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Table 2 SNP marker associations and estimated effects for ADFI and ADG in the discovery population of crossbred steers.

From: Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

       Average Daily Feed Intake (ADFI) Average Daily Gain (ADG)
Marker1 Gene2 Position3 IUB # Genotypes4 MAF Effect5 P -value Correction6 Effect P -value Correction
ARS-BFGL-NGS-77584 37855236 R 1182 G = 0.10 -0.026 0.8 NS -0.0078 0.7 NS
After2Run10KSet7323 37856744 Y 1075 T = 0.30 -0.14 0.01 NS -0.029 0.01 NS
Hapmap31601-BTC-034240 37859827 R 1076 G = 0.28 -0.15 0.005 NS -0.033 0.004 NS
Hapmap28705-BTC-034230 37862818 S 1090 G = 0.31 -0.14 0.010 NS -0.033 0.003 NS
Hapmap25169-BTC-034210 37870369 R 1186 A = 0.30 -0.15 0.006 NS -0.033 0.003 NS
Hapmap30444-BTC-052947 37875093 Y 1164 C = 0.49 0.16 0.004 NS 0.036 0.002 NS
After2Run10KSet5598 37875791 Y 1186 C = 0.30 -0.14 0.01 NS -0.032 0.004 NS
Hapmap32743-BTC-052998 37879284 R 1011 A = 0.23 -0.073 0.2 NS -0.024 0.04 NS
Hapmap23977-BTC-053017 37880952 M 1176 A = 0.30 -0.15 0.006 NS -0.032 0.005 NS
79140_312 LAP3 37964162 INDEL 1165 DEL = 0.09 0.11 0.2 NS -0.013 0.5 NS
Hapmap56977-ss46527055 LAP3 37967630 R 1192 A = 0.13 -0.051 0.5 NS -0.013 0.4 NS
79152_265 LAP3 37977863 Y 1181 C = 0.33 -0.020 0.7 NS -0.021 0.05 NS
79154_194 LAP3 37979109 Y 1078 T = 0.38 -0.0072 0.9 NS -0.021 0.06 NS
79154_347 LAP3 37979262 S 1098 C = 0.34 -0.022 0.7 NS -0.021 0.04 NS
79158_103 LAP3 37984197 S 1193 G = 0.34 0.026 0.6 NS 0.021 0.05 NS
79158_104 LAP3 37984198 R 1190 G = 0.33 -0.021 0.7 NS -0.020 0.07 NS
79160_105 LAP3 37985986 Y 1127 T = 0.34 -0.0086 0.9 NS -0.019 0.08 NS
79162_241 LAP3 37986804 K 1124 T = 0.37 -0.0064 0.9 NS -0.22 0.05 NS
79162_246 LAP3 37986809 Y 1197 C = 0.34 -0.020 0.7 NS -0.21 0.04 NS
ARS-BFGL-NGS-44699 38011603 S 1183 C = 0.10 -0.085 0.3 NS -0.021 0.2 NS
BTA-100891   38076964 Y 1063 T = 0.26 -0.083 0.1 NS -0.028 0.008 NS
83704_2347 NCAPG 38157198 R 1085 A = 0.42 0.18 0.0006 0.03 0.046 2.E-05 0.0009
83704_366 NCAPG 38157330 R 1187 G = 0.12 -0.11 0.2 NS -0.013 0.4 NS
83708_361 NCAPG 38158932 Y 1092 C = 0.41 0.17 0.001 0.05 0.045 4.E-05 0.002
83712_1687 NCAPG 38163729 R 1004 G = 0.47 -0.16 0.003 NS -0.045 9.E-05 0.004
83714_2247 NCAPG 38164403 K 1132 G = 0.34 0.21 8.E-05 0.004 0.059 1.E-07 5.E-06
83724_658 NCAPG 38180790 Y 1100 C = 0.41 0.17 0.001 0.05 0.045 5.E-05 0.002
83730_778 NCAPG 38195339 M 1022 A = 0.42 0.17 0.003 NS 0.058 1.E-06 0.00005
83732_316 NCAPG 38195743 R 1050 G = 0.42 0.14 0.008 NS 0.044 1.E-04 0.005
Hapmap24122-BTC-041153 38217816 K 1193 G = 0.35 0.22 1.E-05 0.0005 0.059 2.E-08 9.E-07
Hapmap24041-BTC-041151 38220879 K 1192 T = 0.35 0.22 1.E-05 0.0005 0.059 2.E-08 9.E-07
Hapmap31609-BTC-041148 38223329 R 1192 A = 0.38 0.17 0.0005 0.02 0.045 1.E-05 0.0005
Hapmap28154-BTC-0411348 LCORL 38228679 R 935 C = 0.38 0.18 0.0003 0.01 0.045 2.E-05 0.0009
Hapmap27082-BTC-041131 LCORL 38233962 R 1121 G = 0.37 0.18 0.0002 0.009 0.047 4.E-06 0.0002
Hapmap26855-BTC-041123 LCORL 38239191 R 1075 G = 0.33 0.21 8.E-05 0.004 0.058 1.E-07 5.E-06
Hapmap23341-BTC-041113 LCORL 38250098 K 1161 T = 0.36 0.21 4.E-05 0.002 0.056 1.E-07 5.E-06
81441_243 LCORL 38255270 S 822 G = 0.28 -0.24 5.E-06 0.0002 -0.058 2.E-07 9E-06
81435_188 LCORL 38284737 Y 892 C = 0.38 0.17 0.0004 0.02 0.042 3.E-05 0.001
Hapmap28589-BTC-041045 9 LCORL 38300298 S 1190 G = 0.33 0.22 2.E-05 0.0009 0.061 1.E-08 5.E-07
Hapmap33629-BTC-041038 LCORL 38313142 Y 999 T = 0.30 0.22 2.E-05 0.0009 0.059 5.E-08 2.E-06
Hapmap28835-BTC-041022 LCORL 38326993 S 1061 G = 0.18 -0.12 0.07 NS -0.027 0.04 NS
81419_461 LCORL 38342145 M 1058 C = 0.05 -0.17 0.1 NS -0.046 0.04 NS
Hapmap33694-BTC-041005 LCORL 38342183 R 1190 G = 0.16 -0.10 0.1 NS -0.038 0.005 NS
81405_282 9 LCORL 38376731 M 1196 A = 0.33 0.22 2.E-05 0.0009 0.061 1.E-08 5.E-07
Hapmap33650-BTC-073421 38409471 Y 1041 C = 0.40 -0.14 0.004 NS -0.036 0.0003 0.01
Hapmap31943-BTC-050642 38427989 Y 1181 C = 0.08 -0.11 0.2 NS -0.039 0.02 NS
BTB-00249053 38481012 Y 1183 T = 0.24 -0.12 0.03 NS -0.029 0.01 NS
  1. 1 Name of publicly available markers from the following references: Van Tassell CP et al. [26], Bovine HapMap Consortium et al. [27], and Bovine Genome Sequencing and Analysis Consortium et al. [28]
  2. 2 SNP located within a gene locus are presented in this column. The gene loci for LAP3, NCAPG, and LCORL are: 37,961,725 - 37,987,164 bp, 38,153,047-38,199,153 bp, and 38,227,955-38,378,385 bp on the Btau 4.0 genome assembly.
  3. 3 Position based on the Btau 4.0 Bovine Genome Assembly.
  4. 4 Number of genotypic calls used for statistical analysis.
  5. 5 ADFI and ADG effects are displayed as kg/d. Effects are presented for the minor allele.
  6. 6 Correction for multiple testing performed by multiplying the P-values by the number of markers tested (n = 47). NS = not significant, P-value > 0.05.
  7. 7 Markers evaluated in Setoguchi et al. [8] and Eberlein et al. [11].
  8. 8 Marker evaluated in Charolais and German Holstein population in Eberlein et al. [11].
  9. 9 Markers in bold font, Hapmap28589-BTC-041045 and 81405_282, were significantly associated with ADG in the validation population of animals (P = 0.04 and 0.03, respectively).
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