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 1 SNP identified in LAP3, LCORL, and NCAPG genes in 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

Gene ¹	Marker Name²	Accession Number	dbSTS _Id	ss #	SNP³	Position in Gene⁴	Location on BTA6⁵	For Primer Name	For Primer Seq	Rev Primer Name	Rev Primer Seq
*LAP3*	79140_312	GF102128	1233209	196003657	INDEL	p.E47del	37964162	*LAP3-EX2F*	GCCTTGTTCTTTTGTCCTTGAG	*LAP3-EX2R*	TTGGGTTGAAGTAGCCTGATTT
LAP3	79144_139	GF102139	1233220	196003658	S	p.D92E	37966065	LAP3-EX4F	ACCAAATTTCTTGGGGAGTTTT	LAP3-EX4R	AACACTGCAAGAGGGAACAAAT
LAP3	79146_218	GF102161	1233242	196003659	Y	c.504C>T	37967629	LAP3-EX5F	GGGAAGAAGTGAAAGCTCAGAA	LAP3-EX5R	AAACTGACTAGGGCCATGAGAG
LAP3	79150_94	GF102129	1233210	196003660	Y	c.834C>T	37971945	LAP3-EX7F	CATTTTTCATTTCCTGCCTTGT	LAP3-EX7R	GTAAGCAAAGGGAAGACAGCAT
*LAP3*	79152_265	GF102108	1233189	196003661	Y		37977863	*LAP3-EX8F*	TGGAAATTTCTTGGTGCTTGTA	*LAP3-EX8R*	CTGACTGCTAACCACATTTTGC
*LAP3*	79154_194	GF102068	1233149	196003662	Y		37979109	*LAP3-EX9F*	CACACTCCATGTTCCTTCATGT	*LAP3-EX9R*	TGCAGGACTTGTTTTCTTCTCA
*LAP3*	79154_347	GF102068	1233149	196003663	S		37979262	*LAP3-EX9F*	CACACTCCATGTTCCTTCATGT	*LAP3-EX9R*	TGCAGGACTTGTTTTCTTCTCA
*LAP3*	79158_103	GF102082	1233163	196003664	S		37984197	*LAP3-EX11F*	AGGATTTGCCAACATCATCTTT	*LAP3-EX11R*	CCATGCCTTCTTTTACAAAGCTA
*LAP3*	79158_104	GF102082	1233163	196003665	R		37984198	*LAP3-EX11F*	AGGATTTGCCAACATCATCTTT	*LAP3-EX11R*	CCATGCCTTCTTTTACAAAGCTA
*LAP3*	79160_105	GF102096	1233177	196003666	Y		37985986	*LAP3-EX12F*	ATTTCAGCAAATGCCCTACAAT	*LAP3-EX12R*	TTGAAAATGCAAAAACCAGTTG
*LAP3*	79162_241	GF102069	1233150	196003667	K	*c.1641T>G**	37986804	*LAP3-EX13F*	TGGGGTTAGATGTTGATTTTTG	*LAP3-EX13R*	GTGAATATGAGAGCCACACCAG
*LAP3*	79162_246	GF102069	1233150	196003668	Y	*c.1646C>T**	37986809	*LAP3-EX13F*	TGGGGTTAGATGTTGATTTTTG	*LAP3-EX13R*	GTGAATATGAGAGCCACACCAG
LAP3	79162_438	GF102069	1233150	196003669	R	c.*1838A>G	37987001	LAP3-EX13F	TGGGGTTAGATGTTGATTTTTG	LAP3-EX13R	GTGAATATGAGAGCCACACCAG
*NCAPG*	83704_234	GF110810	1241907	263198259	R		38157198	*NCAPG-EX4-F*	TCTGTCCTTTTCAAGGGATGTT	*NCAPG-EX4-R*	CAGCCACACAATAATGCGATAG
NCAPG	83704_335	GF110810	1241907	263198262	S		38157299	NCAPG-EX4-F	TCTGTCCTTTTCAAGGGATGTT	NCAPG-EX4-R	CAGCCACACAATAATGCGATAG
NCAPG	83704_358	GF110810	1241907	263198260	W		38157322	NCAPG-EX4-F	TCTGTCCTTTTCAAGGGATGTT	NCAPG-EX4-R	CAGCCACACAATAATGCGATAG
*NCAPG*	83704_366	GF110810	1241907	263198261	R		38157330	*NCAPG-EX4-F*	TCTGTCCTTTTCAAGGGATGTT	*NCAPG-EX4-R*	CAGCCACACAATAATGCGATAG
*NCAPG*	83708_361	GF110811	1241908	263198263	Y		38158932	*NCAPG-EX6-F*	GATGGAAGCTAGAGGGGAACTT	*NCAPG-EX6-R*	CTTTTCATGGTAGGCCTAATGC
*NCAPG*	83712_168	GF110812	1241909	263198264	R	c.1261A>G	38163729	*NCAPG-EX8-F*	TTCTCACTTAATGGGGAGCTGT	*NCAPG-EX8-R*	AAATTTTAAGCAAAAACCTGCAA
NCAPG	83712_422	GF110812	1241909	263198265	R		38163983	NCAPG-EX8-F	TTCTCACTTAATGGGGAGCTGT	NCAPG-EX8-R	AAATTTTAAGCAAAAACCTGCAA
NCAPG	83714_209	GF110813	1241910	263198266	M	c.1357A>C	38164388	NCAPG-EX9-F	TTTCAGAATGTGAATTTTGGCTTA	NCAPG-EX9-R	GTGTGAAAGGGACTGGGTTTTA
*NCAPG*	83714_224	GF110813	1241910	263198267	K	p.I442M	38164403	*NCAPG-EX9-F*	TTTCAGAATGTGAATTTTGGCTTA	*NCAPG-EX9-R*	GTGTGAAAGGGACTGGGTTTTA
*NCAPG*	83724_658	GF110818	1241915	263198273	Y	c.2158T>C	38180790	*NCAPG-EX14-F*	ATTTACTTTTGGTGGGGGATGT	*NCAPG-EX14-R*	CAACCTCCCAATAGTCATTTCA
NCAPG	83726_315	GF110815	1241912	263198269	R		38192653	NCAPG-EX15-F	ATGTAAGGCCTAAAAGGGAGGT	NCAPG-EX15-R	GGAAAGAGCCAAATAATTCAGG
*NCAPG*	83730_778	GF110816	1241913	263198270	M	p.L877M	38195339	*NCAPG-EX17-F*	GAGCGTGAATGGTTCAGTACAC	*NCAPG-EX17-R*	ACTTCAAGAAATGAGCACCAAA
*NCAPG*	83732_316	GF110819	1241916	263198271	R		38195743	*NCAPG-EX18-F*	AGTATTTGGTGCTCATTTCTTGA	*NCAPG-EX18-R*	TCCCAAGTGAATTTAATTAGAAAAA
LCORL	79205_443	GF102113	1233194	196003679	R		38233294	LOC540095-EX6F	CCTATGTAGTGCCTTCCCAGTC	LOC540095-EX6R	CTCGTCCTGCTTCTTAGTTTGT
*LCORL*	81441_243	GF102084	1233165	196003694	Y		38255270	*LOC540095-IN4.4F*	GCATGAATGACAAAACTGTGCT	*LOC540095-IN4.4R*	CATTTTGCCCTTAAGCCTTCTA
LCORL	81439_210	GF102101	1233182	196003693	R		38257174	LOC540095-IN4.3F	TTTGCCTTCAGTTCTCTTAGGC	LOC540095-IN4.3R	TTGCAAAATTATGGCATTTCAC
*LCORL*	81435_188	GF102143	1233224	196003692	Y		38284737	*LOC540095-IN4.1F*	TAGCCTGACTGCATCCATCTAA	*LOC540095-IN4.1R*	GGAAATCCCTGGTTAAGAATCC
LCORL	79197_655	GF110814	1241911	263198268	R		38327100	LOC540095-EX2F	TCTCACGTAGAGTGTATGGATAAGC	LOC540095-EX2R	GAGTTCCAGGCTGCCTATATCA
LCORL	81433_176	GF110817	1241914	263198272	Y		38314844	LOC540095-IN3.1F	GCAGGTGAAAATCCCAATACAC	LOC540095-IN3.1R	GGGCCAAACTAGCCTTATTTCT
*LCORL*	81419_461	GF102100	1233181	196003691	M		38342145	*LOC540095-IN1.9F*	GACTTCAAATTTTTGCCCAGAG	*LOC540095-IN1.9R*	GGTGTTCTTACCCTGTCTCAGC
LCORL	81413_159	GF102115	1233196	196003686	S		38359337	LOC540095-IN1.6F	AGGATCAACCATTAGGATGTGC	LOC540095-IN1.6R	AACTGGGAAGAGAGCAAGTGAG
LCORL	81413_221	GF102115	1233196	196003684	W		38359399	LOC540095-IN1.6F	AGGATCAACCATTAGGATGTGC	LOC540095-IN1.6R	AACTGGGAAGAGAGCAAGTGAG
LCORL	81413_226	GF102115	1233196	196003687	W		38359404	LOC540095-IN1.6F	AGGATCAACCATTAGGATGTGC	LOC540095-IN1.6R	AACTGGGAAGAGAGCAAGTGAG
LCORL	81413_231	GF102115	1233196	196003689	M		38359409	LOC540095-IN1.6F	AGGATCAACCATTAGGATGTGC	LOC540095-IN1.6R	AACTGGGAAGAGAGCAAGTGAG
LCORL	81413_238	GF102115	1233196	196003690	W		38359416	LOC540095-IN1.6F	AGGATCAACCATTAGGATGTGC	LOC540095-IN1.6R	AACTGGGAAGAGAGCAAGTGAG
*LCORL*	81405_282	GF102099	1233180	196003685	M		38376731	*LOC540095-IN1.2F*	TCGGGTCCTCTTTTACTGTCAT	*LOC540095-IN1.2R*	CTTACCACGATCTCCTTTCCAC

¹ SNP in bold were genotyped using the Sequenom MassArray System.
² Marker name in USMARC database.
³ IUB Codes for SNP are K = G/T, M = A/C, R = A/G, S = C/G, W = A/T, Y = C/T.
⁴ Position based on NM_174098 Bos taurus leucine aminopeptidase 3 (LAP3) mRNA; NM_001102376 Bos taurus non-SMC condensin I complex, subunit G (NCAPG), mRNA; and NM_001192357 Bos taurus ligand dependent nuclear receptor corepressor-like (LCORL) mRNA.
⁵ Position based on the Btau 4.0 genome assembly.

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