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 3 The most highly significant SNPs associated with each body conformation 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	BTA^c	Pos. (bp)	MAF	Estimated effect	SE	P-value	Location^d	Gene name
ANG	rs110434046	6	88919352	0.46829	− 2.46	0.40	1.35E−09
ANG	rs137712965	6	88922396	0.46829	2.46	0.40	1.35E−09
ANG	rs136287830	6	88865430	0.46168	− 2.43	0.40	2.21E−09
ANG	rs108983037	6	88913092	0.46499	2.38	0.40	4.01E−09
ANG	rs109512265	6	88485244	0.40611	− 2.19	0.38	1.51E−08	Within	SLC4A4
BD	rs109478645	18	57589121	0.1195	4.49	0.45	2.29E−22	Within	ENSBTAG00000037537
BD	rs136283363	18	57548213	0.1195	− 4.49	0.45	2.29E−22
BD	rs110801791	18	57516245	0.12539	4.00	0.43	9.73E−20	1252 R	CTU1
BD	rs135253383	18	57520290	0.12549	− 3.99	0.43	1.03E−19	Within	CTU1
BD	rs132734257	18	57511637	0.19128	3.13	0.37	1.18E−16
BQ	rs109901274	7	93244933	0.11506	− 2.81	0.43	9.10E−11	Within	ARRDC3
BQ	rs109618368	7	93254737	0.11506	2.81	0.43	9.10E−11	1643 L	ARRDC3
BQ	rs110680622	7	93287387	0.11506	− 2.81	0.43	9.10E−11
BQ	rs110066813	7	93251138	0.13045	− 2.52	0.39	2.59E−10	Within	ARRDC3
BQ	rs109860522	7	93263102	0.13045	2.52	0.39	2.59E−10
CW	rs109901274	7	93244933	0.11506	3.10	0.51	1.47E−09	Within	ARRDC3
CW	rs109618368	7	93254737	0.11506	− 3.10	0.51	1.47E−09	1643 L	ARRDC3
CW	rs110680622	7	93287387	0.11506	3.10	0.51	1.47E−09
CW	rs110434046	6	88919352	0.46829	2.22	0.41	5.90E−08
CW	rs137712965	6	88922396	0.46829	− 2.22	0.41	5.90E−08
DS	rs109478645	18	57589121	0.1195	2.86	0.45	4.48E−10	Within	ENSBTAG00000037537
DS	rs136283363	18	57548213	0.1195	− 2.86	0.45	4.48E−10
DS	rs136514789	18	57486184	0.15844	− 2.29	0.39	5.21E−09	1330 L	LOC540297
DS	rs110801791	18	57516245	0.12539	2.39	0.44	5.02E−08	1252 R	CTU1
DS	rs134321289	18	58053410	0.31698	− 1.73	0.32	5.49E−08
FA	rs109517032	20	26955400	0.26761	2.31	0.40	1.11E−08
FA	rs110521341	20	26957866	0.26761	− 2.31	0.40	1.11E−08
FA	rs109222733	20	26960799	0.26761	− 2.31	0.40	1.11E−08
FA	rs109747498	20	26978980	0.26761	− 2.31	0.40	1.11E−08
FA	rs110486797	20	26990879	0.26761	− 2.31	0.40	1.11E−08
FTP	rs133797664	8	79527489	0.1322	2.55	0.49	2.73E−07
FTP	rs136251125	18	42320881	0.29168	1.67	0.32	3.28E−07
FTP	rs136974352	18	42322043	0.29168	1.67	0.32	3.28E−07
FTP	rs43571286	8	79497558	0.13468	2.42	0.47	3.66E−07
FTP	rs137127919	5	12712534	0.06083	2.71	0.53	3.84E−07
PS	rs42244554	5	1278211	0.3427	2.00	0.36	2.35E−08	694 L	ZFC3H1
PW	rs137169221	13	4626355	0.11558	− 2.73	0.46	5.63E−09
PW	rs109478645	18	57589121	0.1195	2.53	0.43	6.48E−09	Within	ENSBTAG00000037537
PW	rs136283363	18	57548213	0.1195	− 2.53	0.43	6.48E−09
PW	rs42382059	13	4518102	0.1165	− 2.60	0.46	2.12E−08
PW	rs42382046	13	4524429	0.1165	2.60	0.46	2.12E−08
RAH	rs109901274	7	93244933	0.11506	− 3.10	0.49	2.88E−10	Within	ARRDC3
RAH	rs109618368	7	93254737	0.11506	3.10	0.49	2.88E−10	1643 L	ARRDC3
RAH	rs110680622	7	93287387	0.11506	− 3.10	0.49	2.88E−10
RAH	rs109343241	18	59615343	0.27577	1.93	0.35	4.08E−08
RAH	rs135508298	18	59602905	0.20564	2.12	0.39	9.37E−08
ST	rs109882115	18	58067310	0.2799	1.86	0.30	1.19E−09	Within	ENSBTAG00000039491
ST	rs109478645	18	57589121	0.1195	2.53	0.41	1.22E−09	Within	ENSBTAG00000037537
ST	rs136283363	18	57548213	0.1195	− 2.53	0.41	1.22E−09
ST	rs133960300	5	106250561	0.14439	− 2.34	0.39	2.94E−09	3346 R	CCND2
ST	rs109685956	5	106256616	0.14439	− 2.34	0.39	2.94E−09	Within	CCND2
TL	rs110895486	5	12438670	0.21287	3.00	0.41	4.27E−13
TL	rs109194156	5	12444024	0.21318	2.99	0.41	4.92E−13
TL	rs110137797	5	12464607	0.21328	2.93	0.41	1.63E−12	Within	TMTC2
TL	rs109264225	5	12468154	0.21328	2.93	0.41	1.63E−12	Within	TMTC2
TL	rs43435142	5	12468826	0.21328	2.93	0.41	1.63E−12	Within	TMTC2
UD	rs42192551	29	49182244	0.46055	− 1.48	0.27	6.23E−08
UD	rs110432804	6	89036570	0.46932	− 2.00	0.37	8.93E−08
UD	rs108983037	6	88913092	0.46499	− 2.00	0.37	9.11E−08
UD	rs110434046	6	88919352	0.46829	2.00	0.37	1.04E−07
UD	rs137712965	6	88922396	0.46829	− 2.00	0.37	1.04E−07

Conformation trait EBV are standardized to have a mean value of zero and a standard deviation of 5
^aTrait = body depth (BD), bone quality (BQ), chest width (CW), pin width (PW), rear attachment height (RAH), stature (ST), angularity (ANG), body depth (BD), dairy strength (DS), fore udder attachment (FA), front teat placement (FTP), pin setting (PS), rear attachment height (RAH), teat length (TL)
^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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