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Table 4 Most significant SNP regions and candidate genes for production and functional traits in dairy cattle from a large multibreed GWAS

From: Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle

Trait

SNP name

Chr

Position (bp)

log(10)P

  Within Gene

100 kb LD

<500 kb LD

Gene name

Fat

ARS-BFGL-NGS-4939

14

1801116

255.551

  DGAT1

  

diacylglycerol O-acyltransferase 1

BTB-00932332

26

22118554

24.142

  BRTC

  

Beta-transducin repeat containing

BovineHD0500026662

5

93945655

23.718

 

MGST1

 

microsomal glutathione S-transferase 1

BovineHD1800017481

18

60506726

12.907

  LOC788871

  

zinc finger protein 85-like

BovineHD1200015001

12

54273515

12.918

  

RNF219

ring finger protein 219

Milk

ARS-BFGL-NGS-4939

14

1801116

416.491

  DGAT1

  

diacylglycerol O-acyltransferase 1

BovineHD2000009925

20

34582764

44.167

  

LOC782462

sorting nexin-13-like

BovineHD0500026852

5

94562606

24.636

  EPS8

  

epidermal growth factor receptor pathway substrate 8

BovineHD0600024338

6

88865430

22.814

  

GC

group-specific component (vitamin D binding protein)

BovineHD4100003579

5

32784231

19.562

  RPAP3

  

RNA polymerase II associated protein 3

Protein

ARS-BFGL-NGS-4939

14

1801116

144.166

  DGAT1

  

diacylglycerol O-acyltransferase 1

BovineHD4100005296

6

87180731

31.840

  CSN2

  

casein beta

BovineHD2600004009

26

15654751

21.778

  PLCE1

  

phospholipase C, epsilon 1

BovineHD0500029843

5

104307736

19.303

  CD27

  

CD27 molecule

BovineHD2600011254

26

40809501

18.214

  

PPAPDC1A

phosphatidic acid phosphatase type 2 domain containing 1A

Fat%

ARS-BFGL-NGS-4939

14

1801116

1684.117

  DGAT1

  

diacylglycerol O-acyltransferase 1

BovineHD0500026662

5

93945655

93.370

 

MGST1

 

microsomal glutathione S-transferase 1

BovineHD2000009925

20

34582764

61.199

  

LOC782462

sorting nexin-13-like

ARS-BFGL-NGS-57448

27

36155097

32.124

  GINS4

  

GINS complex subunit 4 (Sld5 homolog)

BovineHD0200034371

2

119076939

13.851

 

SP110

 

SP110 nuclear body protein

Protein%

ARS-BFGL-NGS-4939

14

1801116

398.865

  DGAT1

  

diacylglycerol O-acyltransferase 1

BovineHD2000009927

20

34587828

180.352

  

LOC782462

sorting nexin-13-like

BovineHD0600023879

6

87160102

70.809

 

CAS1A

 

casein alpha s1

BovineHD0300005054

3

15451257

44.404

  GBA

  

glucosidase, beta, acid

BovineHD4100003579

5

32784231

34.001

  RPAP3

  

RNA polymerase II associated protein 3

Fertility

BovineHD1800016761

18

57548213

7.445

  LOC786539

  

carcinoembryonic antigen-related cell adhesion molecule 18-like

BovineHD0600024357

6

88922396

6.712

  

NPFFR2

neuropeptide FF receptor 2

BovineHD0500024481

5

86451512

6.441

  

SOX5

SRY (sex determining region Y)-box 5

BovineHD0400015668

4

57384888

6.371

  

LOC100298628

HIG1 domain family, member 1D-like pseudogene

BovineHD0100005095

1

16862494

6.215

  LOC100140852

  

magnesium transporter NIPA2-like

Mamm. System

BovineHD2600006024

26

23379482

9.478

  SUFU

  

suppressor of fused homolog (Drosophila)

BovineHD0200030267

2

105149497

8.263

  SMARCAL1

  

SWI/SNF related, matrix assoc., actin dep. Reg. of chromatin, subfamily a-like 1

BovineHD1100008368

11

28171549

8.175

  PRKCE

  

protein kinase C, epsilon

BovineHD0200035718

2

123208383

8.069

 

SDC3

 

syndecan 3

BovineHD2000008146

20

27565339

7.890

  

ISL1

ISL LIM homeobox 1

Survival

BovineHD1100031193

11

107227039

67.300

 

NLRP6

 

NLR family, pyrin domain containing 6

Hapmap40387-BTA-107848

9

104960154

35.305

 

WDR27

 

WD repeat domain 27

BovineHD3000041679

30

144726003

33.731

  

TBL1X

transducin (beta)-like 1X-linked

BovineHD2000006692

20

22290945

31.258

 

MIER3

 

mesoderm induction early response 1, family member 3-like

BovineHD1700000492

17

2237102

30.497

  

NPY2R

neuropeptide Y receptor Y2

SCC

ARS-BFGL-NGS-92033

1

2582894

12.503

 

MIS18A

 

MIS18 kinetochore protein homolog A (S. pombe)

ARS-BFGL-NGS-57102

3

31219298

10.716

 

CTTNBP2NL

 

CTTNBP2 N-terminal like

BTA-104934-no-rs

7

67940770

10.324

  LARP1

  

La ribonucleoprotein domain family, member 1

BovineHD1100009904

11

32859722

9.169

  NRXN1

  

neurexin 1

 

BovineHD1600008712

16

30646220

8.556

 

ADCK3

 

aarF domain containing kinase 3