Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

Lindholm-Perry, Amanda K; Sexten, Andrea K; Kuehn, Larry A; Smith, Timothy PL; King, D Andy; Shackelford, Steven D; Wheeler, Tommy L; Ferrell, Calvin L; Jenkins, Thomas G; Snelling, Warren M; Freetly, Harvey C

doi:10.1186/1471-2156-12-103

Table 2 SNP marker associations and estimated effects for ADFI and ADG in the discovery population of crossbred steers.

From: Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

						Average Daily Feed Intake (ADFI)			Average Daily Gain (ADG)
Marker¹	Gene²	Position³	IUB	# Genotypes⁴	MAF	Effect⁵	P -value	Correction⁶	Effect	P -value	Correction
ARS-BFGL-NGS-77584		37855236	R	1182	G = 0.10	-0.026	0.8	NS	-0.0078	0.7	NS
After2Run10KSet7323		37856744	Y	1075	T = 0.30	-0.14	0.01	NS	-0.029	0.01	NS
Hapmap31601-BTC-034240		37859827	R	1076	G = 0.28	-0.15	0.005	NS	-0.033	0.004	NS
Hapmap28705-BTC-034230		37862818	S	1090	G = 0.31	-0.14	0.010	NS	-0.033	0.003	NS
Hapmap25169-BTC-034210		37870369	R	1186	A = 0.30	-0.15	0.006	NS	-0.033	0.003	NS
Hapmap30444-BTC-052947		37875093	Y	1164	C = 0.49	0.16	0.004	NS	0.036	0.002	NS
After2Run10KSet5598		37875791	Y	1186	C = 0.30	-0.14	0.01	NS	-0.032	0.004	NS
Hapmap32743-BTC-052998		37879284	R	1011	A = 0.23	-0.073	0.2	NS	-0.024	0.04	NS
Hapmap23977-BTC-053017		37880952	M	1176	A = 0.30	-0.15	0.006	NS	-0.032	0.005	NS
79140_312	LAP3	37964162	INDEL	1165	DEL = 0.09	0.11	0.2	NS	-0.013	0.5	NS
Hapmap56977-ss46527055	LAP3	37967630	R	1192	A = 0.13	-0.051	0.5	NS	-0.013	0.4	NS
79152_265	LAP3	37977863	Y	1181	C = 0.33	-0.020	0.7	NS	-0.021	0.05	NS
79154_194	LAP3	37979109	Y	1078	T = 0.38	-0.0072	0.9	NS	-0.021	0.06	NS
79154_347	LAP3	37979262	S	1098	C = 0.34	-0.022	0.7	NS	-0.021	0.04	NS
79158_103	LAP3	37984197	S	1193	G = 0.34	0.026	0.6	NS	0.021	0.05	NS
79158_104	LAP3	37984198	R	1190	G = 0.33	-0.021	0.7	NS	-0.020	0.07	NS
79160_105	LAP3	37985986	Y	1127	T = 0.34	-0.0086	0.9	NS	-0.019	0.08	NS
79162_241	LAP3	37986804	K	1124	T = 0.37	-0.0064	0.9	NS	-0.22	0.05	NS
79162_246	LAP3	37986809	Y	1197	C = 0.34	-0.020	0.7	NS	-0.21	0.04	NS
ARS-BFGL-NGS-44699		38011603	S	1183	C = 0.10	-0.085	0.3	NS	-0.021	0.2	NS
BTA-100891		38076964	Y	1063	T = 0.26	-0.083	0.1	NS	-0.028	0.008	NS
83704_234⁷	NCAPG	38157198	R	1085	A = 0.42	0.18	0.0006	0.03	0.046	2.E-05	0.0009
83704_366	NCAPG	38157330	R	1187	G = 0.12	-0.11	0.2	NS	-0.013	0.4	NS
83708_361	NCAPG	38158932	Y	1092	C = 0.41	0.17	0.001	0.05	0.045	4.E-05	0.002
83712_168⁷	NCAPG	38163729	R	1004	G = 0.47	-0.16	0.003	NS	-0.045	9.E-05	0.004
83714_224⁷	NCAPG	38164403	K	1132	G = 0.34	0.21	8.E-05	0.004	0.059	1.E-07	5.E-06
83724_658	NCAPG	38180790	Y	1100	C = 0.41	0.17	0.001	0.05	0.045	5.E-05	0.002
83730_778	NCAPG	38195339	M	1022	A = 0.42	0.17	0.003	NS	0.058	1.E-06	0.00005
83732_316	NCAPG	38195743	R	1050	G = 0.42	0.14	0.008	NS	0.044	1.E-04	0.005
Hapmap24122-BTC-041153		38217816	K	1193	G = 0.35	0.22	1.E-05	0.0005	0.059	2.E-08	9.E-07
Hapmap24041-BTC-041151		38220879	K	1192	T = 0.35	0.22	1.E-05	0.0005	0.059	2.E-08	9.E-07
Hapmap31609-BTC-041148		38223329	R	1192	A = 0.38	0.17	0.0005	0.02	0.045	1.E-05	0.0005
Hapmap28154-BTC-041134⁸	LCORL	38228679	R	935	C = 0.38	0.18	0.0003	0.01	0.045	2.E-05	0.0009
Hapmap27082-BTC-041131	LCORL	38233962	R	1121	G = 0.37	0.18	0.0002	0.009	0.047	4.E-06	0.0002
Hapmap26855-BTC-041123	LCORL	38239191	R	1075	G = 0.33	0.21	8.E-05	0.004	0.058	1.E-07	5.E-06
Hapmap23341-BTC-041113	LCORL	38250098	K	1161	T = 0.36	0.21	4.E-05	0.002	0.056	1.E-07	5.E-06
81441_243	LCORL	38255270	S	822	G = 0.28	-0.24	5.E-06	0.0002	-0.058	2.E-07	9E-06
81435_188	LCORL	38284737	Y	892	C = 0.38	0.17	0.0004	0.02	0.042	3.E-05	0.001
Hapmap28589-BTC-041045 ⁹	LCORL	38300298	S	1190	G = 0.33	0.22	2.E-05	0.0009	0.061	1.E-08	5.E-07
Hapmap33629-BTC-041038	LCORL	38313142	Y	999	T = 0.30	0.22	2.E-05	0.0009	0.059	5.E-08	2.E-06
Hapmap28835-BTC-041022	LCORL	38326993	S	1061	G = 0.18	-0.12	0.07	NS	-0.027	0.04	NS
81419_461	LCORL	38342145	M	1058	C = 0.05	-0.17	0.1	NS	-0.046	0.04	NS
Hapmap33694-BTC-041005	LCORL	38342183	R	1190	G = 0.16	-0.10	0.1	NS	-0.038	0.005	NS
81405_282 ⁹	*LCORL*	38376731	M	1196	A = 0.33	0.22	2.E-05	0.0009	0.061	1.E-08	5.E-07
Hapmap33650-BTC-073421		38409471	Y	1041	C = 0.40	-0.14	0.004	NS	-0.036	0.0003	0.01
Hapmap31943-BTC-050642		38427989	Y	1181	C = 0.08	-0.11	0.2	NS	-0.039	0.02	NS
BTB-00249053		38481012	Y	1183	T = 0.24	-0.12	0.03	NS	-0.029	0.01	NS

¹ Name of publicly available markers from the following references: Van Tassell CP et al. [26], Bovine HapMap Consortium et al. [27], and Bovine Genome Sequencing and Analysis Consortium et al. [28]
² SNP located within a gene locus are presented in this column. The gene loci for LAP3, NCAPG, and LCORL are: 37,961,725 - 37,987,164 bp, 38,153,047-38,199,153 bp, and 38,227,955-38,378,385 bp on the Btau 4.0 genome assembly.
³ Position based on the Btau 4.0 Bovine Genome Assembly.
⁴ Number of genotypic calls used for statistical analysis.
⁵ ADFI and ADG effects are displayed as kg/d. Effects are presented for the minor allele.
⁶ Correction for multiple testing performed by multiplying the P-values by the number of markers tested (n = 47). NS = not significant, P-value > 0.05.
⁷ Markers evaluated in Setoguchi et al. [8] and Eberlein et al. [11].
⁸ Marker evaluated in Charolais and German Holstein population in Eberlein et al. [11].
⁹ Markers in bold font, Hapmap28589-BTC-041045 and 81405_282, were significantly associated with ADG in the validation population of animals (P = 0.04 and 0.03, respectively).

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