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. 2017 May 19;18:47. doi: 10.1186/s12863-017-0516-4

Table 2.

Associations of 19 SNPs of ATF3 gene with milk production traits in Chinese Holstein cattle during two lactations (LSM ± SE)

SNPs Lactation Genotype (No.) Milk yield (kg) Fat yield (kg) Fat percentage (%) Protein yield (kg) Protein percentage (%)
g.72834301C > A 1 CC(222) 10,305 ± 73.52a 346.63 ± 3.19Aa 3.37 ± 0.03 306.89 ± 2.32Aa 2.98 ± 0.01
CA(553) 10,339 ± 62Aa 343.59 ± 2.77Aa 3.34 ± 0.026 305.6 ± 2.01Aa 2.96 ± 0.008
AA(299) 10,146 ± 68.79Bb 336.42 ± 3.01B 3.33 ± 0.028 300.12 ± 2.19B 2.96 ± 0.009
P 0.001** 0.0002** 0.2065 0.0003** 0.0737
2 CC(170) 10,707 ± 78.61ab 385.28 ± 3.39ab 3.61 ± 0.032 315.96 ± 2.47Aa 2.96 ± 0.011Aa
CA(371) 10,785 ± 64.99Aa 390.15 ± 2.89Aa 3.63 ± 0.027 322.03 ± 2.1B 2.99 ± 0.009B
AA(212) 10,567 ± 73.79Bb 379.59 ± 3.21Bb 3.59 ± 0.03 312.96 ± 2.34Aa 2.96 ± 0.01Aa
P 0.0051** 0.0004** 0.2901 <.0001** 0.0005**
g.72834229C > A 1 CC(221) 10,318 ± 73 346.25 ± 3.17Aa 3.36 ± 0.03 306.34 ± 2.31Aa 2.97 ± 0.01a
CA(553) 10,315 ± 61.81 341.19 ± 2.75b 3.32 ± 0.026 303.89 ± 2.01ab 2.95 ± 0.008b
AA(299) 10,194 ± 68.95 337.13 ± 3.02Bb 3.31 ± 0.028 301.01 ± 2.2Bb 2.96 ± 0.009ab
P 0.0523 0.003** 0.1234 0.0212* 0.0494*
2 CC(169) 10,691 ± 78.17a 383.01 ± 3.37a 3.6 ± 0.032 314.66 ± 2.45Aa 2.95 ± 0.011Aa
CA(369) 10,802 ± 64.49Aa 388.4 ± 2.86Aa 3.61 ± 0.027 321.87 ± 2.08B 2.99 ± 0.009B
AA(211) 10,493 ± 73.62Bb 374.92 ± 3.19Bb 3.58 ± 0.03 309.72 ± 2.32Ab 2.96 ± 0.01Aa
P <.0001** <.0001** 0.5118 <.0001** 0.001**
g.72833969A > G 1 GG(300) 10,147 ± 68.91Aa 333.48 ± 3.02Aa 3.3 ± 0.028 299.66 ± 2.2A 2.96 ± 0.009
GA(551) 10,318 ± 61.59Bb 338.88 ± 2.74b 3.31 ± 0.025 304.12 ± 2Ba 2.95 ± 0.008
AA(222) 10,273 ± 72.9ab 342.05 ± 3.16Bb 3.35 ± 0.03 304.89 ± 2.3Ba 2.97 ± 0.010
P 0.0049** 0.0033** 0.1466 0.0057** 0.053
2 GG(211) 10,466 ± 75.09A 372.1 ± 3.27A 3.56 ± 0.031 309.3 ± 2.38Aa 2.96 ± 0.010Aa
GA(369) 10,793 ± 65.5Ba 388.2 ± 2.91Ba 3.61 ± 0.027 321.77 ± 2.12B 2.99 ± 0.009B
AA(169) 10,700 ± 78.46Ba 382.28 ± 3.38Bb 3.59 ± 0.032 315.32 ± 2.46Ab 2.95 ± 0.011Aa
P <.0001** <.0001** 0.1837 <.0001** 0.0015**
g.72833562G > T 1 TT(221) 10,340 ± 73.11 347.61 ± 3.17Aa 3.37 ± 0.03 306.84 ± 2.31a 2.97 ± 0.01
TG(552) 10,360 ± 62.09 343.16 ± 2.77a 3.33 ± 0.026 305.18 ± 2.02a 2.95 ± 0.008
GG(299) 10,234 ± 68.85 338.54 ± 3.02Bb 3.32 ± 0.028 301.92 ± 2.2b 2.95 ± 0.009
P 0.0512 0.0029** 0.097 0.0275* 0.0779
2 TT(169) 10,769 ± 78.92Aa 386.76 ± 3.41Aa 3.6 ± 0.032 316.78 ± 2.48Aa 2.95 ± 0.011Aa
TG(370) 10,824 ± 64.37Aa 391.65 ± 2.85Aa 3.63 ± 0.027 322.38 ± 2.07B 2.98 ± 0.009B
GG(210) 10,528 ± 74.13B 377.34 ± 3.22B 3.59 ± 0.03 310.91 ± 2.34Ab 2.96 ± 0.01Aa
P <.0001** <.0001** 0.2651 <.0001** 0.0014**
c.291G > A 1 AA(31) 9757.9 ± 144.69A 326.63 ± 5.95Aa 3.37 ± 0.058 288.83 ± 4.34A 2.98 ± 0.021
AG(345) 10,202 ± 66.08Ba 339.19 ± 2.91b 3.34 ± 0.027 301.61 ± 2.12Ba 2.96 ± 0.009
GG(697) 10,268 ± 60.55Ba 343.04 ± 2.71Bc 3.35 ± 0.025 303.66 ± 1.98Ba 2.96 ± 0.008
P 0.0007** 0.0034** 0.6488 0.0008** 0.752
2 AA(25) 10,866 ± 165.07 400.94 ± 6.75Aa 3.68 ± 0.066 319.04 ± 4.93 2.94 ± 0.024
AG(226) 10,557 ± 73.54 382.33 ± 3.2Bb 3.62 ± 0.03 313.83 ± 2.33 2.98 ± 0.01
GG(503) 10,683 ± 61.69 385.82 ± 2.77b 3.62 ± 0.026 317.26 ± 2.01 2.98 ± 0.008
P 0.0504 0.0172* 0.6436 0.147 0.3771
c.489G > A 1 AA(31) 9774.7 ± 144.35A 326.99 ± 5.93Aa 3.36 ± 0.058 289.58 ± 4.32A 2.98 ± 0.021
AG(344) 10,239 ± 65.93Ba 338.76 ± 2.9c 3.32 ± 0.027 302.48 ± 2.11Ba 2.96 ± 0.009
GG(709) 10,294 ± 60.82Ba 342.86 ± 2.72Bb 3.34 ± 0.025 304.28 ± 1.98Ba 2.96 ± 0.008
P 0.0006** 0.0033** 0.4033 0.0009** 0.5871
2 AA(25) 10,971 ± 164.92ab 399.91 ± 6.75a 3.63 ± 0.066 322.88 ± 4.92ab 2.94 ± 0.024
AG(225) 10,657 ± 73.09Aa 386.05 ± 3.17b 3.61 ± 0.03 318.62 ± 2.31a 2.98 ± 0.01
GG(510) 10,847 ± 60.46Bb 390.87 ± 2.71ab 3.6 ± 0.025 323.16 ± 1.97b 2.97 ± 0.008
P 0.005** 0.0395* 0.8064 0.0461* 0.1971
c.*190A > G 1 AA(584) 10,178 ± 62.42a 338.65 ± 2.78Aa 3.35 ± 0.026 300.85 ± 2.02 2.96 ± 0.008
AG(444) 10,217 ± 63.84Aa 338.37 ± 2.83Aa 3.33 ± 0.026 301.91 ± 2.06 2.96 ± 0.009
GG(56) 9939.48 ± 113.17Bb 323.63 ± 4.7B 3.28 ± 0.046 294.8 ± 3.43 2.98 ± 0.016
P 0.031* 0.0014** 0.2273 0.0705 0.6105
2 AA(423) 10,792 ± 63.54 389.14 ± 2.82 3.61 ± 0.026 321.2 ± 2.05 2.98 ± 0.008
AG(295) 10,671 ± 67.97 387.7 ± 2.98 3.63 ± 0.028 318.92 ± 2.17 2.99 ± 0.009
GG(42) 10,736 ± 131.2 385.86 ± 5.42 3.58 ± 0.053 316.43 ± 3.95 2.94 ± 0.019
P 0.1326 0.7237 0.5687 0.249 0.0664
c.*321G > C 1 CC(53) 10,076 ± 114.66 329.19 ± 4.76 3.29 ± 0.046 298.66 ± 3.47 2.97 ± 0.016
CG(435) 10,277 ± 63.65 339.07 ± 2.82 3.32 ± 0.026 303.06 ± 2.05 2.96 ± 0.009
GG(587) 10,217 ± 62.36 338.28 ± 2.78 3.33 ± 0.026 301.31 ± 2.02 2.96 ± 0.008
P 0.1191 0.0698 0.5569 0.2362 0.583
2 CC(41) 10,584 ± 131.99 380.38 ± 5.45 3.6 ± 0.053 311.06 ± 3.97 2.94 ± 0.019a
CG(290) 10,690 ± 69.23 388.18 ± 3.04 3.64 ± 0.028 319.27 ± 2.21 2.99 ± 0.009b
GG(424) 10,706 ± 64.21 385.69 ± 2.86 3.62 ± 0.026 317.31 ± 2.08 2.97 ± 0.009ab
P 0.6383 0.2827 0.6702 0.0947 0.0371*
c.*326A > G 1 AA(587) 10,223 ± 62.03Aa 337.47 ± 2.77Aa 3.32 ± 0.026 301.41 ± 2.01Aa 2.96 ± 0.008
AG(431) 10,295 ± 63.85Aa 338.53 ± 2.83Aa 3.31 ± 0.026 303.33 ± 2.06Aa 2.95 ± 0.009
GG(57) 9904.58 ± 111.55B 322.04 ± 4.64B 3.28 ± 0.045 292.88 ± 3.38B 2.97 ± 0.016
P 0.0008** 0.0004** 0.5042 0.0026** 0.4722
2 AA(425) 10,789 ± 64.31 389.29 ± 2.86 3.62 ± 0.027 319.31 ± 2.08 2.97 ± 0.009
AG(285) 10,706 ± 68.79 387.76 ± 3.02 3.63 ± 0.028 318.88 ± 2.2 2.98 ± 0.009
GG(43) 10,572 ± 129.83 382.68 ± 5.36 3.62 ± 0.052 310.75 ± 3.91 2.95 ± 0.019
P 0.1309 0.3978 0.9601 0.0689 0.0988
c.*640G > A 1 AA(31) 9805.53 ± 145.34A 328.47 ± 5.97Aa 3.36 ± 0.058 290.54 ± 4.36A 2.97 ± 0.021
AG(340) 10,228 ± 66.3Ba 341.02 ± 2.92c 3.34 ± 0.027 302.39 ± 2.13Ba 2.95 ± 0.009
GG(709) 10,299 ± 60.44Ba 345.29 ± 2.7Bb 3.36 ± 0.025 304.73 ± 1.97Ba 2.96 ± 0.008
P 0.0009** 0.0018** 0.5681 0.0009** 0.655
2 AA(25) 10,910 ± 164.71 396.49 ± 6.74 3.63 ± 0.066 2.93 ± 0.024 2.93 ± 0.024
AG(221) 10,653 ± 73.17 381.19 ± 3.18 3.58 ± 0.03 2.97 ± 0.01 2.97 ± 0.01
GG(510) 10,763 ± 61.24 384.41 ± 2.75 3.58 ± 0.025 2.97 ± 0.008 2.97 ± 0.008
P 0.107 0.0533 0.7617 0.2326 0.2326
c.*685G > C 1 CC(30) 9978.84 ± 146.26 328.2 ± 6 3.32 ± 0.059 294.37 ± 4.38a 2.96 ± 0.021
CG(337) 10,272 ± 66.72 336.86 ± 2.94 3.3 ± 0.027 303.87 ± 2.14b 2.96 ± 0.009
GG(713) 10,302 ± 60.16 339.63 ± 2.69 3.31 ± 0.025 304.85 ± 1.96b 2.96 ± 0.008
P 0.0617 0.0588 0.6272 0.0331* 0.9781
2 CC(25) 11,131 ± 164.65Aa 398.09 ± 6.74a 3.57 ± 0.066 323.53 ± 4.92ab 2.92 ± 0.024
CG(221) 10,600 ± 73.44B 383.03 ± 3.19b 3.61 ± 0.03 314.94 ± 2.33a 2.97 ± 0.01
GG(511) 10,774 ± 61.52Ab 388.76 ± 2.77a 3.61 ± 0.025 319.05 ± 2.01b 2.97 ± 0.008
P 0.0008** 0.0168* 0.8299 0.0384* 0.05
c.*735 T > C 1 CC(30) 10,031 ± 146.66 330.74 ± 6.02 3.32 ± 0.059 296.27 ± 4.39 2.96 ± 0.021
CT(338) 10,256 ± 66.98 337.13 ± 2.95 3.3 ± 0.028 303.04 ± 2.15 2.96 ± 0.009
TT(712) 10,306 ± 60.38 339.99 ± 2.7 3.32 ± 0.025 304.31 ± 1.97 2.96 ± 0.008
P 0.1031 0.1125 0.7774 0.1133 0.9598
2 CC(25) 11,178 ± 166.12Aa 397.7 ± 6.82a 3.56 ± 0.067 326.05 ± 4.97a 2.92 ± 0.024
CT(222) 10,608 ± 73.59B 383.22 ± 3.2b 3.61 ± 0.03 315.95 ± 2.33b 2.98 ± 0.01
TT(511) 10,791 ± 61.3Ab 388.01 ± 2.75ab 3.6 ± 0.025 320.43 ± 2a 2.97 ± 0.008
P 0.0003** 0.0358* 0.7454 0.0166* 0.0571
c.*1064G > A 1 AA(30) 9789.35 ± 145.71A 324.33 ± 5.97Aa 3.34 ± 0.058 290.87 ± 4.35A 2.98 ± 0.021
AG(346) 10,225 ± 66.48Ba 336.45 ± 2.93b 3.31 ± 0.027 302.73 ± 2.13Ba 2.96 ± 0.009
GG(699) 10,290 ± 60.6Ba 340.29 ± 2.71Bb 3.33 ± 0.025 304.73 ± 1.97Ba 2.96 ± 0.008
P 0.0011** 0.0046** 0.6409 0.0019** 0.5754
2 AA(24) 11,065 ± 169.52a 411.69 ± 6.93A 3.7 ± 0.068 324.69 ± 5.05 2.94 ± 0.024
AG(227) 10,639 ± 72.64b 386.11 ± 3.16Ba 3.62 ± 0.03 317.56 ± 2.3 2.98 ± 0.01
GG(501) 10,797 ± 61.59a 391.84 ± 2.76Bb 3.63 ± 0.025 321.28 ± 2.01 2.98 ± 0.008
P 0.0062** 0.0004** 0.5116 0.0823 0.1711
g.72819977 T > C 1 TT(709) 10,252 ± 60.58Aa 341.13 ± 2.71Aa 3.34 ± 0.025 303.11 ± 1.97Aa 2.96 ± 0.008
TC(345) 10,190 ± 66.68Aa 336.44 ± 2.94b 3.32 ± 0.027 301.02 ± 2.14a 2.96 ± 0.009
CC(31) 9810.39 ± 144.46B 326.61 ± 5.93Bb 3.35 ± 0.058 290.6 ± 4.33Bb 2.97 ± 0.021
P 0.0037** 0.0034** 0.391 0.0044** 0.6802
2 TT(510) 10,795 ± 60.71 388.17 ± 2.72 3.6 ± 0.025 321.11 ± 1.98 2.97 ± 0.008
TC(225) 10,673 ± 72.24 385.16 ± 3.13 3.6 ± 0.03 318.52 ± 2.28 2.98 ± 0.01
CC(25) 10,953 ± 165.5 399.73 ± 6.77 3.64 ± 0.066 321.39 ± 4.94 2.94 ± 0.024
P 0.0686 0.0736 0.777 0.3541 0.2628
g.72819850A > G 1 GG(31) 9737.41 ± 143.71A 322.7 ± 5.9Aa 3.34 ± 0.058 287.79 ± 4.3A 2.97 ± 0.021
GA(342) 10,221 ± 66.54Ba 336.58 ± 2.93b 3.3 ± 0.027 301.93 ± 2.13Ba 2.95 ± 0.009
AA(706) 10,282 ± 60.43Ba 340.2 ± 2.7Bb 3.32 ± 0.025 303.63 ± 1.97Ba 2.95 ± 0.008
P 0.0003** 0.0021** 0.6324 0.0003** 0.7239
2 GG(25) 10,948 ± 164.92b 404.59 ± 6.75Aa 3.69 ± 0.066 321.58 ± 4.92ab 2.94 ± 0.024
GA(224) 10,546 ± 73.43Aa 381.72 ± 3.19B 3.62 ± 0.03 313.96 ± 2.32Aa 2.98 ± 0.01
AA(508) 10,773 ± 61.24Bb 388.75 ± 2.75Ab 3.61 ± 0.025 320.15 ± 2Bb 2.98 ± 0.008
P 0.0005** 0.0004** 0.5079 0.003** 0.2881
g.72818819A > G 1 GG(305) 10,154 ± 68.15Aa 336.43 ± 2.98A 3.33 ± 0.028 299.24 ± 2.17A 2.95 ± 0.009a
GA(557) 10,314 ± 61.4Bb 341.97 ± 2.74Ba 3.33 ± 0.025 303.62 ± 1.99Ba 2.95 ± 0.008Aa
AA(218) 10,301 ± 73.25b 346.69 ± 3.17Bb 3.38 ± 0.03 305.87 ± 2.31Ba 2.97 ± 0.01Bb
P 0.0068** 0.0004** 0.1048 0.0012** 0.0108*
2 GG(216) 10,481 ± 73.65A 374.35 ± 3.2A 3.57 ± 0.03 309.56 ± 2.33A 2.96 ± 0.01Aa
GA(373) 10,845 ± 64.47Ba 391.01 ± 2.86Ba 3.61 ± 0.027 323.76 ± 2.08B 2.99 ± 0.009B
AA(167) 10,778 ± 79.59Ba 384.6 ± 3.44Bb 3.57 ± 0.033 317.22 ± 2.51C 2.95 ± 0.011Aa
P <.0001** <.0001** 0.1906 <.0001** 0.0003**
g.72818818C > T 1 TT(305) 10,224 ± 68.77Aa 337.97 ± 3.01A 3.31 ± 0.028 301.6 ± 2.19A 2.95 ± 0.009ab
TC(555) 10,382 ± 61.58Bb 344.22 ± 2.75Ba 3.33 ± 0.025 305.98 ± 2Ba 2.95 ± 0.008a
CC(221) 10,330 ± 72.84ab 346.52 ± 3.16Ba 3.36 ± 0.03 306.65 ± 2.3Ba 2.97 ± 0.01b
P 0.0106* 0.0019** 0.1484 0.0075** 0.0355*
2 TT(216) 10,466 ± 74A 374.26 ± 3.22A 3.58 ± 0.03 308.75 ± 2.34A 2.96 ± 0.01Aa
TC(372) 10,767 ± 64.62Ba 389.23 ± 2.87Ba 3.63 ± 0.027 320.3 ± 2.09Ba 2.99 ± 0.009B
CC(169) 10,737 ± 78.69Ba 385.23 ± 3.4Ba 3.6 ± 0.032 315.35 ± 2.48Bb 2.95 ± 0.011Aa
P <.0001** <.0001** 0.1591 <.0001** 0.0006**
g.72818292 T > C 1 TT(709) 10,300 ± 60.49Aa 341.5 ± 2.71a 3.33 ± 0.025 304.06 ± 1.97a 2.96 ± 0.008
TC(336) 10,249 ± 66.63a 337.35 ± 2.93b 3.31 ± 0.027 302.39 ± 2.13a 2.95 ± 0.009
CC(33) 9929.1 ± 140.09Bb 330.35 ± 5.74b 3.34 ± 0.056 294.03 ± 4.19b 2.97 ± 0.02
P 0.0156* 0.0197* 0.453 0.0253* 0.632
2 TT(509) 10,683 ± 61.62c 382.44 ± 2.77Aa 3.6 ± 0.026 316.43 ± 2.02a 2.97 ± 0.008
TC(219) 10,522 ± 72.71Aa 377.12 ± 3.15Ab 3.6 ± 0.03 312.89 ± 2.3Aa 2.98 ± 0.01
CC(27) 11,074 ± 159.67Bb 405.34 ± 6.54B 3.64 ± 0.064 326.97 ± 4.77Bb 2.95 ± 0.023
P 0.0006** <.0001** 0.7811 0.0057** 0.4872
g.72818161 T > C 1 TT(711) 10,326 ± 60.82Aa 343.62 ± 2.72A 3.34 ± 0.025 305.45 ± 1.98Aa 2.96 ± 0.008
TC(322) 10,206 ± 67.05Ab 338.41 ± 2.95Ba 3.32 ± 0.028 302.22 ± 2.15Ab 2.96 ± 0.009
CC(30) 9725.31 ± 145.87B 325.45 ± 5.98Bb 3.36 ± 0.059 287.93 ± 4.36B 2.97 ± 0.021
P <.0001** 0.0004** 0.7091 <.0001** 0.6543
2 TT(511) 10,714 ± 61.04Aa 383.57 ± 2.74a 3.59 ± 0.025 317.97 ± 1.99 2.97 ± 0.008ab
TC(208) 10,546 ± 73.84Bb 378.91 ± 3.19Aa 3.6 ± 0.03 315.19 ± 2.33 2.99 ± 0.01a
CC(24) 10,933 ± 168.72a 397.23 ± 6.9Bb 3.63 ± 0.068 319.26 ± 5.03 2.93 ± 0.024b
P 0.0078** 0.014* 0.7997 0.2957 0.0239*

* indicates P < 0.05; ** indicates P < 0.01; a, b, c within the same column with different superscripts means P < 0.05; A, B, C within the same column with different superscripts means P < 0.01.