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Table 4 Allele effects for lactose QTL tag variants in Holstein-Friesian and Jersey Cows

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

    

Holstein-Friesian (n=14,857)

 

Jersey (n=8,995)

 

Pheno

Chr

Mbp

Tag variant

Beta±SE

PVal

Beta±SE

PVal

LC

1

154.14

rs43282035

−0.014±0.002

1 . 7 7 × 10−12

−0.016±0.002

3 . 5 9 × 10−11

LC

2

127.64

rs208702482

−0.019±0.002

2 . 2 6 × 10−24

−0.013±0.003

1.04×10−4

LC

3

15.52

rs211336034

−0.015±0.002

1 . 9 1 × 10−18

−0.018±0.002

1 . 7 4 × 10−19

LC

3

53.84

rs109613143

−0.020±0.002

2 . 0 6 × 10−33

−0.001±0.002

0.595

LC

5

21.14

rs377953581

0.006±0.002

6.30×10−4

0.002±0.002

0.300

LC

5

31.56

rs137534989

−0.014±0.002

6 . 8 5 × 10−15

−0.010±0.002

2.25×10−7

LC

5

44.16

rs383349320

0.009±0.002

2.37×10−5

0.005±0.002

0.0205

LC

6

37.76

rs43702337

−0.329±0.009

< 1 . 0 5 × 10−308

−0.294±0.019

1 . 5 1 × 10−54

LC

6

89.04

rs478177439

−0.022±0.002

6 . 0 7 × 10−36

−0.018±0.009

0.0417

LC

7

8.77

rs210686953

0.005±0.002

7.02×10−3

0.015±0.002

6 . 8 1 × 10−14

LC

10

2.14

rs137774567

−0.012±0.002

2 . 5 4 × 10−12

−0.020±0.003

2 . 5 5 × 10−9

LC

15

28.36

rs211369213

−0.034±0.002

1 . 2 0 × 10−43

−0.026±0.009

5.07×10−3

LC

16

24.99

rs109379517

−0.018±0.002

6 . 4 7 × 10−24

−0.015±0.003

4 . 8 5 × 10−9

LC

16

67.77

rs380467601

0.015±0.002

3 . 9 2 × 10−20

0.009±0.002

1.27×10−5

LC

17

56.47

rs134672113

−0.012±0.002

3 . 7 0 × 10−13

−0.011±0.003

2.07×10−5

LC

19

33.51

rs109514832

−0.023±0.002

6 . 0 5 × 10−37

−0.009±0.002

4.46×10−6

LC

19

42.99

rs517084099

−0.018±0.003

1 . 2 2 × 10−10

0.022±0.003

2 . 4 9 × 10−12

LC

19

61.13

rs41923843

−0.025±0.002

4 . 4 7 × 10−46

−0.007±0.002

3.47×10−4

LC

20

58.45

rs135934727

−0.011±0.002

5.46×10−7

−0.019±0.002

2 . 7 2 × 10−20

LC

27

36.21

rs209987511

0.018±0.002

2 . 5 8 × 10−22

0.021±0.002

1 . 3 2 × 10−26

LC

28

6.56

rs110674951

−0.013±0.002

4 . 6 4 × 10−15

−0.017±0.003

7 . 3 7 × 10−9

LC

29

9.61

rs378183369

0.029±0.002

1 . 4 8 × 10−58

0.023±0.002

8 . 8 6 × 10−22

LY

5

93.94

rs211210569

0.021±0.002

9 . 1 6 × 10−37

0.016±0.004

1.91×10−4

LY

11

63.45

rs210726760

0.010±0.002

9 . 8 1 × 10−9

0.005±0.004

0.205

LY

14

1.77

rs109234250

−0.046±0.002

9 . 0 3 × 10−170

−0.035±0.002

1 . 0 8 × 10−61

LY

20

31.69

rs208881195

−0.010±0.002

5.15×10−8

−0.005±0.002

5.97×10−3

LY

26

22.96

rs208730573

0.008±0.002

1.12×10−6

0.042±0.006

1 . 6 1 × 10−13

  1. Allele effects for each WGS tag variant for Holstein-Friesian and Jersey cows, assuming an additive model. P-values in bold font indicate tag variants which pass the genome-wide Bonferroni-corrected threshold (4.58×10−8) for that breed. All but three variants pass Bonferroni in at least one breed; one of these three tags the QTL which failed validation. The direction of the allele effect is the same in both breeds for all but one (rs517084099) of the variants. Allele effects are relative to the allele present in the reference bovine genome. Phenotypes are lactose concentration (top) and lactose yield (bottom)
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BMC Genomics

ISSN: 1471-2164

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