Table 1.

Genome scan for milk production traits in a daughter design of 1,941 dairy goats, based on haplotype-based linkage analyses.

CH I	Trait	Breed	Significance level	LRT	Position (Mb)	95% –CI (min max)	Substitution effect	Candidate genes
1	PC	Alpine	***	41.6	1.382	1.362–1.449	0.36	PDE9A
1	PC	All	**	51.8	1.418	1.404–1.434	0.30
2	FY	All	**	51.8	0.239	0.237–0.241	0.33
5	PC	Saanen	**	31.5	0.205	0.196–0.224	0.32
6	FC	All	***	66.2	0.764	0.743–0.812	0.32
6	FC	Saanen	***	44.3	0.805	0.746–0.872	0.44	Caseins cluster
6	PC	Alpine	***	62.5	0.814	0.786–0.848	0.37	Caseins cluster
6	PC	All	***	161.3	0.824	0.792–0.842	0.50	Caseins cluster
6	PC	Saanen	***	99.6	0.824	0.791–0.845	0.66	Caseins cluster
7	FC	Alpine	**	36.8	0.037	0.013–0.042	0.30	SLC27A1
11	PC	Alpine	**	39.9	0.900	0.887–0.906	0.35	PAEP
14	FY	Alpine	***	39.9	0.034	0.025–0.046	0.30
14	FY	All	**	53.8	0.037	0.025–0.048	0.28
14	FC	All	***	126.2	0.111	0.092–0.124	0.48	DGAT1
14	FC	Saanen	***	60.8	0.123	0.092–0.143	0.50
14	FC	Alpine	***	70.8	0.155	0.146–0.160	0.42
19	PY	All	**	52.3	0.285	0.248–0.290	0.27	PLD2 GGT6 ALOX12, ALOX 12B, ALOX 15
21	FC	All	**	52.0	0.554	0.526–0.576	0.27
21	FC	Alpine	**	37.2	0.571	0.538–0.588	0.27
21	PC	All	**	49.9	0.578	0.570–0.585	0.27
21	PY	All	***	58.0	0.634	0.627–0.640	0.31
21	MY	All	**	53.2	0.635	0.627–0.642	0.29
25	FC	Saanen	**	32.4	0.101	0.099–0.103	0.35
28	PC	Alpine	**	33.7	0.322	0.295–0.361	0.31

Significance level: ***: 5% genome-wide; ** 1% chromosome-wide. The 95% confidence intervals of the QTL locations were estimated by logarithm of odds drop-off.