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Table 3 Detailed information on the nearest and most significant SNPs from previous GWAS to the 22 differentially expressed genes in bovine liver at different lactation stages

From: Identification of candidate genes for milk production traits by RNA sequencing on bovine liver at different lactation stages

Gene name

Early vs.

Peak vs.

Peak vs.

Gene position (bp)a

Nearest and most significant SNPs of GWAS

Traits

Raw p value

dry

dry

early

Distance

Name

Position (bp)b

APOA1

+

 

–

Chr15:27932198–27,934,085

1.77 Mb

BTB-00590603

29,702,877

FY,PY,FP,PP

7.05E-22 ∼ 4.71E-16

    

3.59 Mb

BTB-00590405

31,527,773

FY,PY

4.12E-11 ∼ 1.22E-10

ABCG8

–

  

Chr11: 26156365–26,175,034

1.34 Mb

BTB-00470332

27,519,615

FY,PY

3.66E-09 ∼ 1.25E-08

    

1.78 Mb

BFGL-NGS-115431

24,379,969

MY,FY,PY,FP,PP

3.18E-29 ∼ 1.92E-07

    

2.46 Mb

BTB-01556917

23,700,685

PP

3.46E-12

    

2.56 Mb

Hapmap59290-rs29022016

23,599,074

PY,PP

1.87E-22 ∼ 7.11E-08

    

3.49 Mb

BFGL-NGS-116483

22,666,445

MY,FY,PY,FP,PP

1.60E-24 ∼ 1.14E-08

    

3.57 Mb

ARS-BFGL-NGS-43804

22,588,525

MY,FY,PY,FP

2.85E-26 ∼ 5.15E-08

    

4.03 Mb

ARS-BFGL-NGS-100459

22,128,569

FY,PY,PP

1.03E-24 ∼ 7.98E-08

APOC2

+

  

Chr18: 53057717–53,059,957

888.61 Kb

BFGL-NGS-117985

53,948,569

MY,FY,PY,FP,PP

9.83E-55 ∼ 1.71E-19

    

910.9 Kb

Hapmap41540-BTA-43915

53,970,861

FY,PY,FP

3.07E-18 ∼ 2.19E-09

    

2.83 Mb

Hapmap47618-BTA-43817

55,892,476

PP

1.07E-08

    

4.11 Mb

ARS-BFGL-NGS-98028

57,174,711

FY,PY,FP,PP

1.40E-21 ∼ 1.04E-10

APOA4

+

+

 

Chr15: 27906598–27,919,592

1.78 Mb

BTB-00590603

29,702,877

FY,PY,FP,PP

7.05E-22 ∼ 4.71E-16

    

3.61 Mb

BTB-00590405

31,527,773

FY,PY

4.12E-11 ∼ 1.22E-10

SAA1

+

+

 

Chr29:26696726–26,714,918

6.41 Kb

ARS-BFGL-NGS-24998

26,721,324

PP

2.96E-08

    

4.19 Mb

UA-IFASA-8605

30,901,735

FY,FP,PP

1.50E-16 ∼ 1.50E-07

PC

+

  

Chr29: 45508279–45,611,042

2.89 Mb

ARS-BFGL-NGS-2893

48,501,273

FY,PY,FP,PP

1.98E-12 ∼ 8.87E-08

    

3.28 Mb

Hapmap40456-BTA-66218

48,895,237

FY

1.35E-08

    

3.75 Mb

BFGL-NGS-117323

49,357,135

MY,FY,PY,FP

4.32E-19 ∼ 3.58E-08

PPP1R3B

–

  

Chr27: 24316623–24,317,477

259.32 Kb

ARS-BFGL-NGS-43776

24,576,801

MY,FY,PY,FP,PP

6.30E-26 ∼ 1.20E-07

    

4.07 Mb

BTB-01063707

28,386,241

MY,FY,PY,FP,PP

1.55E-45 ∼ 1.35E-17

GALE

+

  

Chr2:129706509–129,711,871

1.27 Mb

BTA-31250-no-rs

128,437,731

PY,FP,PP

1.26E-24 ∼ 3.25E-08

SDS

+

  

Chr17: 63302876–63,311,105

162.16 Kb

BFGL-NGS-110646

63,140,712

FY,PY,FP,PP

2.61E-14 ∼ 3.54E-08

    

230.59 Kb

Hapmap52830-rs29014800

63,541,690

FP,PP

4.31E-11 ∼ 3.38E-07

    

1.41 Mb

BTB-00682411

61,891,068

PP

2.65E-08

    

1.76 Mb

BTB-01992588

65,071,599

MY,FY,PY

3.55E-15 ∼ 2.01E-10

    

2.93 Mb

ARS-BFGL-NGS-17192

66,236,750

MY,PY

2.97E-15 ∼ 1.30E-12

    

3.31 Mb

ARS-BFGL-NGS-34106

66,619,908

FY,FP,PP

4.65E-25 ∼ 3.68E-14

    

3.36 Mb

Hapmap40427-BTA-41914

66,671,839

FP,PP

6.15E-19 ∼ 3.07E-11

FBP2

+

+

 

Chr8:82396095–82,438,817

1.45 Mb

BTA-14515-no-rs

83,888,935

FY,PY,PP

6.36E-12 ∼ 7.78E-09

    

3.95 Mb

ARS-BFGL-NGS-20324

86,384,898

FY,PY,FP,PP

7.96E-22 ∼ 3.80E-14

PKLR

–

  

Chr3:15396974–15,408,994

1.31 Mb

UA-IFASA-8925

14,084,731

PY

3.48E-07

SGLT1

–

  

Chr17: 72690558–72,741,954

3.96 Mb

BTA-90512-no-rs

68,732,546

FP,PP

6.81E-19 ∼ 4.33E-13

GK

+

  

ChrX:118110570–118,186,827

2.14 Mb

Hapmap34068-BES2_Contig513_1168

115,968,607

MY,FY,PY,FP,PP

2.30E-27 ∼ 6.86E-09

    

2.47 Mb

BTA-30585-no-rs

120,654,979

FY,FP,PP

2.02E-16 ∼ 1.36E-08

    

2.50 Mb

Hapmap39109-BTA-30591

120,691,496

FP,PP

6.01E-13 ∼ 1.28E-07

    

2.89 Mb

Hapmap33343-BTA-111447

121,076,442

FY,PY,FP,PP

6.03E-13 ∼ 7.03E-08

    

3.41 Mb

BTA-98858-no-rs

121,600,055

FY,FP,PP

7.03E-21 ∼ 1.01E-09

    

3.79 Mb

Hapmap45528-BTA-102311

114,319,576

FY,FP,PP

3.01E-18 ∼ 5.13E-09

CYP7A1

+

+

 

Chr14:26348324–26,358,692

3.76 Mb

ARS-BFGL-BAC-12159

22,587,081

MY,FY,PY,PP

4.94E-24 ∼ 6.01E-11

    

4.41 Mb

ARS-BFGL-NGS-3198

21,933,950

FY,PY,FP,PP

1.21E-25 ∼ 1.45E-12

ANGPTL4

+

+

 

Chr7:18236482–18,243,588

1.84 Mb

Hapmap23865-BTA-111820

16,397,706

PP

1.51E-08

    

4.60 Mb

BFGL-NGS-119066

13,632,174

FP,PP

9.49E-20 ∼ 7.48E-10

    

4.63 Mb

ARS-BFGL-NGS-109534

13,608,935

FP,PP

8.42E-20 ∼ 1.94E-09

    

4.65 Mb

BFGL-NGS-111315

13,584,721

FY,PY,FP,PP

4.90E-29 ∼ 7.03E-12

IGF-1R

–

–

 

Chr21:7967718–8,268,246

769.19 Kb

ARS-BFGL-NGS-10704

9,037,431

FP,PP

2.60E-13 ∼ 4.77E-08

    

1.07 Mb

ARS-BFGL-NGS-77061

6,900,116

PP

9.32E-10

CDKN1A

–

 

+

Chr23:10551755–10,568,782

2.68 Mb

BFGL-NGS-115177

7,874,236

MY,FY,PY

1.83E-24 ∼ 6.49E-17

    

3.28 Mb

ARS-BFGL-NGS-41214

13,846,320

MY,FY,PY,PP

2.10E-24 ∼ 3.13E-11

    

4.20 Mb

ARS-BFGL-NGS-17887

14,769,068

MY,FY,PY,PP

3.76E-24 ∼ 6.86E-09

ODC1

+

+

 

Chr11:87175389–87,182,661

74.93 Kb

BTA-110370-no-rs

87,257,595

FY,PY,FP

3.10E-12 ∼ 2.68E-07

    

96.35 Kb

BFGL-NGS-114578

87,279,008

FY,PY

2.85E-11 ∼ 1.82E-08

    

197.94 Kb

ARS-BFGL-NGS-42014

87,380,604

FY

9.34E-09

    

249.36 Kb

ARS-BFGL-NGS-17731

86,926,025

FY,PY,FP

3.31E-16 ∼ 3.55E-07

    

605.73 Kb

Hapmap53648-rs29021240

86,569,656

FY,PY

1.00E-10 ∼ 2.14E-08

    

641.51 Kb

ARS-BFGL-NGS-70263

87,824,167

MY,FY,PY,PP

1.16E-17 ∼ 2.25E-08

    

789.42 Kb

ARS-BFGL-NGS-41670

87,972,079

FY,PP

1.41E-08 ∼ 2.53E-07

    

817.29 Kb

ARS-BFGL-BAC-16207

87,999,946

FY,PY,FP,PP

4.08E-10 ∼ 3.65E-07

    

2.02 Mb

Hapmap52066-rs29015690

85,153,576

FY

1.10E-07

    

2.16 Mb

ARS-BFGL-NGS-28030

89,338,824

FY,PY

2.08E-12 ∼ 1.33E-07

    

2.19 Mb

Hapmap31724-BTA-126967

89,371,911

FY,PY,FP

1.05E-15 ∼ 1.43E-08

    

2.30 Mb

ARS-BFGL-NGS-2015

84,872,349

FY,PY,FP,PP

1.83E-18 ∼ 6.84E-05

    

2.35 Mb

ARS-BFGL-NGS-104652

84,828,071

MY,FY,PY

1.05E-18 ∼ 2.22E-09

    

3.54 Mb

ARS-BFGL-NGS-63978

83,637,998

FY,PY,FP,PP

2.27E-15 ∼ 1.78E-07

    

3.65 Mb

Hapmap40477-BTA-105881

83,526,455

FY,PY,FP,PP

1.80E-24 ∼ 2.41E-11

    

4.19 Mb

Hapmap56387-rs29014077

82,982,779

FY

1.25E-07

    

4.25 Mb

ARS-BFGL-NGS-93601

82,920,732

FY,PY,FP,PP

1.88E-21 ∼ 2.96E-13

    

4.53 Mb

Hapmap46768-BTA-117394

82,643,114

MY,FY,PY

1.78E-13 ∼ 1.73E-07

GADD45B

 

+

+

Chr7:22411968–22,414,079

2.24 Mb

Hapmap49309-BTA-78604

24,655,689

PP

4.34E-14

LPIN1

 

+

+

Chr11:86050742–86,128,538

2.38 Kb

ARS-BFGL-NGS-14236

86,048,363

FY,PY

1.29E-12 ∼ 4.60E-08

    

441.12 Kb

Hapmap53648-rs29021240

86,569,656

FY,PY

1.00E-10 ∼ 2.14E-08

    

797.49 Kb

ARS-BFGL-NGS-17731

86,926,025

FY,PY,FP

3.31E-16 ∼ 3.55E-07

    

897.17 Kb

Hapmap52066-rs29015690

85,153,576

FY

1.10E-07

    

1.13 Mb

BTA-110370-no-rs

87,257,595

FY,PY,FP

3.10E-12 ∼ 2.68E-07

    

1.15 Mb

BFGL-NGS-114578

87,279,008

FY,PY

2.85E-11 ∼ 1.82E-08

    

1.18 Mb

ARS-BFGL-NGS-2015

84,872,349

FY,PY,FP,PP

1.83E-18 ∼ 6.84E-05

    

1.22 Mb

ARS-BFGL-NGS-104652

84,828,071

MY,FY,PY

1.05E-18 ∼ 2.22E-09

    

1.25 Mb

ARS-BFGL-NGS-42014

87,380,604

FY

9.34E-09

    

1.70 Mb

ARS-BFGL-NGS-70263

87,824,167

MY,FY,PY,PP

1.16E-17 ∼ 2.25E-08

    

1.84 Mb

ARS-BFGL-NGS-41670

87,972,079

FY,PP

1.41E-08 ∼ 2.53E-07

    

1.87 Mb

ARS-BFGL-BAC-16207

87,999,946

FY,PY,FP,PP

4.08E-10 ∼ 3.65E-07

    

2.41 Mb

ARS-BFGL-NGS-63978

83,637,998

FY,PY,FP,PP

2.27E-15 ∼ 1.78E-07

    

2.52 Mb

Hapmap40477-BTA-105881

83,526,455

FY,PY,FP,PP

1.80E-24 ∼ 2.41E-11

    

3.07 Mb

Hapmap56387-rs29014077

82,982,779

FY

1.25E-07

    

3.13 Mb

ARS-BFGL-NGS-93601

82,920,732

FY,PY,FP,PP

1.88E-21 ∼ 2.96E-13

    

3.21 Mb

ARS-BFGL-NGS-28030

89,338,824

FY,PY

2.08E-12 ∼ 1.33E-07

    

3.24 Mb

Hapmap31724-BTA-126967

89,371,911

FY,PY,FP

1.05E-15 ∼ 1.43E-08

    

3.41 Mb

Hapmap46768-BTA-117394

82,643,114

MY,FY,PY

1.78E-13 ∼ 1.73E-07

    

4.21 Mb

ARS-BFGL-NGS-105586

81,845,043

FY,PY,FP

2.47E-15 ∼ 3.00E-08

    

4.23 Mb

ARS-BFGL-NGS-52709

81,819,453

FY,PY,FP,PP

3.01E-25 ∼ 1.28E-08

DUSP1

 

+

 

Chr20:4449106–4,452,189

44.19 Kb

ARS-BFGL-NGS-48030

4,496,376

PP

2.07E-08

    

53.45 Kb

Hapmap54098-rs29010434

4,395,656

FY,PY,PP

1.35E-12 ∼ 1.66E-08

    

3.32 Mb

Hapmap49207-BTA-51446

7,770,495

MY,FY,PY,FP,PP

5.02E-27 ∼ 9.06E-11

    

3.50 Mb

Hapmap36217-SCAFFOLD290026_21689

7,954,374

FY,PY

7.19E-09 ∼ 7.36E-09

    

3.74 Mb

ARS-BFGL-NGS-27058

712,232

FY,PY,FP

1.11E-10 ∼ 3.92E-07

LMNA

+

  

Chr3:14695234–14,724,663

0.61 Mb

UA-IFASA-8925

14,084,731

PY

3.48E-07

  1. a,bMeans the position on the bovine genome sequence of UMD3.1.80
  2. MY milk yield; FY milk fat yield; PY milk protein yield; FP milk fat percentage; PP milk protein percentage.