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Table 2 QTL locations for lactose QTL in bovine milk

From: DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

   

HD+RNA

  

Sequence

   

Pheno

Chr

Mbp

QTL PVal

Tag Var

Var effect

QTL PVal

Tag Var

SNP effect

Validation

LC

1

154.14

4.98×10−12

rs43280825

−0.0143±0.0021

2.25×10−13

rs43282035

−0.0155±0.0021

3.09×10−24

LC

2

127.64

3.93×10−13

rs209230743

−0.0160±0.0022

1.37×10−13

rs208702482

−0.0164±0.0022

2.84×10−19

LC

3

15.52

2.25×10−14

rs210326427

−0.0136±0.0018

1.26×10−14

rs211336034

−0.0137±0.0018

3.82×10−22

LC

3

53.84

7.86×10−16

rs136784524

−0.0152±0.0019

6.02×10−16

rs109613143

−0.0153±0.0019

3.52×10−23

LC

5

21.14

7.55×10−12

rs133198838

0.0128±0.0019

3.46×10−12

rs377953581

0.0130±0.0019

0.210

LC

5

31.56

4.18×10−13

rs109681546

0.0138±0.0019

1.40×10−14

rs137534989

−0.0140±0.0018

6.90×10−23

LC

5

44.16

4.25×10−11

rs378337086

0.0134±0.0020

3.51×10−11

rs383349320

0.0134±0.0020

2.91×10−10

LC

6

37.76

1 . 9 5 × 10−221

rs381223633

0.2656±0.0084

<1.05×10−308

rs43702337

−0.3379±0.0090

<1.05×10−308

LC

6

89.04

6 . 9 6 × 10−20

rs110432804

−0.0208±0.0023

1.25×10−20

rs478177439

−0.0213±0.0023

1.73×10−29

LC

7

8.77

4.55×10−11

rs137176653

0.0115±0.0017

5.92×10−11

rs210686953

0.0120±0.0017

4.02×10−11

LC

10

2.14

2.94×10−13

rs137007518

−0.0143±0.0020

2.63×10−13

rs137774567

−0.0145±0.0020

6.63×10−10

LC

15

28.36

1 . 0 6 × 10−21

rs209807357

−0.0281±0.0029

2.70×10−21

rs211369213

−0.0278±0.0029

2.02×10−45

LC

16

24.99

3 . 9 6 × 10−20

rs109379517

−0.0183±0.0020

1.25×10−21

rs109379517

−0.0192±0.0020

1.60×10−29

LC

16

67.77

1.11×10−12

rs137354702

0.0124±0.0017

1.11×10−12

rs380467601

0.0128±0.0018

1.43×10−23

LC

17

56.47

7.97×10−14

rs109194382

−0.0142±0.0019

7.40×10−14

rs134672113

−0.0142±0.0019

8.35×10−07

LC

19

33.51

5.19×10−15

rs109898712

−0.0149±0.0019

1.01×10−15

rs109514832

−0.0149±0.0019

2.14×10−38

LC

19

42.99

9.38×10−14

rs133057731

0.0233±0.0031

6.85×10−14

rs517084099

0.0248±0.0033

8.68×10−31

LC

19

61.13

1 . 2 3 × 10−24

rs41923843

−0.0187±0.0018

1.23×10−24

rs41923843

−0.0187±0.0018

1.63×10−34

LC

20

58.45

2 . 0 1 × 10−18

rs135594014

−0.0175±0.0020

9.37×10−19

rs135934727

−0.0178±0.0020

1.34×10−27

LC

27

36.21

2 . 8 4 × 10−22

rs208675276

0.0173±0.0018

2.34×10−22

rs209987511

0.0175±0.0018

2.71×10−41

LC

28

6.56

5.47×10−13

rs110674951

0.0133±0.0019

5.47×10−13

rs110674951

−0.0138±0.0019

3.90×10−35

LC

29

9.61

4 . 0 3 × 10−35

rs471922429

0.0252±0.0020

5.96×10−36

rs378183369

0.0245±0.0020

2.32×10−90

LY

5

93.94

8 . 5 4 × 10−19

rs134637616

0.0175±0.0020

4.35×10−22

rs211210569

0.0183±0.0019

1.09×10−26

LY

11

63.45

7.94×10−12

rs210726760

0.0133±0.0019

2.65×10−11

rs210726760

0.0130±0.0019

3.60×10−9

LY

14

1.77

2 . 0 0 × 10−138

rs134364612

−0.0421±0.0017

1.09×10−137

rs109234250

−0.0420±0.0017

9.43×10−179

LY

20

31.69

7.18×10−12

rs110728486

−0.0114±0.0017

6.54×10−12

rs208881195

−0.0114±0.0017

7.52×10−9

LY

26

22.96

4.06×10−15

rs110996268

0.0150±0.0019

1.30×10−15

rs208730573

0.0152±0.0019

1.50×10−6

  1. Loci identified using GWAS on the lactose concentration (LC) and lactose yield (LY) phenotypes. Chromosomes and base positions are from the UMD 3.1 bovine reference genome, with positions in millions of bases. The p-values are for the variant at each locus that was most strongly associated with the phenotype: values in bold pass genome-wide significance after both Bonferroni correction and adjustment for inflation. Allele effects are relative to the allele present in the reference bovine genome