Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

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

doi:10.1186/s12864-019-6273-1

Table 3 A summary of SNP allele substitution effects and additive genetic variance for each class based on imputed 7.8 M WGS variant GWAS for carcass merit traits 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: II: carcass merit traits

Trait^a	Class^b	no_of_SNP^c	class_mean^d	Ratio^e	Vgf ± SE^f	Vgo ± SE^g	Vg_total ± SE^h	Vgf/SNPⁱ	Vgf_Ratio^j
HCW	Intergenic region variants	5,251,680	7.168859	1.0004	222.95 ± 49.14	188.13 ± 47.74	411.08 ± 48.44	4.24531	0.512854
	Downstream gene variants	253,163	7.520336	1.0495	60.97 ± 39.03	349.56 ± 49.21	410.53 ± 44.47	24.082334	2.909263
	Upstream gene variants	285,798	7.505758	1.0474	39.13 ± 38.31	370.24 ± 49.29	409.37 ± 44.22	13.691187	1.653962
	Synonymous variants	32,019	7.087438	0.9890	2.05 ± 32.98	406.81 ± 46.26	408.86 ± 40.3	6.411609	0.774554
	Intron variants	1,987,366	7.055907	0.9846	143.3 ± 45.55	266.95 ± 49.52	410.25 ± 47.59	7.210423	0.871054
	Missense variants	17,654	7.920537	1.1053	0.000836 ± 26.23	413.7 ± 42.31	413.7 ± 35.35	0.004735	0.000572
	3′ UTR variants	15,851	7.229731	1.0089	2.98 ± 21.86	406 ± 39.82	408.98 ± 32.28	18.816321	2.273103
	5′ UTR variants	3309	7.408689	1.0339	0.000836 ± 16.51	421.81 ± 37.35	421.81 ± 29.07	0.025264	0.003052
	Other regulatory regions	6371	7.792834	1.0875	0.000836 ± 23.25	411.98 ± 40.68	411.98 ± 33.29	0.013122	0.001585
AFAT	Intergenic region variants	5,251,680	0.022854	1.0049	2.75 ± 0.69	0.67 ± 0.64	3.42 ± 0.67	0.052299	0.155457
	Downstream gene variants	253,163	0.023221	1.0210	0.000011 ± 0.55	3.91 ± 0.7	3.91 ± 0.63	0.000004	0.000013
	Upstream gene variants	285,798	0.02344	1.0306	0.000011 ± 0.51	3.6 ± 0.67	3.60 ± 0.60	0.000004	0.000011
	Synonymous variants	32,019	0.022847	1.0046	0.47 ± 0.47	2.98 ± 0.63	3.45 ± 0.56	1.482551	4.406805
	Intron variants	1,987,366	0.022241	0.9779	0.65 ± 0.64	2.78 ± 0.7	3.43 ± 0.67	0.032884	0.097746
	Missense variants	17,654	0.025805	1.1346	0.06 ± 0.37	3.39 ± 0.57	3.44 ± 0.48	0.314206	0.933962
	3′ UTR variants	15,851	0.024082	1.0589	0.18 ± 0.34	3.27 ± 0.54	3.45 ± 0.45	1.145354	3.404504
	5′ UTR variants	3309	0.024767	1.0890	0.000011 ± 0.25	3.45 ± 0.5	3.45 ± 0.40	0.000332	0.000988
	Other regulatory regions	6371	0.024345	1.0704	0.000011 ± 0.36	3.54 ± 0.56	3.55 ± 0.47	0.000173	0.000513
REA	Intergenic region variants	5,251,680	0.138587	0.9972	13.81 ± 4.49	19.18 ± 4.42	32.99 ± 4.46	0.262918	0.032449
	Downstream gene variants	253,163	0.145748	1.0488	6.55 ± 3.73	26.32 ± 4.63	32.87 ± 4.21	2.587783	0.319378
	Upstream gene variants	285,798	0.144594	1.0405	6.7 ± 3.76	26.01 ± 4.66	32.71 ± 4.24	2.343388	0.289216
	Synonymous variants	32,019	0.13927	1.0022	3.89 ± 3.14	28.81 ± 4.34	32.7 ± 3.79	12.144655	1.498865
	Intron variants	1,987,366	0.138017	0.9931	14.76 ± 4.27	18.2 ± 4.57	32.96 ± 4.42	0.742811	0.091676
	Missense variants	17,654	0.160403	1.1542	2.12 ± 2.49	30.79 ± 3.88	32.91 ± 3.27	12.029908	1.484703
	3′ UTR variants	15,851	0.144689	1.0411	1.73 ± 2.1	30.97 ± 3.73	32.71 ± 3.03	10.944533	1.350749
	5′ UTR variants	3309	0.145881	1.0497	0.09 ± 1.48	32.7 ± 3.45	32.79 ± 2.66	2.69595	0.332728
	Other regulatory regions	6371	0.152593	1.0980	1.86 ± 2.28	31.04 ± 3.77	32.9 ± 3.12	29.171151	3.600236
LMY	Intergenic region variants	5,251,680	0.021969	1.0046	2.85 ± 0.68	0.8 ± 0.64	3.66 ± 0.66	0.054312	0.379217
	Downstream gene variants	253,163	0.022022	1.0070	0.00001 ± 0.55	4.09 ± 0.69	4.09 ± 0.62	0.000004	0.000028
	Upstream gene variants	285,798	0.022437	1.0260	0.00001 ± 0.51	3.72 ± 0.66	3.72 ± 0.59	0.000003	0.000024
	Synonymous variants	32,019	0.021771	0.9956	0.31 ± 0.46	3.39 ± 0.62	3.70 ± 0.54	0.95339	6.656776
	Intron variants	1,987,366	0.021469	0.9818	0.73 ± 0.63	2.94 ± 0.69	3.67 ± 0.66	0.036739	0.256519
	Missense variants	17,654	0.024785	1.1334	0.04 ± 0.35	3.65 ± 0.55	3.69 ± 0.46	0.244018	1.703789
	3′ UTR variants	15,851	0.02225	1.0175	0.00001 ± 0.33	3.81 ± 0.54	3.81 ± 0.45	0.000063	0.000440
	5′ UTR variants	3309	0.023045	1.0538	0.00001 ± 0.25	3.72 ± 0.5	3.72 ± 0.4	0.000302	0.002110
	Other regulatory regions	6371	0.022794	1.0423	0.00001 ± 0.36	3.84 ± 0.56	3.84 ± 0.47	0.000157	0.001096
CMAR	Intergenic region variants	5,251,680	6.845916	0.9963	667.29 ± 214.86	600.03 ± 205.38	1267.33 ± 210.16	12.706271	0.015578
	Downstream gene variants	253,163	7.285638	1.0603	192.91 ± 169.25	1081.56 ± 206.95	1274.47 ± 189.17	76.199958	0.093423
	Upstream gene variants	285,798	7.377171	1.0736	330.95 ± 170.69	927.5 ± 208.27	1258.45 ± 190.46	115.797731	0.141971
	Synonymous variants	32,019	7.213334	1.0498	363.28 ± 151.71	897.33 ± 193.21	1260.61 ± 173.75	1134.569787	1.391014
	Intron variants	1,987,366	6.79074	0.9883	385.01 ± 200.95	883.24 ± 220.43	1268.25 ± 210.94	19.372642	0.023751
	Missense variants	17,654	8.065681	1.1738	215.62 ± 124.41	1044.92 ± 177.69	1260.54 ± 153.51	1221.362297	1.497424
	3′ UTR variants	15,851	7.0756	1.0297	0.004 ± 99.99	1284.05 ± 166.53	1284.05 ± 137.72	0.024427	0.000030
	5′ UTR variants	3309	7.507205	1.0925	30.35 ± 72.08	1237.79 ± 152.58	1268.14 ± 119.70	917.210033	1.124525
	Other regulatory regions	6371	8.107115	1.1798	244.87 ± 110.14	1010.4 ± 168.07	1255.27 ± 142.21	3843.536337	4.712283

^aHCW hot carcass weight in kg, AFAT average backfat thickness in mm, REA rib eye area in cm², LMY lean meat yield in %, CMAR carcass marbling score from 100 (trace marbling) to 499 (more marbling).^bOther regulatory regions consisted of splice regions in intron variants, disruptive in-frame deletion, splice region variants, etc. Detail functional class assignments of DNA variants can be found in (Additional file 3: Table S1). ^cNumber of DNA variants (or SNPs in text for simplicity). ^dclass_mean is the average of squared SNP allele substitution effects (class_mean) for the functional class. ^eRatio is ratio of the class_mean of the functional class over the weighted average of class_means of all functional classes. ^fV_gf ± SE is additive genetic variance of the functional class ± standard error (SE). ^gV_go ± SE is additive genetic variance of the rest of SNPs in other functional classes ± standard error (SE). ^hVg_total ± SE is total additive genetic variance of all 7.8 M WGS variants ± standard error (SE). ⁱV_gf/SNP is additive genetic variance of the functional class per SNP × 10⁵. ^jVgf_Ratio is ratio of additive genetic variance of the functional class per SNP over the average of additive genetic variance per SNP of all functional classes based on the imputed 7.8 M WGS variant GWAS

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