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Table 5 Results of a genome scan for QTL associated with stress response using linkage disequilibrium and linkage analysis

From: QTL affecting stress response to crowding in a rainbow trout broodstock population

Omy

cM

Trait

LR1

P 2

P GenomeWide 3

LOD score4

h u 2 5

h addQTL 2 6

h domQTL 2 7

Flanking markers

Left

Right

3

79.0

EBV

173.77**

1.8E-38

6.6E-36

36.2

0.00

0.00

0.98

OMM3120

OMM5109

3

98.0

BLUP3

16.65*

2.4E-04

8.5E-02

2.6

0.00

0.00

0.84

OMM1263

OMM1391b

4

7.0

EBV

39.75**

2.3E-09

1.0E-06

7.5

0.00

0.03

0.81

OMM11948

OMM1211

5

90.0

BLUP3

58.23**

2.3E-13

8.3E-11

11.4

0.00

0.76

0.11

OMM5025

OMM1774

5

99.0

EBV

20.63**

3.3E-05

1.2E-02

3.5

0.00

0.00

0.70

OMM5025

OMM1774

6

67.0

EBV

53.03**

3.1E-12

1.1E-09

10.3

0.00

0.00

0.71

OMM1753

OMM1628

7

35.0

EBV

31.27**

1.6E-07

5.9E-05

5.7

0.43

0.00

0.48

OMM1468

OMM17408

8

55.0

EBV

46.24**

9.1E-11

3.3E-08

8.8

0.00

0.37

0.29

OMM1295

OMM1632

9

71.0

EBV

18.83**

8.1E-05

2.9E-02

3.1

0.00

0.10

0.36

OMM5179

OMM1089

10

100.0

EBV

81.7**

1.8E-18

6.6E-16

16.4

0.00

0.00

0.64

CR3729718

OMY1000UW

11

34.0

EBV

22.36**

1.4E-05

5.1E-03

3.8

0.00

0.00

0.61

OMM1333

OMM3042

12

33.0

EBV

50.87**

9.0E-12

3.3E-09

9.8

0.52

0.00

0.38

OMY105INRA

OMM1096

13

50.0

EBV

26.45**

2.0E-06

6.6E-04

4.7

0.00

0.00

0.54

OMY1UoG

OMM5165a

13

51.0

BLUP3

15.05*

5.4E-04

1.8E-01

2.3

0.16

0.00

0.35

OMY1UoG

OMM5165a

14

46.0

EBV

16.05*

3.3E-04

1.1E-01

2.5

0.14

0.00

0.47

OMM1038

OMM1415

16

54.0

EBV

21.32**

2.3E-05

8.5E-03

3.6

0.18

0.13

0.34

OmyRGT6TUFa

OMM1362

16

69.0

BLUP3

22.89**

1.1E-05

3.9E-03

3.9

0.00

0.61

0.00

OMM1150

OMM1221

17

75.0

EBV

49.57**

1.7E-11

6.3E-09

9.5

0.00

0.45

0.23

OMM3126

OMM1808

18

108.0

EBV

16.64*

2.4E-04

8.5E-02

2.6

0.48

0.00

0.42

OMM1352

BX873238

19

84.0

EBV

45.14**

1.6E-10

5.8E-08

8.6

0.47

0.00

0.46

OMM5106a8

OMM1412b

21

16.0

EBV

17.23*

1.8E-04

6.4E-02

2.8

0.00

0.00

0.54

OMM12568

OMM5298

25

0.0

EBV

19.97**

4.6E-05

1.7E-02

3.3

0.00

0.00

0.68

OMM3142

BX881655a

26

56.0

EBV

29.97**

3.1E-07

1.1E-04

5.4

0.00

0.00

0.83

OMY1189UWa

OMM1752b

27

28.0

EBV

19.3**

6.4E-05

2.3E-02

3.2

0.33

0.00

0.49

OMM13158

OMM5309

28

48.0

EBV

19.71**

5.2E-05

1.9E-02

3.3

0.00

0.00

0.53

CR3734048

OMY1013UW

Sex

20.0

EBV

53.66**

2.2E-12

8.1E-10

10.4

0.00

0.28

0.48

OMM1026

OMM1461

Sex

44.0

BLUP3

16.56*

2.5E-04

8.8E-02

2.6

0.47

0.00

0.38

BX076085

OMM17728

  1. 1The likelihood ratio (LR) test statistic is defined as L R = − 2 l n l ^ r z l ^ z where ln stands for natural logarithm, Î(z) is the likelihood function evaluated at the maximum likelihood estimate (MLE) for the full model that includes polygenic and QTL effects, and Î r (z) is the MLE for the restricted model under which r parameters of the full model are assigned fixed values. The QTL was declared as suggestive if it had a LR ≥ 13.82 or nominal P ≤ 0.001 (*), and as significant if it had a P GenomeWide ≤0.05 (**).
  2. 2The nominal P-value was estimated assuming the LR test statistic follows a chi-square distribution with two degrees of freedom.
  3. 3The genome-wide significance level for detected QTL was estimated as P GenomeWide  = 1 − (1 − P)g[37] where P is the nominal P-value, and g = 365 STR loci used with LDLA method of QTL analysis.
  4. 4Logarithm of odds (LOD) score was calculated as LOD = log10[L(QTL)/L(polygenic)] where L = likelihood of the model.
  5. 5h u 2 is the residual genetic variance or proportion of the total variance due to the polygenic component.
  6. 6h addQTL 2 is the proportion of the total variance due to additive effect QTL.
  7. 7h domQTL 2 is the proportion of the total variance due to dominance effect QTL.
  8. 8These QTL flanking markers had significant Mendelian segregation distortion (P <0.01): OMM1194, OMM1740, OMM5106a and OMM1772 in family 2; CR372971 and CR373404 in family 3; OMM1256 in family 4; OMM1315 in family 5; and OMM1752b in family 7.
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BMC Genomic Data

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