Table 3

Haplotype statistics and analysis of suggested QTL regions.

Haplotype analysis


SSC#

Trait

HF

SNP-set

Haplotypes$

Percent$

Significance

Fixed effect (μg/g)


Duroc

3

log Skatole

68.9

10

5

93

0.05023

0.022

3

log Androstenone

33.7

12

10

97.4

0.03365 *

0.844

5

log S/I-index

81.6

5

2

99.4

0.00304 **

0.015

6

log Androstenone

56.1

4

4

99.4

2.106e-4 ***

0.775

10a

log Indole

55.4

10

13

78

6.92e-4 ***

0.012

10b

log Indole

34.1

15

12

77.2

0.0225 *

0.008 (0.003*)a

12

log Androstenone

51.5

9

9

93.4

1.027e-4 ***

1.292

14

log Androstenone

82.8

12

4

94.9

7.4e-3 **

1.183

Landrace

1

log Androstenone

19.8S

6

8

99.2

3.35e-4 ***

1.279

2a

log Androstenone

23.4

7

14

85.7

6.48e-3 **

0.838

2b

log Androstenone

54.9

6

6

94.2

0.02133 *

1.172

5

log S/I-index

44.5

10

9

79.6

6.138e-3 **

-0.031

6

log Indole

27.6

11

10

89.3

0.01616 *

-0.012

7

log Androstenone

38.6

15

13

58.7

8.094e-3 **

1.240

14

log S/I-index

52.4

24

9

92.2

3.86e-5 ***

-0.038 (-0.011***)a

14

log Indole

30

24

7

93.3

8.815e-5 ***

-0.013 (-0.004***)a

15

log Indole

48.1

18

7

96

5.451e-3 **

-0.056

Yorkshire

6a

log S/I-index

73.9

15

3

95.8

4.706e-5 ***

0.015 (0.004***)b

6b

log S/I-index

30.6

10

7

94.4

0.01399 *

0.009

7

log S/I-index

44.8

16

5

97.2

3.538e-3 **

0.013

8

log S/I-index

63

11

5

97.2

1.741e-3 **

0.013 (0.003**)a

9

log Skatole

33.5

11

10

90.5

0.03686 *

-0.012

11b

log Androstenone

57.1

5

6

98.4

0.0125 *

0.838 (0.059**)a

12

log Androstenone

61

16

10

94.3

0.03257 *

0.827

14

log Indole

43.8

12

8

95.1

1.028e-3 **

-0.007


***,**,* = p < 0.001, 0.01, 0.05, # = Sus scrofa chromosome

HF = Haplotype frequency of the most common haplotype,S = The second most common haplotype

$ = Amount of haplotypes with a frequency above 1.5%

a,b = Test including slaughter weight, slaughter weight and meat content as covariate

Gregersen et al. BMC Genomics 2012 13:22   doi:10.1186/1471-2164-13-22

Open Data