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Table 2 Results of a genome scan for QTL associated with stress response using half-sib regression interval mapping

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

Omy

cM

Trait

Sire-dam family4

LR1

F-value2

F ChromWide P=0.05 3

F ExperWide P=0.05 4

P-value 5

P GenomeWide 6

h q 2 7

Left flanking marker

Right flanking marker

6

32.0

BLUP3

Dam

21.14

3.14*

2.85

4.16

0.00350

0.736

0.26

OMY105DU

OMM5254

10

70.0

BLUP3

Dam

18.41

2.72

2.91

4.16

0.01002

0.978

0.21

OMM1544

OMM5108

10

72.0

EBV

Dam

23.19

3.46*

2.88

4.15

0.00155

0.445

0.30

OMM1544

OMM3102

12

36.0

EBV

Dam

19.83

2.93*

2.75

4.15

0.00594

0.896

0.24

OMM1096

OMM11308

12

60.0

EBV

Sire

19.88

4.14*

2.71

4.48

0.00129

0.388

0.27

OMM1341

OMM1711

14

95.0

EBV

Sire

15.8

3.26*

2.78

4.48

0.00733

0.939

0.20

OMM1643

OMM51538

16

45.09

BLUP3

Sire

17.4

3.60*

2.59

4.53

0.00108

0.336

0.23

OMM1559

OMM5162

16

65.0

BLUP3

Dam

20.44

3.03*

2.77

4.16

0.00462

0.828

0.25

OMM1150

OMM1221

16

71.09

BLUP3

Sire

22.64

4.75**

2.61

4.53

0.00005

0.020

0.32

OMM1150

OMM1221

19

40.0

EBV

Sire

14.33

2.94*

2.93

4.48

0.01365

0.995

0.17

OMM1241

OMM3067

19

45.0

BLUP3

Sire

14.59

3.00*

2.95

4.53

0.01215

0.990

0.18

OMM1241

OMM3067

19

64.0

BLUP3

Dam

18.34

2.70

2.77

4.16

0.01052

0.982

0.21

OMM5327

OMM5216

22

35.0

EBV

Dam

19.61

2.90*

2.54

4.15

0.00640

0.913

0.23

OMM1292

BX9130598

29

50.010

EBV

Sire

14.76

3.04*

2.73

4.48

0.01125

0.986

0.18

OMM17728

OMM1118

29

56.010

EBV

Sire

14.6

3.01*

2.70

4.48

0.01192

0.990

0.18

OMM1118

OMM1405

  1. 1The likelihood ratio (LR) test statistic.
  2. 2Asymptotically F- test statistic with the degrees of freedom(DF) being the number of sires or dams included for the numerator, and the total number of offspring minus twice the number of sires or dams for the denominator. The QTL with F-value ≥ F ChromWide P=0.05 was defined as suggestive QTL (*); and QTL with F-value ≥ F ExperWide P=0.05 or P GenomeWide ≤ 0.05 was defined as significant QTL (**).
  3. 3Chromosome-wide F-value at P=0.05 was estimated using 10,000 permutations with software GridQTL.
  4. 4Experiment-wide F-value at P=0.05 was estimated using 10,000 bootstraps with re-sampling with software GridQTL.
  5. 5The nominal P-value was calculated assuming an F-value distributed with numerator DF equal to the number of sires or dams, and denominator DF equal to the total number of offspring minus twice the number of sires or dams.
  6. 6The genome-wide significance level for detected QTL.
  7. 7The proportion of phenotypic variance explained by the QTL.
  8. 8The QTL flanking markers OMM1772, OMM1130, BX913059 and OMM5153 had significant Mendelian segregation distortion (P <0.01) in families 2, 4, 5 and 6, respectively.
  9. 9The Omy16 QTL had significant statistical support for two QTL segregating (F2QTL vs. 0QTL; DF=10=3.58; F1QTL vs. 0QTL; DF=5=3.60; LR2QTL vs. 0QTL = 33.62) for BLUP3 when fitting a two-QTL model with sire HS families.
  10. 10The Sex chromosome QTL had significant statistical support for two QTL segregating (F2QTL vs. 0QTL; DF=10=3.45; F1QTL vs. 0QTL; DF=5=3.10; LR2QTL vs. 0QTL = 32.50) for EBV when fitting a two-QTL model with sire HS families.
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BMC Genomic Data

ISSN: 2730-6844

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