Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Abo-Ismail, Mohammed K.; Brito, Luiz F.; Miller, Stephen P.; Sargolzaei, Mehdi; Grossi, Daniela A.; Moore, Steve S.; Plastow, Graham; Stothard, Paul; Nayeri, Shadi; Schenkel, Flavio S.

doi:10.1186/s12711-017-0356-8

Genetics Selection Evolution

Table 2 The 10 most significant SNPs associated with each calving performance trait at the genome-wise false discovery rate of 5%

From: Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Trait^a	RefSNP (rs)^b	c	Pos. (bp)	MAF	Estimated effect	SE	P-value	Location^d	Gene name
CA	rs109478645	18	57589121	0.12	− 5.55	0.39	3.69E−41	5484 L	LOC100138951
CA	rs136283363	18	57548213	0.12	5.55	0.39	3.69E−41	5497L	LOC615876
CA	rs110801791	18	57516245	0.13	− 4.86	0.38	4.51E−35	1252 R	CTU1
CA	rs135253383	18	57520290	0.13	4.83	0.38	1.27E−34	Within	CTU1
CA	rs136514789	18	57486184	0.16	3.92	0.34	1.50E−28	1330 L	LOC540297
CA	rs109882115	18	58067310	0.28	− 3.15	0.29	1.71E−25	Within	ENSBTAG00000039491
CA	rs132734257	18	57511637	0.19	− 3.54	0.33	2.04E−25	5860 R	CTU1
CA	rs135508298	18	59602905	0.21	3.52	0.33	2.12E−25	75902 L	ENSBTAG00000048191
CA	rs134539659	18	59612379	0.21	− 3.52	0.33	2.12E−25
CA	rs109540436	18	59890631	0.20	3.37	0.33	2.98E−23	3982 R	LOC100300095
CEc	rs110801791	18	57516245	0.13	− 3.93	0.49	2.72E−15	1252 R	CTU1
CEc	rs135253383	18	57520290	0.13	3.90	0.49	4.08E−15	Within	CTU1
CEc	rs109478645	18	57589121	0.12	− 3.86	0.51	7.21E−14	5484 L	LOC100138951
CEc	rs136283363	18	57548213	0.12	3.86	0.51	7.21E−14	5497L	LOC615876
CEc	rs137554975	18	56944300	0.15	− 2.98	0.45	4.04E−11	Within	MYH14
CEc	rs136113894	18	56959011	0.16	− 2.82	0.44	2.25E−10	Within	KCNC3
CEc	rs136514789	18	57486184	0.16	2.79	0.44	5.19E−10	1330 L	LOC540297
CEc	rs133544315	18	60019327	0.21	2.61	0.42	7.62E−10	47852 L	ZNF836
CEc	rs109540436	18	59890631	0.20	2.45	0.42	9.69E−09	3982 R	LOC100300095
CEc	rs135033267	18	60043680	0.20	− 2.45	0.43	1.13E−08	25523 R	ENSBTAG00000011844
CEh	rs110801791	18	57516245	0.13	− 3.73	0.46	1.33E−15	1252 R	CTU1
CEh	rs135253383	18	57520290	0.13	3.69	0.46	2.77E−15	Within	CTU1
CEh	rs109478645	18	57589121	0.12	− 3.73	0.48	1.92E−14	5484 L	LOC100138951
CEh	rs136283363	18	57548213	0.12	3.73	0.48	1.92E−14	5497L	LOC615876
CEh	rs133544315	18	60019327	0.21	2.45	0.40	9.84E−10	47852 L	ZNF836
CEh	rs109540436	18	59890631	0.20	2.41	0.40	2.17E−09	3982 R	LOC100300095
CEh	rs135033267	18	60043680	0.20	− 2.41	0.40	2.69E−09	25523 R	ENSBTAG00000011844
CEh	rs137436636	18	60006650	0.20	2.41	0.40	2.69E−09	35175 L	ZNF836
CEh	rs136514789	18	57486184	0.16	2.49	0.42	3.36E−09	1330 L	LOC540297
CEh	rs133144614	18	59242260	0.41	− 1.99	0.34	4.68E−09	13197 L	ZNF845
CSh	rs43264905	1	118222449	0.04	4.91	0.85	9.51E−09	15187 L	ENSBTAG00000038069
DCA	rs110801791	18	57516245	0.13	− 4.27	0.57	1.26E−13	1252 R	CTU1
DCA	rs135253383	18	57520290	0.13	4.23	0.57	2.06E−13	Within	CTU1
DCA	rs109478645	18	57589121	0.12	− 4.25	0.59	1.59E−12	5484 L	LOC100138951
DCA	rs136283363	18	57548213	0.12	4.25	0.59	1.59E−12	5497L	LOC615876
DCA	rs136514789	18	57486184	0.16	3.18	0.51	8.24E−10	1330 L	LOC540297
DCA	rs41601357	18	58800104	0.49	2.33	0.40	5.86E−09	7804 L	LOC101904049
DCA	rs133144614	18	59242260	0.41	− 2.41	0.42	8.66E−09	13197 L	ZNF845
DCA	rs109011289	18	59058582	0.48	− 2.27	0.40	1.99E−08	7587 L	LOC101904371
DCA	rs41582522	18	58666276	0.41	− 2.33	0.41	2.47E−08
DCA	rs133544315	18	60019327	0.21	2.76	0.49	2.55E−08	47852 L	ZNF836
SCEc	rs109478645	18	57589121	0.12	− 6.19	0.40	1.07E−47	5484 L	LOC100138951
SCEc	rs136283363	18	57548213	0.12	6.19	0.40	1.07E−47	5497L	LOC615876
SCEc	rs110801791	18	57516245	0.13	− 5.66	0.39	1.36E−43	1252 R	CTU1
SCEc	rs135253383	18	57520290	0.13	5.65	0.39	1.66E−43	Within	CTU1
SCEc	rs136514789	18	57486184	0.16	4.38	0.36	1.81E−32	1330 L	LOC540297
SCEc	rs132734257	18	57511637	0.19	− 4.05	0.34	1.21E−30	5860 R	CTU1
SCEc	rs137554975	18	56944300	0.15	− 4.21	0.35	1.42E−30	Within	MYH14
SCEc	rs136113894	18	56959011	0.16	− 4.07	0.35	3.22E−29	Within	KCNC3
SCEc	rs135508298	18	59602905	0.21	3.90	0.34	7.48E−29	75902 L	ENSBTAG00000048191
SCEc	rs134539659	18	59612379	0.21	− 3.90	0.34	7.48E−29
SCEh	rs109478645	18	57589121	0.12	− 6.13	0.46	4.12E−37	5484 L	LOC100138951
SCEh	rs136283363	18	57548213	0.12	6.13	0.46	4.12E−37	5497L	LOC615876
SCEh	rs110801791	18	57516245	0.13	− 5.42	0.44	4.98E−32	1252 R	CTU1
SCEh	rs135253383	18	57520290	0.13	5.38	0.44	1.17E−31	Within	CTU1
SCEh	rs136514789	18	57486184	0.16	4.39	0.40	3.24E−26	1330 L	LOC540297
SCEh	rs132734257	18	57511637	0.19	− 4.03	0.39	2.30E−24	5860 R	CTU1
SCEh	rs109882115	18	58067310	0.28	− 3.53	0.34	1.33E−23	Within	ENSBTAG00000039491
SCEh	rs135508298	18	59602905	0.21	3.90	0.39	5.03E−23	75902 L	ENSBTAG00000048191
SCEh	rs134539659	18	59612379	0.21	− 3.90	0.39	5.03E−23
SCEh	rs43038601	18	57491196	0.22	− 3.59	0.36	4.60E−22	4128 R	KLK14
SCSc	rs109478645	18	57589121	0.12	− 5.59	0.82	1.50E−11	5484 L	LOC100138951
SCSc	rs136283363	18	57548213	0.12	5.59	0.82	1.50E−11	5497L	LOC615876
SCSc	rs136113894	18	56959011	0.16	− 4.41	0.71	9.17E−10	Within	KCNC3
SCSc	rs110801791	18	57516245	0.13	− 4.73	0.79	3.63E−09	1252 R	CTU1
SCSc	rs135253383	18	57520290	0.13	4.73	0.79	3.63E−09	Within	CTU1
SCSc	rs134066287	18	62844651	0.23	3.84	0.65	3.70E−09	Within	FCAR
SCSc	rs109882115	18	58067310	0.28	− 3.56	0.60	3.96E−09	Within	ENSBTAG00000039491
SCSc	rs109844326	18	63415091	0.16	4.19	0.72	9.77E−09	2950 L	MBOAT7
SCSc	rs134353106	18	62839617	0.26	3.47	0.61	2.13E−08	5900 L	KIR2DL5A
SCSc	rs133544315	18	60019327	0.21	3.74	0.67	2.82E−08	47852 L	ZNF836
SCSh	rs109478645	18	57589121	0.12	− 7.95	0.86	1.86E−19	5484 L	LOC100138951
SCSh	rs136283363	18	57548213	0.12	7.95	0.86	1.86E−19	5497L	LOC615876
SCSh	rs133544315	18	60019327	0.21	5.91	0.71	1.97E−16	47852 L	ZNF836
SCSh	rs110801791	18	57516245	0.13	− 6.94	0.83	2.84E−16	1252 R	CTU1
SCSh	rs135253383	18	57520290	0.13	6.86	0.83	5.87E−16	Within	CTU1
SCSh	rs109540436	18	59890631	0.20	5.76	0.71	1.05E−15	3982 R	LOC100300095
SCSh	rs135033267	18	60043680	0.20	− 5.72	0.71	1.98E−15	25523 R	ENSBTAG00000011844
SCSh	rs137436636	18	60006650	0.20	5.72	0.71	1.98E−15	35175 L	ZNF836
SCSh	rs136514789	18	57486184	0.16	6.02	0.75	3.07E−15	1330 L	LOC540297
SCSh	rs136766893	18	58494682	0.26	− 5.02	0.63	6.02E−15	Within	BOSTAUV1R416

^aTraits = evaluated calving traits included calving ability (CA), daughter calving ability (DCA), maternal calving ease at first calving (heifer; CEh), maternal calf survival at first calving (heifer; CSh), maternal calving ease at later calvings (cow; CEc), maternal calf survival at later calvings (cow; CSc), direct calving ease at first calving (heifer; SCEh), direct calf survival at first calving (heifer; SCSh), direct calving ease at later calvings (cow; SCEc), direct calf survival at later calvings (cow; SCSc) and sire conception rate (SCR). Calving performance traits are expressed as relative breeding values with a population average of 100 and standard deviation of 5
^bRefSNP (rs) = assigned reference SNP (rs) number for a SNP by the National Center for Biotechnology Information
^cBTA = Bos taurus autosomes
^dLocation = gene location (within L left or R right) from the SNP of interest

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ISSN: 1297-9686

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