Table 2 Associations of 19 SNPs of ATF3 gene with milk production traits in Chinese Holstein cattle during two lactations (LSM ± SE)

g.72834301C > A

1

CC(222)

10,305 ± 73.52^a

346.63 ± 3.19^Aa

3.37 ± 0.03

306.89 ± 2.32^Aa

2.98 ± 0.01

CA(553)

10,339 ± 62^Aa

343.59 ± 2.77^Aa

3.34 ± 0.026

305.6 ± 2.01^Aa

2.96 ± 0.008

AA(299)

10,146 ± 68.79^Bb

336.42 ± 3.01^B

3.33 ± 0.028

300.12 ± 2.19^B

2.96 ± 0.009

P

0.001**

0.0002**

0.2065

0.0003**

0.0737

2

CC(170)

10,707 ± 78.61^ab

385.28 ± 3.39^ab

3.61 ± 0.032

315.96 ± 2.47^Aa

2.96 ± 0.011^Aa

CA(371)

10,785 ± 64.99^Aa

390.15 ± 2.89^Aa

3.63 ± 0.027

322.03 ± 2.1^B

2.99 ± 0.009^B

AA(212)

10,567 ± 73.79^Bb

379.59 ± 3.21^Bb

3.59 ± 0.03

312.96 ± 2.34^Aa

2.96 ± 0.01^Aa

P

0.0051**

0.0004**

0.2901

<.0001**

0.0005**

g.72834229C > A

1

CC(221)

10,318 ± 73

346.25 ± 3.17^Aa

3.36 ± 0.03

306.34 ± 2.31^Aa

2.97 ± 0.01^a

CA(553)

10,315 ± 61.81

341.19 ± 2.75^b

3.32 ± 0.026

303.89 ± 2.01^ab

2.95 ± 0.008^b

AA(299)

10,194 ± 68.95

337.13 ± 3.02^Bb

3.31 ± 0.028

301.01 ± 2.2^Bb

2.96 ± 0.009^ab

P

0.0523

0.003**

0.1234

0.0212*

0.0494*

2

CC(169)

10,691 ± 78.17^a

383.01 ± 3.37^a

3.6 ± 0.032

314.66 ± 2.45^Aa

2.95 ± 0.011^Aa

CA(369)

10,802 ± 64.49^Aa

388.4 ± 2.86^Aa

3.61 ± 0.027

321.87 ± 2.08^B

2.99 ± 0.009^B

AA(211)

10,493 ± 73.62^Bb

374.92 ± 3.19^Bb

3.58 ± 0.03

309.72 ± 2.32^Ab

2.96 ± 0.01^Aa

P

<.0001**

<.0001**

0.5118

<.0001**

0.001**

g.72833969A > G

1

GG(300)

10,147 ± 68.91^Aa

333.48 ± 3.02^Aa

3.3 ± 0.028

299.66 ± 2.2^A

2.96 ± 0.009

GA(551)

10,318 ± 61.59^Bb

338.88 ± 2.74^b

3.31 ± 0.025

304.12 ± 2^Ba

2.95 ± 0.008

AA(222)

10,273 ± 72.9^ab

342.05 ± 3.16^Bb

3.35 ± 0.03

304.89 ± 2.3^Ba

2.97 ± 0.010

P

0.0049**

0.0033**

0.1466

0.0057**

0.053

2

GG(211)

10,466 ± 75.09^A

372.1 ± 3.27^A

3.56 ± 0.031

309.3 ± 2.38^Aa

2.96 ± 0.010^Aa

GA(369)

10,793 ± 65.5^Ba

388.2 ± 2.91^Ba

3.61 ± 0.027

321.77 ± 2.12^B

2.99 ± 0.009^B

AA(169)

10,700 ± 78.46^Ba

382.28 ± 3.38^Bb

3.59 ± 0.032

315.32 ± 2.46^Ab

2.95 ± 0.011^Aa

P

<.0001**

<.0001**

0.1837

<.0001**

0.0015**

g.72833562G > T

1

TT(221)

10,340 ± 73.11

347.61 ± 3.17^Aa

3.37 ± 0.03

306.84 ± 2.31^a

2.97 ± 0.01

TG(552)

10,360 ± 62.09

343.16 ± 2.77^a

3.33 ± 0.026

305.18 ± 2.02^a

2.95 ± 0.008

GG(299)

10,234 ± 68.85

338.54 ± 3.02^Bb

3.32 ± 0.028

301.92 ± 2.2^b

2.95 ± 0.009

P

0.0512

0.0029**

0.097

0.0275*

0.0779

2

TT(169)

10,769 ± 78.92^Aa

386.76 ± 3.41^Aa

3.6 ± 0.032

316.78 ± 2.48^Aa

2.95 ± 0.011^Aa

TG(370)

10,824 ± 64.37^Aa

391.65 ± 2.85^Aa

3.63 ± 0.027

322.38 ± 2.07^B

2.98 ± 0.009^B

GG(210)

10,528 ± 74.13^B

377.34 ± 3.22^B

3.59 ± 0.03

310.91 ± 2.34^Ab

2.96 ± 0.01^Aa

P

<.0001**

<.0001**

0.2651

<.0001**

0.0014**

c.291G > A

1

AA(31)

9757.9 ± 144.69^A

326.63 ± 5.95^Aa

3.37 ± 0.058

288.83 ± 4.34^A

2.98 ± 0.021

AG(345)

10,202 ± 66.08^Ba

339.19 ± 2.91^b

3.34 ± 0.027

301.61 ± 2.12^Ba

2.96 ± 0.009

GG(697)

10,268 ± 60.55^Ba

343.04 ± 2.71^Bc

3.35 ± 0.025

303.66 ± 1.98^Ba

2.96 ± 0.008

P

0.0007**

0.0034**

0.6488

0.0008**

0.752

2

AA(25)

10,866 ± 165.07

400.94 ± 6.75^Aa

3.68 ± 0.066

319.04 ± 4.93

2.94 ± 0.024

AG(226)

10,557 ± 73.54

382.33 ± 3.2^Bb

3.62 ± 0.03

313.83 ± 2.33

2.98 ± 0.01

GG(503)

10,683 ± 61.69

385.82 ± 2.77^b

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 ± 144.35^A

326.99 ± 5.93^Aa

3.36 ± 0.058

289.58 ± 4.32^A

2.98 ± 0.021

AG(344)

10,239 ± 65.93^Ba

338.76 ± 2.9^c

3.32 ± 0.027

302.48 ± 2.11^Ba

2.96 ± 0.009

GG(709)

10,294 ± 60.82^Ba

342.86 ± 2.72^Bb

3.34 ± 0.025

304.28 ± 1.98^Ba

2.96 ± 0.008

P

0.0006**

0.0033**

0.4033

0.0009**

0.5871

2

AA(25)

10,971 ± 164.92^ab

399.91 ± 6.75^a

3.63 ± 0.066

322.88 ± 4.92^ab

2.94 ± 0.024

AG(225)

10,657 ± 73.09^Aa

386.05 ± 3.17^b

3.61 ± 0.03

318.62 ± 2.31^a

2.98 ± 0.01

GG(510)

10,847 ± 60.46^Bb

390.87 ± 2.71^ab

3.6 ± 0.025

323.16 ± 1.97^b

2.97 ± 0.008

P

0.005**

0.0395*

0.8064

0.0461*

0.1971

c.*190A > G

1

AA(584)

10,178 ± 62.42^a

338.65 ± 2.78^Aa

3.35 ± 0.026

300.85 ± 2.02

2.96 ± 0.008

AG(444)

10,217 ± 63.84^Aa

338.37 ± 2.83^Aa

3.33 ± 0.026

301.91 ± 2.06

2.96 ± 0.009

GG(56)

9939.48 ± 113.17^Bb

323.63 ± 4.7^B

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 ± 0.019^a

CG(290)

10,690 ± 69.23

388.18 ± 3.04

3.64 ± 0.028

319.27 ± 2.21

2.99 ± 0.009^b

GG(424)

10,706 ± 64.21

385.69 ± 2.86

3.62 ± 0.026

317.31 ± 2.08

2.97 ± 0.009^ab

P

0.6383

0.2827

0.6702

0.0947

0.0371*

c.*326A > G

1

AA(587)

10,223 ± 62.03^Aa

337.47 ± 2.77^Aa

3.32 ± 0.026

301.41 ± 2.01^Aa

2.96 ± 0.008

AG(431)

10,295 ± 63.85^Aa

338.53 ± 2.83^Aa

3.31 ± 0.026

303.33 ± 2.06^Aa

2.95 ± 0.009

GG(57)

9904.58 ± 111.55^B

322.04 ± 4.64^B

3.28 ± 0.045

292.88 ± 3.38^B

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 ± 145.34^A

328.47 ± 5.97^Aa

3.36 ± 0.058

290.54 ± 4.36^A

2.97 ± 0.021

AG(340)

10,228 ± 66.3^Ba

341.02 ± 2.92^c

3.34 ± 0.027

302.39 ± 2.13^Ba

2.95 ± 0.009

GG(709)

10,299 ± 60.44^Ba

345.29 ± 2.7^Bb

3.36 ± 0.025

304.73 ± 1.97^Ba

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 ± 4.38^a

2.96 ± 0.021

CG(337)

10,272 ± 66.72

336.86 ± 2.94

3.3 ± 0.027

303.87 ± 2.14^b

2.96 ± 0.009

GG(713)

10,302 ± 60.16

339.63 ± 2.69

3.31 ± 0.025

304.85 ± 1.96^b

2.96 ± 0.008

P

0.0617

0.0588

0.6272

0.0331*

0.9781

2

CC(25)

11,131 ± 164.65^Aa

398.09 ± 6.74^a

3.57 ± 0.066

323.53 ± 4.92^ab

2.92 ± 0.024

CG(221)

10,600 ± 73.44^B

383.03 ± 3.19^b

3.61 ± 0.03

314.94 ± 2.33^a

2.97 ± 0.01

GG(511)

10,774 ± 61.52^Ab

388.76 ± 2.77^a

3.61 ± 0.025

319.05 ± 2.01^b

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 ± 166.12^Aa

397.7 ± 6.82^a

3.56 ± 0.067

326.05 ± 4.97^a

2.92 ± 0.024

CT(222)

10,608 ± 73.59^B

383.22 ± 3.2^b

3.61 ± 0.03

315.95 ± 2.33^b

2.98 ± 0.01

TT(511)

10,791 ± 61.3^Ab

388.01 ± 2.75^ab

3.6 ± 0.025

320.43 ± 2^a

2.97 ± 0.008

P

0.0003**

0.0358*

0.7454

0.0166*

0.0571

c.*1064G > A

1

AA(30)

9789.35 ± 145.71^A

324.33 ± 5.97^Aa

3.34 ± 0.058

290.87 ± 4.35^A

2.98 ± 0.021

AG(346)

10,225 ± 66.48^Ba

336.45 ± 2.93^b

3.31 ± 0.027

302.73 ± 2.13^Ba

2.96 ± 0.009

GG(699)

10,290 ± 60.6^Ba

340.29 ± 2.71^Bb

3.33 ± 0.025

304.73 ± 1.97^Ba

2.96 ± 0.008

P

0.0011**

0.0046**

0.6409

0.0019**

0.5754

2

AA(24)

11,065 ± 169.52^a

411.69 ± 6.93^A

3.7 ± 0.068

324.69 ± 5.05

2.94 ± 0.024

AG(227)

10,639 ± 72.64^b

386.11 ± 3.16^Ba

3.62 ± 0.03

317.56 ± 2.3

2.98 ± 0.01

GG(501)

10,797 ± 61.59^a

391.84 ± 2.76^Bb

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 ± 60.58^Aa

341.13 ± 2.71^Aa

3.34 ± 0.025

303.11 ± 1.97^Aa

2.96 ± 0.008

TC(345)

10,190 ± 66.68^Aa

336.44 ± 2.94^b

3.32 ± 0.027

301.02 ± 2.14^a

2.96 ± 0.009

CC(31)

9810.39 ± 144.46^B

326.61 ± 5.93^Bb

3.35 ± 0.058

290.6 ± 4.33^Bb

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 ± 143.71^A

322.7 ± 5.9^Aa

3.34 ± 0.058

287.79 ± 4.3^A

2.97 ± 0.021

GA(342)

10,221 ± 66.54^Ba

336.58 ± 2.93^b

3.3 ± 0.027

301.93 ± 2.13^Ba

2.95 ± 0.009

AA(706)

10,282 ± 60.43^Ba

340.2 ± 2.7^Bb

3.32 ± 0.025

303.63 ± 1.97^Ba

2.95 ± 0.008

P

0.0003**

0.0021**

0.6324

0.0003**

0.7239

2

GG(25)

10,948 ± 164.92^b

404.59 ± 6.75^Aa

3.69 ± 0.066

321.58 ± 4.92^ab

2.94 ± 0.024

GA(224)

10,546 ± 73.43^Aa

381.72 ± 3.19^B

3.62 ± 0.03

313.96 ± 2.32^Aa

2.98 ± 0.01

AA(508)

10,773 ± 61.24^Bb

388.75 ± 2.75^Ab

3.61 ± 0.025

320.15 ± 2^Bb

2.98 ± 0.008

P

0.0005**

0.0004**

0.5079

0.003**

0.2881

g.72818819A > G

1

GG(305)

10,154 ± 68.15^Aa

336.43 ± 2.98^A

3.33 ± 0.028

299.24 ± 2.17^A

2.95 ± 0.009^a

GA(557)

10,314 ± 61.4^Bb

341.97 ± 2.74^Ba

3.33 ± 0.025

303.62 ± 1.99^Ba

2.95 ± 0.008^Aa

AA(218)

10,301 ± 73.25^b

346.69 ± 3.17^Bb

3.38 ± 0.03

305.87 ± 2.31^Ba

2.97 ± 0.01^Bb

P

0.0068**

0.0004**

0.1048

0.0012**

0.0108*

2

GG(216)

10,481 ± 73.65^A

374.35 ± 3.2^A

3.57 ± 0.03

309.56 ± 2.33^A

2.96 ± 0.01^Aa

GA(373)

10,845 ± 64.47^Ba

391.01 ± 2.86^Ba

3.61 ± 0.027

323.76 ± 2.08^B

2.99 ± 0.009^B

AA(167)

10,778 ± 79.59^Ba

384.6 ± 3.44^Bb

3.57 ± 0.033

317.22 ± 2.51^C

2.95 ± 0.011^Aa

P

<.0001**

<.0001**

0.1906

<.0001**

0.0003**

g.72818818C > T

1

TT(305)

10,224 ± 68.77^Aa

337.97 ± 3.01^A

3.31 ± 0.028

301.6 ± 2.19^A

2.95 ± 0.009^ab

TC(555)

10,382 ± 61.58^Bb

344.22 ± 2.75^Ba

3.33 ± 0.025

305.98 ± 2^Ba

2.95 ± 0.008^a

CC(221)

10,330 ± 72.84^ab

346.52 ± 3.16^Ba

3.36 ± 0.03

306.65 ± 2.3^Ba

2.97 ± 0.01^b

P

0.0106*

0.0019**

0.1484

0.0075**

0.0355*

2

TT(216)

10,466 ± 74^A

374.26 ± 3.22^A

3.58 ± 0.03

308.75 ± 2.34^A

2.96 ± 0.01^Aa

TC(372)

10,767 ± 64.62^Ba

389.23 ± 2.87^Ba

3.63 ± 0.027

320.3 ± 2.09^Ba

2.99 ± 0.009^B

CC(169)

10,737 ± 78.69^Ba

385.23 ± 3.4^Ba

3.6 ± 0.032

315.35 ± 2.48^Bb

2.95 ± 0.011^Aa

P

<.0001**

<.0001**

0.1591

<.0001**

0.0006**

g.72818292 T > C

1

TT(709)

10,300 ± 60.49^Aa

341.5 ± 2.71^a

3.33 ± 0.025

304.06 ± 1.97^a

2.96 ± 0.008

TC(336)

10,249 ± 66.63^a

337.35 ± 2.93^b

3.31 ± 0.027

302.39 ± 2.13^a

2.95 ± 0.009

CC(33)

9929.1 ± 140.09^Bb

330.35 ± 5.74^b

3.34 ± 0.056

294.03 ± 4.19^b

2.97 ± 0.02

P

0.0156*

0.0197*

0.453

0.0253*

0.632

2

TT(509)

10,683 ± 61.62^c

382.44 ± 2.77^Aa

3.6 ± 0.026

316.43 ± 2.02^a

2.97 ± 0.008

TC(219)

10,522 ± 72.71^Aa

377.12 ± 3.15^Ab

3.6 ± 0.03

312.89 ± 2.3^Aa

2.98 ± 0.01

CC(27)

11,074 ± 159.67^Bb

405.34 ± 6.54^B

3.64 ± 0.064

326.97 ± 4.77^Bb

2.95 ± 0.023

P

0.0006**

<.0001**

0.7811

0.0057**

0.4872

g.72818161 T > C

1

TT(711)

10,326 ± 60.82^Aa

343.62 ± 2.72^A

3.34 ± 0.025

305.45 ± 1.98^Aa

2.96 ± 0.008

TC(322)

10,206 ± 67.05^Ab

338.41 ± 2.95^Ba

3.32 ± 0.028

302.22 ± 2.15^Ab

2.96 ± 0.009

CC(30)

9725.31 ± 145.87^B

325.45 ± 5.98^Bb

3.36 ± 0.059

287.93 ± 4.36^B

2.97 ± 0.021

P

<.0001**

0.0004**

0.7091

<.0001**

0.6543

2

TT(511)

10,714 ± 61.04^Aa

383.57 ± 2.74^a

3.59 ± 0.025

317.97 ± 1.99

2.97 ± 0.008^ab

TC(208)

10,546 ± 73.84^Bb

378.91 ± 3.19^Aa

3.6 ± 0.03

315.19 ± 2.33

2.99 ± 0.01^a

CC(24)

10,933 ± 168.72^a

397.23 ± 6.9^Bb

3.63 ± 0.068

319.26 ± 5.03

2.93 ± 0.024^b

P

0.0078**

0.014*

0.7997

0.2957

0.0239*