Table 3.

QTL identified for milk mineral and citrate content on Bos taurus (BTA) autosomes 1 to 10 (when a QTL region affected multiple traits, the most significantly affected trait is indicated in bold).

Region	QTL	Trait	BTA	Confidence Interval of the QTL				Variant with the most significant effect (frequency p and effect b of the ALT allele)
				From (bp)	To (bp)	# variants	# genes	Position (bp)	ID	p	R2	−log10P	b	SE	Name of gene(s)	Impact
1	1	P	1	135,384,680	136,262,601	8	3	136,262,601	rs210630730	0.199	0.69	11.5	8.57	1.23	TMEM108	Intron
2	4	Mg	1	142,826,156	142,837,365	9	1	142,834,737	rs109459130	0.576	0.85	64.1	1.48	0.09	SLC37A1	Intron
2	5	P	1	142,826,156	142,835,551	7	1	142,834,737	rs109459130	0.576	0.85	219.3	30.2	0.95	SLC37A1	Intron
2	6	K	1	142,826,156	142,838,477	31	1	142,835,551	rs109717634	0.613	1.00	138.1	22.4	0.89	SLC37A1	Intron
2	7	Na	1	142,826,156	142,835,551	7	1	142,835,551	rs109717634	0.613	1.00	19.5	− 3.77	0.41	SLC37A1	Intron
3	9	Mg	1	145,114,056	146,804,023	64	3	146,775,338	rs43048006	0.630	0.33	10.3	− 0.70	0.11	–	–
4	11	Na	2	5,738,340	7,483,560	104	7	5,739,439	rs209271012	0.111	0.86	10.4	3.85	0.58	LOC104971101	lncRNA
5	12	Na	2	131,111,763	131,742,987	206	9	131,197,793	rs133533873	0.672	0.99	13.8	2.84	0.37	ALPL	Intron
6	13	Na	3	15,459,107	15,540,579	7	6	15,470,670	rs110073735	0.026	0.92	8.9	− 5.20	0.86	EFNA1 / LOC107132270	Intron / lncRNA
7	14	Ca	4	48,711,128	48,835,496	22	4	48,711,294	rs381111559	0.291	0.59	13.0	− 10.5	1.42	SLC26A4	Intron
8	15	Na	4	75,153,659	77,188,370	14	7	77,147,308	rs386097640	0.024	0.87	9.5	6.65	1.06	GCK	Intron
8	16	Ca	4	77,147,308	77,257,775	9	7	77,173,366	rs133824313	0.025	0.98	9.1	14.8	2.40	GCK	Intron
8	17	Mg	4	77,037,103	77,188,370	8	4	77,173,366	rs133824313	0.025	0.98	11.1	1.34	0.20	GCK	Intron
9	18	Ca	4	91,807,789	92,192,288	182	6	92,192,288	rs42451422	0.028	0.95	9.5	13.4	2.13	LRRC4 / SND1	Intron / Intron
10	19	Ca	5	108,256,181	109,217,271	87	11	109,141,258	rs383141568	0.570	0.82	8.4	5.73	0.98	BID	Intron
11	20	Ca	5	111,637,039	111,848,859	47	7	111,745,513	rs384814366	0.231	0.94	16.6	− 9.38	1.11	MRTFA = MKL1	Intron
12	21	Ca	5	116,403,262	116,463,104	48	8	116,429,840	rs382268272	0.049	0.58	60.5	− 34.8	2.11	LOC101903383	lncRNA
12	22	Na	5	116,403,262	116,907,862	72	17	116,429,922	rs110716509	0.050	0.67	9.3	5.05	0.81	LOC101903383	lncRNA
12	23	Citrate	5	116,403,262	116,468,630	50	8	116,439,760	rs110048000	0.042	0.56	9.5	− 0.25	0.04	PPARA	Intron
12	24	Mg	5	116,403,806	116,463,104	36	6	116,448,403	rs110659119	0.048	0.97	24.2	− 1.38	0.13	PPARA	Intron
12	25	P	5	116,420,172	117,323,874	28	5	116,448,403	rs110659119	0.048	0.97	19.5	− 13.5	1.46	PPARA	Intron
13	26	Ca	5	119,066,644	119,069,138	25	1	119,068,337	rs134583661	0.046	0.95	48.4	− 24.8	1.69	–	Intergenic
13	27	Mg	5	119,066,644	119,069,138	25	1	119,068,337	rs134583661	0.046	0.95	20.1	− 1.29	0.14	–	Intergenic
13	28	P	5	119,066,644	119,069,138	25	1	119,068,337	rs134583661	0.046	0.95	17.9	− 13.2	1.50	–	Intergenic
14	29	K	6	40,012,262	40,518,049	18	2	40,024,540	rs43610452	0.064	0.99	11.7	− 11.6	1.66	SLIT2	Intron
15	30	P	6	42,855,236	43,032,274	17	3	42,870,371	rs42610629	0.523	0.97	9.2	5.59	0.91	–	Intergenic
16	31	K	6	43,297,568	43,322,676	12	1	43,322,676	rs43463132	0.778	0.97	40.7	13.2	0.98	–	Intergenic
17	32	P	6	45,018,531	45,401,570	78	4	45,056,055	rs378008740	0.713	0.76	30.6	12.7	1.09	–	Intergenic
17	33	K	6	45,018,882	45,401,570	66	4	45,328,581	rs135848932	0.174	1.00	120.0	− 27.4	1.17	SEL1L3	Intron
17	34	Ca	6	45,328,392	45,411,116	17	4	45,393,335	rs134399380	0.183	0.91	8.6	7.24	1.22	–	Intergenic
17	35	Na	6	45,215,035	45,401,570	17	4	45,401,485	rs108972810	0.177	0.99	10.2	− 3.39	0.52	SMIM20 / LOC112447060	Upstream BS DOF5.3 / lncRNA
18	36	K	6	47,687,737	49,094,600	79	1	48,145,964	rs43461552	0.336	0.92	26.9	− 10.6	0.98	–	Intergenic
19	37	K	6	50,277,420	51,315,936	82	2	51,311,430	rs110769289	0.555	0.53	9.1	− 5.72	0.93	–	Intergenic
20	38	K	6	56,960,135	56,970,541	6	1	56,968,022	rs134533189	0.091	0.41	9.4	− 8.37	1.34	RELL1	Intron
21	39	Na	6	85,409,619	86,104,900	312	15	85,512,651	rs110772556	0.660	0.98	8.6	2.79	0.47	–	Intergenic
21	40	Mg	6	85,587,260	85,599,456	41	2	85,594,649	rs209134503	0.481	0.85	29.8	− 1.09	0.10	ODAM	Synonymous
21	41	Ca	6	85,406,891	85,599,456	44	5	85,594,717	rs135113545	0.485	0.79	17.0	− 10.6	1.24	ODAM	Intron
21	42	P	6	85,564,407	87,276,896	1004	6	87,033,142	rs110121930	0.613	1.00	12.3	− 7.88	1.09	–	Intergenic
22	43	Mg	6	88,380,434	88,436,951	4	1	88,390,406	rs133413027	0.252	0.99	9.8	− 0.56	0.09	–	Intergenic
23	44	Citrate	6	117,331,679	117,456,476	30	7	117,407,851	rs43489995	0.306	0.30	10.4	0.22	0.03	TMEM175 / DGKQ	Downstream / Synonymous
23	45	Ca	6	117,331,679	117,457,454	42	6	117,442,167	–	0.407	0.41	19.8	12.7	1.37	GAK	Intron
24	46	Na	7	1,055,458	1,365,056	387	3	1,057,563	rs210648426	0.346	0.91	14.3	− 2.85	0.36	RASGEF1C	Intron
25	47	Ca	7	37,353,946	39,223,460	24	16	39,194,875	rs41567828	0.068	0.99	9.1	12.8	2.08	LOC107132625	lncRNA
25	48	P	7	38,917,914	40,541,631	10	5	40,541,609	rs1116258782	0.009	0.22	16.9	31.7	3.71	–	Intergenic
25	49	Ca	7	39,528,343	42,832,365	179	16	41,321,781	rs209051255	0.059	0.76	11.6	18.4	2.63	ENSBTAG00000053872	Upstream BS FOXD3
26	50	Ca	7	43,090,012	44,848,268	250	19	44,836,642	rs210107035	0.068	0.98	17.1	21.6	2.51	FSTL4 / LOC101902643	Intron / lncRNA