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. 2020 Jan 13;21:38. 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

Traita Classb no_of_SNPc class_meand Ratioe Vgf ± SEf Vgo ± SEg Vg_total ± SEh Vgf/SNPi Vgf_Ratioj
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. fVgf ± SE is additive genetic variance of the functional class ± standard error (SE). gVgo ± 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). iVgf/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