Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

Zhang, Feng; Wang, Yining; Mukiibi, Robert; Chen, Liuhong; Vinsky, Michael; Plastow, Graham; Basarab, John; Stothard, Paul; Li, Changxi

doi:10.1186/s12864-019-6362-1

Table 4 A summary of top lead SNPs of each chromosome in significant associations with RFI and its component traits DMI, ADG, and MWT based on the imputed 7.8 M WGS variant GWAS with a threshold value of P-value < 10⁻⁵ (1.00E-05) in a beef cattle multibreed population

From: Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

Trait¹	Lead SNP	Num²	Chr	Pos (bp)	Nearest Gene³	Distance (bp)⁴	Annotation⁵	P-value	FDR⁶	b ± SE⁷	Var_Phe (%)⁸
RFI	rs109479784	38	1	121,176,492	SNORA70	50,597	intergenic_region	8.27E-06	7.23E-01	− 0.06 ± 0.01	0.35
RFI	rs379241952	41	2	28,511,594	B3GALT1	109,859	intergenic_region	9.69E-07	7.23E-01	0.10 ± 0.020	0.43
RFI	rs110523019	123	3	6,835,555	DDR2	Within	intron_variant	1.74E-07	6.60E-01	−0.14 ± 0.03	0.43
RFI	rs42645457	7	4	89,834,757	GPR37	11,146	intergenic_region	6.12E-06	7.23E-01	−0.07 ± 0.02	0.35
RFI	rs446215391	24	5	9,075,556	SYT1	13,259	intergenic_region	6.77E-07	7.23E-01	0.14 ± 0.03	0.39
RFI	Chr10:18890829	1	10	18,890,829	ENSBTAG00000033344	Within	intron_variant	4.70E-06	7.23E-01	−0.12 ± 0.03	0.36
RFI	rs382972340	154	12	54,262,083	U6	61,906	intergenic_region	8.21E-06	7.23E-01	0.10 ± 0.02	0.33
RFI	rs382536070	1	13	35,856,785	LYZL1	61,216	intergenic_region	6.60E-06	7.23E-01	−0.18 ± 0.04	0.30
RFI	Chr15:82875910	23	15	82,875,910	ENSBTAG00000039917	270	upstream_gene_variant	6.20E-06	7.23E-01	0.18 ± 0.04	0.30
RFI	Chr16:13105979	86	16	13,105,979	RGS2	60,759	intergenic_region	8.38E-06	7.23E-01	−0.07 ± 0.02	0.38
RFI	rs382491772	2	23	48,775,591	F13A1	Within	3’UTR_variant	8.90E-06	7.23E-01	0.14 ± 0.03	0.30
RFI	rs209862831	4	28	10,939,077	ENSBTAG00000046453	4795	upstream_gene_variant	7.19E-06	7.23E-01	0.10 ± 0.02	0.32
DMI	rs211318336	5	1	25,084,372	U2	266,897	intergenic_region	8.30E-06	3.41E-02	−0.18 ± 0.04	0.31
DMI	rs109570141	142	2	112,157,337	U6atac	104,324	intergenic_region	1.96E-06	1.19E-02	0.14 ± 0.03	0.40
DMI	rs472695088	8	4	3,153,240	SNORA31	367,620	intergenic_region	2.80E-06	1.57E-02	−0.20 ± 0.04	0.37
DMI	rs207689046	139	6	39,105,359	LCORL	113,247	intergenic_region	2.77E-25	8.49E-19	0.25 ± 0.02	3.04
DMI	rs109256612	64	10	31,282,009	DPH6	172,888	intergenic_region	7.06E-06	3.10E-02	0.09 ± 0.02	0.35
DMI	rs382972340	154	12	54,262,083	U6	61,906	intergenic_region	1.03E-06	8.63E-03	0.15 ± 0.03	0.40
DMI	rs384869645	425	13	19,004,111	PARD3	Within	intron_variant	5.56E-06	2.64E-02	−0.13 ± 0.03	0.34
DMI	rs110092040	32	14	24,973,953	MOS	1997	downstream_gene_variant	1.12E-08	2.61E-04	−0.15 ± 0.03	0.69
DMI	rs380573663	87	16	78,179,941	CRB1	Within	intron_variant	3.66E-06	1.94E-02	−0.13 ± 0.03	0.36
DMI	rs43357086	73	20	4,791,751	5S_rRNA	14,480	intergenic_region	4.33E-09	1.20E-04	0.12 ± 0.02	0.66
DMI	rs211404023	41	22	30,879,104	5S_rRNA	74,025	intergenic_region	3.71E-06	1.96E-02	−0.09 ± 0.02	0.35
ADG	rs134607538	155	2	93,780,831	ENSBTAG00000010293	77,522	intergenic_region	2.44E-07	1.30E-03	−0.02 ± 0.00	0.47
ADG	Chr4:112725016	34	4	112,725,016	CUL1	31,822	intergenic_region	3.79E-06	1.39E-02	−0.03 ± 0.01	0.37
ADG	rs137822220	151	5	106,247,266	CCND2	6641	intergenic_region	8.25E-07	3.53E-03	0.03 ± 0.01	0.43
ADG	rs110987922	124	6	39,113,335	LCORL	121,223	intergenic_region	3.28E-37	1.74E-30	0.07 ± 0.01	4.23
ADG	rs109901274	62	7	93,244,933	ARRDC3	Within	missense_variant	8.44E-08	5.14E-04	0.03 ± 0.00	0.59
ADG	rs41693642	65	13	45,111,501	ENSBTAG00000046128	57,267	intergenic_region	1.32E-07	7.58E-04	−0.03 ± 0.01	0.48
ADG	rs134215421	59	14	25,006,125	PLAG1	1166	downstream_gene_variant	4.82E-13	1.58E-08	−0.04 ± 0.01	1.09
ADG	rs42661323	50	20	4,916,731	STC2	Within	missense_variant	3.65E-09	4.17E-05	0.03 ± 0.01	0.67
ADG	rs111029508	52	24	15,100,338	snoU54	472,490	intergenic_region	5.47E-06	1.89E-02	0.02 ± 0.00	0.38
ADG	rs448890458	6	25	40,587,255	CARD11	373,301	intergenic_region	5.31E-06	1.86E-02	−0.06 ± 0.01	0.32
ADG	rs469759962	15	28	45,058,986	TMEM72	5434	intergenic_region	9.68E-06	2.96E-02	−0.05 ± 0.01	0.31
ADG	rs137389740	32	29	41,512,334	SCGB1A1	7615	intergenic_region	3.74E-06	1.37E-02	−0.02 ± 0.00	0.36
MWT	rs210255011	37	1	118,345,325	ERICH6	26,609	intergenic_region	3.85E-06	8.48E-03	0.60 ± 0.13	0.40
MWT	rs43320298	7	2	113,058,683	ENSBTAG00000040156	73,281	intergenic_region	7.62E-07	2.07E-03	−1.36 ± 0.28	0.43
MWT	rs110358394	58	5	106,266,665	CCND2	Within	intron_variant	3.20E-07	1.08E-03	0.84 ± 0.17	0.46
MWT	Chr6:39111019	179	6	39,111,019	LCORL	118,907	intergenic_region	1.59E-44	5.39E-38	2.30 ± 0.16	5.80
MWT	rs109901274	88	7	93,244,933	ARRDC3	Within	missense_variant	9.61E-09	5.22E-05	0.76 ± 0.13	0.70
MWT	rs446606774	4	11	68,821,419	GALNT14	Within	intron_variant	7.92E-07	2.12E-03	1.97 ± 0.40	0.39
MWT	rs134215421	59	14	25,006,125	PLAG1	1166	downstream_gene_variant	2.08E-28	1.59E-23	−1.91 ± 0.17	2.69
MWT	rs41934045	193	20	4,563,925	ERGIC1	Within	intron_variant	6.12E-21	2.52E-16	1.42 ± 0.15	1.77
MWT	rs209660822	74	21	21,679,784	AP3S2	Within	3’UTR_variant	8.25E-06	1.65E-02	0.74 ± 0.17	0.35
MWT	rs133223744	6	26	8,545,128	A1CF	Within	intron_variant	3.27E-06	7.45E-03	2.12 ± 0.45	0.30

¹RFI residual feed intake in kg of DMI per day, DMI daily dry matter intake in kg per day, ADG average daily gain in kg, MWT metabolic body weight in kg
²The number of significant support SNPs associated with a lead SNP within 70 k bps
³The nearest annotated gene to the significant SNP. The annotated gene database was downloaded from https://www.ensembl.org/index.html
⁴SNP designated as in a gene or distance (bp) from a gene region in the UMD3.1 bovine genome assembly
⁵Functional annotation for the SNP
⁶FDR = genome-wise false discovery rate (FDR) calculated followed the Benjamini-Hochberg procedure [32]
^7,8The allele substitution effect (b) ± standard error (SE) and phenotypic variance explained by the significant SNP, respectively

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