. 2020 Jan 13;21:36. doi: 10.1186/s12864-019-6362-1

Table 3.

A summary of SNP allele substitution effect and additive genetic variance for each functional class based on imputed 7.8 M variant GWAS for RFI and its component traits in a beef cattle multibreed population

Trait¹	Class²	no_of_SNP³	class_mean⁴	Ratio⁵	Vgf ± SE⁶	Vgo ± SE⁷	Vg_total ± SE⁸	Vgf/SNP⁹	Vgf_Ratio¹⁰
RFI	Intergenic region variants	5,251,680	0.000461	0.997835	0.067 ± 0.015	0.048 ± 0.014	0.12 ± 0.01	0.001283	0.05765900
	Downstream gene variants	253,163	0.000478	1.034632	0.01 ± 0.012	0.105 ± 0.015	0.12 ± 0.01	0.004142	0.18608265
	Upstream gene variants	285,798	0.000480	1.038961	0.002 ± 0.011	0.114 ± 0.015	0.12 ± 0.01	0.000644	0.02894225
	Synonymous variants	32,019	0.000454	0.982684	0.01 ± 0.01	0.106 ± 0.014	0.12 ± 0.01	0.031869	1.43185934
	Intron variants	1,987,366	0.000461	0.997835	0.039 ± 0.014	0.077 ± 0.015	0.12 ± 0.01	0.001966	0.08835385
	Missense variants	17,654	0.000522	1.129870	0.006 ± 0.008	0.11 ± 0.013	0.12 ± 0.01	0.036643	1.64638613
	3′ UTR variants	15,851	0.000490	1.060606	0.011 ± 0.007	0.105 ± 0.012	0.12 ± 0.01	0.070273	3.15738258
	5′ UTR variants	3309	0.000515	1.114719	0.002 ± 0.005	0.114 ± 0.011	0.12 ± 0.01	0.053490	2.40333421
	Other regulatory regions	6371	0.000501	1.084416	0 ± 0.007	0.119 ± 0.012	0.12 ± 0.01	0.000000	0.0000000
DMI	Intergenic region variants	5,251,680	0.000946	0.998944	0.219 ± 0.032	0.141 ± 0.03	0.36 ± 0.03	0.004173	0.15156143
	Downstream gene variants	253,163	0.000970	1.024287	0.011 ± 0.025	0.348 ± 0.033	0.36 ± 0.03	0.004527	0.16439637
	Upstream gene variants	285,798	0.000967	1.021119	0.00001 ± 0.024	0.362 ± 0.033	0.36 ± 0.03	0.000000	0.00001300
	Synonymous variants	32,019	0.000924	0.975713	0.009 ± 0.021	0.35 ± 0.031	0.36 ± 0.03	0.029379	1.06696756
	Intron variants	1,987,366	0.000944	0.996832	0.119 ± 0.029	0.241 ± 0.032	0.36 ± 0.03	0.005984	0.21733452
	Missense variants	17,654	0.001038	1.096093	0.00001 ± 0.02	0.362 ± 0.029	0.36 ± 0.02	0.000006	0.00020571
	3′ UTR variants	15,851	0.001009	1.065470	0.032 ± 0.016	0.327 ± 0.027	0.36 ± 0.02	0.203703	7.39785415
	5' UTR variants	3309	0.000978	1.032735	0.00001 ± 0.011	0.365 ± 0.026	0.37 ± 0.02	0.000030	0.00109752
	Other regulatory regions	6371	0.001017	1.073918	0.00001 ± 0.015	0.362 ± 0.028	0.36 ± 0.02	0.000016	0.00057003
ADG	Intergenic region variants	5,251,680	0.000052	1.000000	0.009 ± 0.002	0.004 ± 0.002	0.014 ± 0.002	0.000178	0.05631654
	Downstream gene variants	253,163	0.000054	1.038462	0.0004 ± 0.001	0.013 ± 0.002	0.014 ± 0.002	0.000143	0.04529727
	Upstream gene variants	285,798	0.000054	1.038462	0 ± 0.001	0.014 ± 0.002	0.014 ± 0.001	0.000000	0.00000000
	Synonymous variants	32,019	0.000051	0.980769	0.001 ± 0.001	0.013 ± 0.002	0.014 ± 0.001	0.003891	1.22935097
	Intron variants	1,987,366	0.000051	0.980769	0.003 ± 0.002	0.01 ± 0.002	0.014 ± 0.002	0.000176	0.05555651
	Missense variants	17,654	0.000058	1.115385	0 ± 0.001	0.014 ± 0.001	0.014 ± 0.001	0.000000	0.00000000
	3′ UTR variants	15,851	0.000054	1.038462	0.001 ± 0.001	0.013 ± 0.001	0.014 ± 0.001	0.005924	1.87143409
	5' UTR variants	3309	0.000055	1.057692	0 ± 0.001	0.014 ± 0.001	0.014 ± 0.001	0.000000	0.00000000
	Other regulatory regions	6371	0.000060	1.153846	0.001 ± 0.001	0.013 ± 0.001	0.014 ± 0.001	0.018176	5.74204463
MWT	Intergenic region variants	5,251,680	0.040609	0.998795	13.14 ± 1.47	7.93 ± 1.38	21.07 ± 1.42	0.250139	0.43808451
	Downstream gene variants	253,163	0.041833	1.028900	0.9 ± 1.1	20.14 ± 1.53	21.04 ± 1.34	0.354482	0.62082809
	Upstream gene variants	285,798	0.041653	1.024472	0.76 ± 1.09	20.27 ± 1.53	21.03 ± 1.33	0.265853	0.46560607
	Synonymous variants	32,019	0.040382	0.993212	0.71 ± 0.97	20.34 ± 1.45	21.05 ± 1.24	2.216215	3.88140336
	Intron variants	1,987,366	0.040446	0.994786	6.3 ± 1.32	14.77 ± 1.48	21.07 ± 1.4	0.317024	0.55522447
	Missense variants	17,654	0.044912	1.104629	0.00004 ± 0.75	21.14 ± 1.33	21.14 ± 1.08	0.000227	0.00039682
	3′ UTR variants	15,851	0.041232	1.014118	0.27 ± 0.63	20.75 ± 1.27	21.03 ± 1.01	1.733070	3.03524000
	5' UTR variants	3309	0.041624	1.023759	0.00004 ± 0.45	21.29 ± 1.19	21.29 ± 0.91	0.001209	0.00211709
	Other regulatory regions	6371	0.043722	1.075360	0.00004 ± 0.65	21.05 ± 1.28	21.05 ± 1.02	0.000628	0.00109959

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

²Other 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 S2)

³Number of DNA variants (or SNPs in text for simplicity)

⁴class_mean is the average of squared SNP allele substitution effects (class_mean) for the functional class

⁵Ratio is ratio of the class_mean of the functional class over the weighted average of class_means of all functional classes

⁶V_gf ± SE is additive genetic variance of the functional class ± standard error (SE)

⁷V_go ± SE is additive genetic variance of the rest of SNPs in other functional classes ± standard error (SE)

⁸Vg_total ± SE is total additive genetic variance of all 7.8 M WGS variants ± standard error (SE)

⁹V_gf/SNP is additive genetic variance of the functional class per SNP × 10⁵

¹⁰Vgf_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