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Table 1 SNPs significantly associated with milk production traits in the combined population

From: Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits

SNP-ID

Gene

Amino acid sub

Chr

Positiona

Traitsb

P valuec

N7

PDE9A

 

1

144562226

PP

4.68E-05

C8

DIP2A

K → Q

1

147894635

PP

1.01E-05

U71

SLC30A7

 

3

42465645

PP

1.13E-04

C30

SLC30A7

H → Y

3

42530986

PP

4.88E-06

U36

STXBP1

 

11

98393605

PP

1.43E-05

C204

EGFL7

I → M

11

104152101

PP

2.71E-07

U41

LY6D

 

14

1155474

MY,FY,FP,PP

9.62E-05

U42

LY6H

 

14

1449253

MY,PY,FP

5.84E-05

C109

ZNF34

H → R

14

1494039

MY,FP,PY,PP

1.74E-04

P18

RPL8*

 

14

1508300

MY,PY,FP

6.63E-05

S12

LOC785799

 

14

1524572

MY,PY,FP

5.63E-05

P23

GPT*

 

14

1628421

All

8.08E-08

C110

PPP1R16A

A → T

14

1629600

All

2.39E-07

S4

CYHR1*

 

14

1677522

All

3.14E-08

U46

VPS28*

 

14

1694862

All

1.99E-09

C111

CPSF1*

T → I

14

1736599

All

1.40E-10

C199

DGAT1*

K → A

14

1802265

All

2.96E-10

U47

HSF1*

 

14

1806340

FP

2.95E-08

C112

HEATR7A*

Q → R

14

1851040

FP

2.30E-11

C113

HEATR7A*

N → S

14

1878165

All

2.66E-10

U48

LOC509113*

 

14

1907315

All

2.39E-10

N10

MAF1

 

14

1924112

MY,FP,PP

2.31E-06

P24

GPAA1

 

14

1946673

MY,FP,PP

1.15E-06

P25

OPLAH

 

14

1957462

MY,FP,PP

1.48E-06

C114

SPATC1

P → A

14

1977494

MY,FP,PP

1.27E-06

U50

GRINA

 

14

2019072

FP

6.36E-06

C115

PARP10

G → D

14

2026781

MY,FP,PP

4.39E-07

C116

PARP10

G → S

14

2027812

MY,FP,PP

3.13E-07

C119

LOC786966*

D → A

14

2086893

MY,FP,PP

2.97E-06

C120

LOC786966*

L → G

14

2087763

All

1.66E-07

C125

EPPK1

R → Q

14

2138115

PP

9.31E-05

P29

PUF60

 

14

2163044

FP

5.29E-06

P33

LOC506831*

 

14

2221616

FY,FP,PP

2.29E-04

C127

FAM83H*

V → G

14

2231494

MY,FY,FP,PP

1.08E-04

C128

MAPK15

T → M

14

2239085

MY,FY,FP,PP

2.12E-04

C130

PYCRL

R → C

14

2308255

PY

2.04E-06

P35

EEF1D*

 

14

2311270

MY,FP,PP

9.23E-06

P90

EEF1D*

 

14

2314560

MY,FP,FP

1.21E-04

C132

ZC3H3*

P → L

14

2358243

MY,PY,FP,PP

6.77E-06

C133

ZC3H3*

A → D

14

2358255

MY,PY,FP,PP

8.05E-06

U52

RHPN1

 

14

2462476

MY,FP,FP

1.49E-05

C207

RHPN1

T → A

14

2465250

FP,PP

2.29E-04

P89

GPIHBP1*

 

14

2553652

MY,PY,FP

2.17E-08

C206

CYP11B1

A → V

14

2705205

FP

1.57E-10

N8

CYP11B1

 

14

2706012

FY,FP

7.98E-05

C198

CYP11B1

E → K

14

2708768

FP

1.87E-05

C136

GML

Q → P

14

2715807

FP

1.57E-09

C137

LYNX1

L → F

14

2816429

MY,FP,PP

7.22E-05

S8

GPR20

 

14

3640627

MY,FP,PP

8.90E-05

C138

PTK2*

I → M

14

4061098

MY,FY,FP

3.16E-05

P48

EIF2C2*

 

14

4129075

MY,FY,FP

1.62E-04

C139

TRAPPC9*

C → G

14

4352117

MY,PY,FP

3.45E-07

C140

TRAPPC9*

G → R

14

4472220

MY,FY,FP

1.29E-04

U70

KCNK9

 

14

4743187

MY,FP

6.83E-05

C147

FAM135B

M → V

14

5603441

MY,FY,PP

1.24E-04

C194

GHR*

F → Y

20

31909476

MY,FY,PP

6.44E-09

P63

PLCXD3

 

20

33027949

FP,PP

1.96E-04

U60

PLCXD3

 

20

33229971

PP

7.47E-07

C163

C6

P → L

20

33376024

MY,FP,PP

3.34E-05

C168

C7

T → I

20

33578727

MY,FP,PP

8.33E-05

C169

C7

T → M

20

33582457

PP

2.81E-09

C171

DAB2

A → V

20

35073744

FP,PP

1.88E-05

C175

OSMR

R → M

20

35544340

PP

1.56E-05

C176

OSMR

M → L

20

35561705

PP

5.21E-05

P72

GDNF

 

20

36634182

FP,PP

4.81E-07

C184

NIPBL*

I → V

20

37238542

FP,PP

1.97E-06

  1. a: based on the UMD_3.1 genome assembly.
  2. b: MY = milk yield, FY = fat yield, PY = protein yield, FP = fat percentage, PP = protein percentage
  3. c: These values were from the combined population. For SNPs whichwere significant for more than one trait, the maximum P values are presented.
  4. *: These genes were selected for mRNA expression analysis.
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BMC Genomics

ISSN: 1471-2164

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