Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Abo-Ismail, Mohammed K; Vander Voort, Gordon; Squires, James J; Swanson, Kendall C; Mandell, Ira B; Liao, Xiaoping; Stothard, Paul; Moore, Stephen; Plastow, Graham; Miller, Stephen P

doi:10.1186/1471-2156-15-14

BMC Genomic Data

Table 3 Significant and suggestive SNP based on false discovery rate (FDR) q threshold of 0.05 and 0.2 for feed efficiency traits using single locus regression model (SLRM) on 339 SNPs

From: Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Trait¹	Gene ID²	BTA³	Ref. SNP⁴	Pos. ( bp)⁵	MAF⁶	Alleles⁷	n⁸	Estimate ± SE⁹	*P-value*
ADG	523789	3	rs42417924	75523597	0.102	C/G	726	-0.062 ± 0.02	0.0104&
DMI	616055	5	ss914082855	119551668	0.37	A/G	726	-0.234 ± 0.08	0.0025^*
DMI	616055	5	ss914082856	119557146	0.37	T/C	720	-0.237 ± 0.08	0.0023^*
MMWT	616908	6	rs41574929	36099801	0.388	T/G	716	0.992 ± 0.40	0.0132&
ADG	616908	6	rs41574929	36099801	0.388	T/G	716	0.049 ± 0.01	0.0009^*
MMWT	540329	6	ss914082878	37288379	0.152	T/C	726	1.342 ± 0.54	0.0128&
MMWT	536203	6	ss914082880	37386084	0.16	A/G	725	1.293 ± 0.53	0.0148&
MMWT	530393	6	rs43702346	37439120	0.272	T/G	723	1.421 ± 0.43	0.0009^*
DMI	784720	8	ss914082889	10674426	0.041	A/G	726	0.620 ± 0.18	0.0006^*
RFI	784720	8	ss914082889	10674426	0.041	A/G	726	0.483 ± 0.15	0.0017^*
MMWT	282689	10	ss914082689	50256553	0.197	T/C	725	-1.210 ± 0.48	0.01&
MMWT	282689	10	ss914082690	50259055	0.046	A/G	726	2.184 ± 0.89	0.015&
MMWT	614507	10	ss914082694	79315960	0.364	T/C	718	0.933 ± 0.39	0.0176&
RFI	533166	15	rs41755948	30710940	0.207	T/C	726	-0.201 ± 0.07	0.007&
RFI	533166	15	ss914082737	30717928	0.207	T/C	726	-0.201 ± 0.07	0.007&
RFI	521326	16	rs41821600	64875340	0.037	A/T	726	0.496 ± 0.17	0.0033^*
RFI	521326	16	rs41820824	64950387	0.012	A/G	726	0.785 ± 0.29	0.0064^*
RFI	508025	18	ss914082760	17150858	0.365	T/C	723	0.191 ± 0.06	0.0028^*
FCR	282411	19	rs41914675	37278418	0.072	A/G	726	0.278 ± 0.10	0.004&
RFI	282411	19	rs41914675	37278418	0.072	A/G	726	0.342 ± 0.12	0.004&
DMI	282411	19	rs41914675	37278418	0.072	A/G	726	0.462 ± 0.14	0.0008^*
RFI	524684	21	rs43020736	29054823	0.371	T/C	726	-0.162 ± 0.07	0.016&
DMI	524684	21	rs43020736	29054823	0.371	T/C	726	-0.248 ± 0.08	0.0018^*
RFI	524684	21	rs43020769	29060759	0.478	A/G	726	0.172 ± 0.07	0.009&
MMWT	532512	25	ss914082815	36278405	0.11	T/C	719	1.555 ± 0.63	0.014&
MMWT	532512	25	ss914082816	36279504	0.02	T/C	726	3.099 ± 1.31	0.018&
MMWT	515895	27	ss914082827	39798548	0.08	A/G	726	-2.298 ± 0.71	0.0013^*
DMI	508697	28	ss914082834	7727734	0.426	A/G	726	-0.211 ± 0.08	0.0067^*
RFI	508697	28	ss914082834	7727734	0.426	A/G	726	-0.183 ± 0.07	0.005^*
RFI	780878	28	ss914082829	13580673	0.187	T/A	726	-0.208 ± 0.08	0.009^*

¹average daily gain (ADG), kg d^-1, average daily dry matter intake (DMI), kg d^-1, mid-point metabolic weight (MMWT), kg⁷⁵, feed efficiency conversion ratio (FCR), kg gainkg-¹ DM and residual feed intake (RFI) kg d^-1.
^*is a significant SNP after adjusting for chromosome-wise 5% false discovery rate.
& is a suggestive SNP after adjusting for chromosome-wise 20% false discovery rate.
Gene ID² = Entrez gene identifier.
BTA³ = Bos taurus autosome.
Ref. SNP⁴ = (rs#) is a reference SNP ID number and (ss#) ID is the National Center for Biotechnology Information (NCBI) assay ID number assigned by NCBI to submitted SNPs for discovered SNPs using RNA-Seq.
Pos. (bp)⁵ = the SNP’s position in a base pair.
MAF⁶ = minor allele frequency.
Alleles⁷ = first allele/second allele, the second allele is the minor allele which the phenotypes regressed on its number (0, 1, and 2).
n⁸ = Number of animals’ phenotypes and genotypes for testing the association.
Estimate ± SE⁹ = allele substitution effect ± standard error.

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