	−2.6	0.16	−6.54	0.31	−2.84	0.15
SCEL	−6.85	0.36	−2.75	0.18	−7.46	0.35	−3.03	0.17
SSBF	−5.86	0.48	−3.66	0.24	−6.58	0.47	−3.90	0.24
SSBL	−5.35	0.47	−2.90	0.24	−5.96	0.46	−3.12	0.24
SCSF	5.74	0.29	2.07	0.14	6.23	0.28	2.30	0.14
SCSL	6.05	0.28	1.88	0.14	6.51	0.27	2.12	0.13
SCI	−6.78	0.49	−3.78	0.25	−7.54	0.48	−4.05	0.24
BCI	4.79	0.41	4.36	0.24	5.66	0.39	4.65	0.24

SNP from the LCORL gene exhibiting the most significant association with calf size were used for constructing HAP1. SNPs indicating the most significant association with body conformation were used to construct HAP2.