Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle

Cai, Zexi; Dusza, Magdalena; Guldbrandtsen, Bernt; Lund, Mogens Sandø; Sahana, Goutam

doi:10.1186/s12711-020-00538-6

Genetics Selection Evolution

Table 4 The lead SNP and its nearest genes in the multi-trait meta-analysis of milk yield (MY), fat yield (FY) and protein yield (PY)

From: Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle

Chr	Lead SNP (bp)	rsid	− log₁₀(p)	Nearest gene (distance)	Annotation	Single trait significant^a
1	63177947	rs42409534	12.19	ENSBTAG00000046854 (7850,66 bp)	Intergenic	FY, PY
1	71250238	rs210007164	9.51	TFRC (9830 bp)	Intergenic	FY
1	120470021	rs109519395	13.92	AGTR1 (67,012 bp)	Intergenic	FY, MY, PY
1	148567669	rs108957710	9.97	ENSBTAG00000046447	Upstream	Novel
2	86095020	rs110457337	10.76	ANKRD44	Intron	FY, PY
2	124837669	–	13.34	PTPRU	Intron	FY, PY
3	15459025	rs132797166	23.45	GBA	Intron	Novel
4	101547644	–	11.18	CHRM2	Upstream	MY
5	31335325	rs447206924	23.61	LALBA (12,536 bp)	Intergenic	MY
5	93945991	rs208248675	126.98	MGST1	Intron	FY, MY
6	38031954	rs454966322	72.75	ABCG2 (1371 bp)	Downstream	FY, MY
6	88442678	rs211069111	76.92	SLC4A4	Intron	PY
7	57287990	–	21.70	KCTD16	Intron	FY, MY, PY
8	40627140	rs381636155	9.38	bta-mir-2471 (64,540 bp)	Intergenic	MY
8	73877814	rs381189656	10.50	ENSBTAG00000010829 (171 bp)	Upstream	MY, PY
8	93065787	rs211543235	8.88	GRIN3A	Intron	PY
9	33179984	rs211241852	11.33	SLC35F1 (83,834 bp)	intergenic	MY, PY
10	1989907	rs109274615	9.01	ENSBTAG00000047622 (109,990 bp)	Intergenic	MY
10	46591115	rs211044009	19.41	USP3 (20,126 bp)	Intergenic	Novel
10	93933304	–	8.73	SEL1L	Intron	PY
11	15339847	rs110446044	12.01	TTC27	Intron	FY, PY
11	35270918	rs109956079	13.52	ENSBTAG00000027786 (241,298 bp)	Intergenic	PY
11	55692712	rs208208268	11.86	CTNNA2	Intron	FY, PY
11	63203084	rs110286816	9.96	ENSBTAG00000046117 (87,338 bp)	intergenic	Novel
11	88771449	rs109730673	9.41	ENSBTAG00000047976 (150,709 bp)	Intergenic	FY
11	103301805	rs110788821	15.43	PAEP	Intron	Novel
12	75309869	rs43128997	8.78	ENSBTAG00000026070 (148,028 bp)	Intergenic	Novel
13	20194953	rs41602070	9.06	ITGB1 (53,992 bp)	Intergenic	PY
13	37208793	rs385962673	10.43	MKX (10,635 bp)	Intergenic	MY, PY
13	46391099	rs42442665	10.03	ADARB2	Intron	MY
13	60701113	rs108986421	8.61	RSPO4 (9143 bp)	Intergenic	PY
14	1802265	rs109234250	705.26	DGAT1	Missense	FY, MY, PY
14	1802266	rs109326954	705.26	DGAT1	Missense	FY, MY, PY
14	66649826	rs445616049	59.08	MGC148714 (2105 bp)	Downstream	Novel
15	28357864	rs208325660	17.79	RNF214	Missense	Novel
15	53640417	rs380720492	25.33	ARHGEF17	Synonymous	MY
15	66103726	rs41775109	16.64	EHF (72,762 bp)	Intergenic	FY
16	32262983	rs384531912	12.03	SMYD3	Intron	PY
16	49798794	rs380930173	9.40	AJAP1 (33,340 bp)	intergenic	PY
16	67736535	rs385935762	9.64	SWT1	intron	Novel
17	62543160	rs211016475	11.60	TBX5	Intron	FY
18	15058306	rs211386971	10.04	VPS35	Intron	PY
18	46583596	rs110398208	11.19	UPK1A (662 bp)	Upstream	MY, PY
18	57064406	rs433130247	18.74	MYBPC2	Intron	PY
19	27522927	rs210334173	13.09	ASGR1 (6170 bp)	Intergenic	FY, PY
19	51383847	rs136067046	19.23	FASN (1075 bp)	Upstream	Novel
20	9608408	rs519502268	10.57	CARTPT (183,253 bp)	Intergenic	MY, PY
20	31909478	rs385640152	112.79	GHR	Missense	FY, MY
20	69006609	rs134612291	10.41	IRX1 (466,030 bp)	Intergenic	PY
22	60087443	rs462776871	8.51	EEFSEC	Intron	Novel
23	10974968	rs136158431	9.29	FGD2 (56,619 bp)	Intergenic	PY
23	25076739	rs210864958	8.70	GCM	Downstream	MY
25	6984796	rs110991040	8.71	RBFOX1 (298,008 bp)	Intergenic	Novel
25	36299420	rs210351939	10.92	ACHE (1112 bp)	Upstream	Novel
26	20527926	rs453802222	20.87	ENSBTAG00000023629 (175 bp)	Downstream	FY
26	37869471	rs458256022	14.61	KCNK18	Synonymous	FY, MY, PY
27	36212352	rs208675276	20.10	GPAT4	5_prime_UTR	Novel
28	34972377	rs137526033	9.90	ZMIZ1 (60,078 bp)	Intergenic	MY
29	21075705	rs382642281	10.42	ENSBTAG00000000853 (161,330 bp)	Intergenic	FY, PY
29	41825511	–	16.32	STX5	Intron	Novel

The distance in base pairs from the nearest gene is in brackets
^aNovel hit from multi-trait meta-analysis, not identified by any of the single trait analysis

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ISSN: 1297-9686

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