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. 2020 Jan 13;21:36. 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

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