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. 2013 Dec 26;8(12):e83625. doi: 10.1371/journal.pone.0083625

Table 3. Associations of SNPs with EBVs of five milk production traits (LSM±SE).

SNP ID Genotype MY FY PY FP PP
SNP1 TT 538.94±151.12A 2.21±4.78 14.65±4.33Aa −17.91±4.99B −2.53±2.27
TG 397.51±150.05B 5.06±4.75 10.79±4.29b −9.39±4.95A −1.88±2.25
GG 284.31±157.94B 4.02±5.02 6.48±4.52Bb −6.36±5.26A −2.54±2.37
P-value 0.0002* 0.1849 <.0001* <.0001* 0.6132
σ2 a/σ2 P 1.28E-02 1.46E-04 1.76E-02 1.75E-02 9.36E-05
SNP2 TT 434.81±148.54 3.87±4.69 11.62±4.26 −12.14±4.89 −2.24±2.23
CT 508.20±200.83 4.61±6.52 16.86±5.73 −14.24±6.90 0.69±3.05
P-value 0.5916 0.8706 0.1769 0.6700 0.1644
σ2 a/σ2 P 1.14E-02 8.57E-04 1.54E-02 7.16E-03 8.01E-05
SNP3 GG 459.49±152.55 0.45±4.83 11.40±4.37 −16.83±5.05B −3.25±2.29
GA 453.63±149.91 5.43±4.74 12.37±4.29 −11.12±4.95A −2.08±2.25
AA 354.44±154.36 4.51±4.89 10.24±4.42 −8.42±5.12A −1.07±2.32
P-value 0.1532 0.0121 0.3828 0.0003* 0.0691
σ2 a/σ2 P 2.70E-03 2.75E-03 4.97E-04 1.19E-02 4.43E-03
SNP4 CC 431.17±156.89 −1.32±4.99 9.82±4.49 −17.71±5.22 −3.91±2.36
CT 424.36±149.83 4.81±4.74 11.68±4.29 −10.76±4.94 −1.84±2.25
TT 457.63±151.76 4.69±4.81 12.55±4.35 −12.00±5.02 −2.04±2.28
P-value 0.7771 0.0089 0.3382 0.0079 0.0890
σ2 a/σ2 P 2.46E-04 4.56E-03 1.70E-03 2.97E-03 1.89E-03
SNP5 GG 344.41±150.02C 2.66±4.74 8.82±4.29C −10.05±4.95A −2.12±2.25
GA 495.03±150.64B 5.12±4.77 13.62±4.32B −13.12±4.97A −2.19±2.26
AA 823.33±170.87A 5.55±5.48 23.26±4.88A −24.40±5.76B −3.06±2.58
P-value <.0001* 0.2244 <.0001* <.0001* 0.8023
σ2 a/σ2 P 5.49E-02 6.19E-04 5.99E-02 4.59E-02 1.27E-03
SNP6 TT 462.08±148.76A 3.79±4.70 12.14±4.26 −13.26±4.90B −2.61±2.23B
TC 243.24±159.42B 3.91±5.08 8.36±4.56 −4.82±5.32A 0.77±2.39A
CC 692.83±560.50AB 42.14±18.70 13.94±15.92 20.02±20.08AB −7.34±8.62AB
P-value 0.0036* 0.1070 0.1282 0.0005* 0.0032*
σ2 a/σ2 P 3.38E-02 2.39E-01 6.27E-03 9.24E-02 4.75E-02
SNP7 AA 339.04±150.02C 2.53±4.74 8.68±4.29C −9.97±4.95A −2.08±2.25
AG 501.70±150.64B 5.22±4.77 13.82±4.31B −13.28±4.97A −2.21±2.26
GG 834.06±171.36A 6.04±5.49 23.36±4.89A −24.24±5.78B −3.30±2.59
P-value <.0001* 0.1558 <.0001* <.0001* 0.6942
σ2 a/σ2 P 5.73E-02 1.13E-03 6.01E-02 4.43E-02 2.05E-03
SNP8 TT 344.62±150.02Ba 2.66±4.74 8.82±4.29C −10.05±4.95A −2.12±2.25
TC 494.59±150.61Bb 5.12±4.77 13.71±4.31B −13.11±4.97A −2.09±2.26
CC 843.98±171.90A 5.54±5.51 23.05±4.91A −25.15±5.79B −3.92±2.59
P-value <.0001* 0.2246 <.0001* <.0001* 0.4362
σ2 a/σ2 P 1.58E-02 3.13E-05 1.41E-02 1.49E-02 1.79E-03
SNP9 AA 63.93±148.71 3.85±4.69 12.23±4.26 −13.26±4.90a −2.58±2.23a
AG 158.72±164.82 4.10±5.27 6.31±4.71 −1.44±5.53b 1.52±2.48b
P-value 0.0001* 0.9233 0.0081 <.0001* 0.0007*
σ2 a/σ2 P 5.66E-03 5.46E-03 3.32E-02 1.01E-02 2.72E-08
SNP10 CC 501.00±150.82Aa 1.85±4.77 13.29±4.32Aa −16.89±4.98B −2.70±2.26
CT 422.36±150.25a 5.99±4.75 11.57±4.30a −9.31±4.96A −1.89±2.25
TT 259.26±157.97Bb 2.35±5.02 6.45±4.52Bb −7.21±5.26A −1.72±2.38
P-value 0.0012* 0.0201 0.0013* <.0001* 0.4489
σ2 a/σ2 P 1.43E-02 4.55E-03 1.50E-02 1.18E-02 6.12E-04
SNP11 CC 598.73±151.49A 5.93±4.79 15.94±4.34A −16.12±5.01B −3.16±2.27
CA 383.22±150.00B 3.06±4.74 10.37±4.29B −11.07±4.95A −1.88±2.25
AA 255.05±157.43B 2.09±5.01 6.77±4.51B −7.19±5.24A −1.21±2.37
P-value <.0001* 0.1087 <.0001* 0.0003* 0.0926
σ2 a/σ2 P 2.20E-02 6.18E-04 1.97E-02 1.26E-02 2.95E-03
SNP12 AA 808.89±168.51A 8.45±5.39 22.09±4.82A −20.81±5.67B −3.73±2.54
AC 583.80±154.65A 7.42±4.91 17.17±4.43A −13.98±5.13AB −1.49±2.32
CC 367.38±149.03B 2.59±4.71 9.43±4.27B −10.99±4.91A −2.26±2.23
P-value <.0001* 0.0069 <.0001* 0.0035* 0.2912
σ2 a/σ2 P 2.39E-02 8.04E-03 3.27E-02 5.38E-03 1.37E-04
SNP13 TT 521.16±150.22A 4.11±4.75 13.67±4.30Aa −15.15±4.96Bc −2.95±2.25
TG 384.39±150.51Ba 3.61±4.76 10.59±4.31a −10.49±4.97b −1.66±2.26
GG 157.36±167.47Bb 3.95±5.36 4.48±4.79Bb −1.64±5.63Aa −0.40±2.52
P-value <.0001* 0.9473 0.0002* <.0001* 0.0521
σ2 a/σ2 P 2.89E-02 7.47E-06 2.43E-02 3.36E-02 4.86E-03
A, B

Within the same column with different superscripts means P<0.01; a,b within the same column with different superscripts means P<0.05.

*

P indicates the significant association after Bonferroni correction for multiple testing at the significance level α = 0.05; σ2 a/σ2 P represents the proportion of variance explained by a SNP.