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Table 2 Location of QTL and magnitude of QTL effects

From: A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer)

Trait

QTL name

LG

Nearest marker

LOD

LOD threshold

PVE (%)

Phenotype means

     

Genome-wide

Linkage-group-wide

 

m1f1

m1f2

m2f1

m2f2

Significance

Body weight (g)

qBW2-a

2

Lca287

5.25*

4.5

3.4

28.8

27.0

23.3

39.1

27.0

†‡

 

qBW2-b

2

Lca371

4.62*

4.5

3.4

6.4

25.7

29.0

28.9

34.0

†‡

 

qBW3

3

Lca154

5.33*

4.5

2.3

8.8

30.7

26.6

34.6

26.4

‡

 

qBW12

12

Lca178

3.34

4.5

3.0

18.7

23.4

34.2

25.5

34.1

‡

 

qBW16

16

LcaE22

1.96

4.5

1.7

2.5

28.5

26.9

30.9

31.3

†

 

qBW20

20

Lca234

3.16

4.5

3.0

3.8

32.8

26.4

29.6

29.7

‡§

Total length (mm)

qTL1

1

Lca148

4.65

6.1

4.4

8.8

134.8

111.7

106.8

135.8

§

 

qTL2-a

2

Lca287

6.59*

6.1

5.4

58.9

119.7

104.2

138.5

131.5

†‡

 

qTL2-b

2

Lca371

5.45

6.1

5.4

7.6

117.1

123.2

122.9

130.9

†‡

 

qTL3

3

Lca154

5.08

6.1

2.3

8.3

125.9

119.1

131.0

119.4

‡

 

qTL12

12

Lca178

3.26

6.1

3.3

22.6

113.8

131.6

116.7

131.4

‡

 

qTL16

16

LcaE22

2.06

6.1

1.7

2.6

121.5

120.3

126.5

126.2

†

Standard length (mm)

qSL1

1

Lca148

4.65

6.1

4.5

8.3

111.4

92.3

88.3

112.3

§

 

qSL2-a

2

Lca287

6.30*

6.1

5.4

59.7

98.3

86.1

114.7

108.9

†‡

 

qSL2-b

2

Lca371

5.05

6.1

5.4

7.2

99.4

100.9

99.0

108.4

†‡

 

qSL3

3

Lca154

5.16

6.1

2.3

8.4

104.1

98.3

108.4

98.7

‡

 

qSL12

12

Lca178

3.32

6.1

3.2

21.9

93.7

109.2

97.0

108.1

‡

 

qSL16

16

LcaE22

2.19

6.1

1.7

2.7

100.4

99.3

104.7

104.3

†

KTL

qKTL6-a

6

Lca409

2.76

4.6

2.6

8.1

1.51

1.50

1.43

1.50

†‡

 

qKTL6-b

6

Lca223

3.99

4.6

2.6

10.7

1.46

1.45

1.49

1.55

†

 

qKTL7

7

Lca436

3.55

4.6

2.3

4.3

1.50

1.52

1.46

1.46

†

 

qKTL11-a

11

Lca315

2.48

4.6

2.4

6.7

1.46

1.45

1.52

1.51

†

 

qKTL11-b

11

Lca058

2.43

4.6

2.4

5.9

1.51

1.51

1.45

1.45

†

 

qKTL12

12

Lca115

2.87

4.6

2.8

18.3

1.50

1.44

1.44

1.55

†‡

 

qKTL16

16

LcaE22

1.99

4.6

1.7

2.5

1.51

1.48

1.46

1.48

†

 

qKTL21

21

Lca349

3.78

4.6

2.3

4.9

1.53

1.47

1.47

1.46

‡

KSL

qKSL6-a

6

Lca409

2.38

6.1

2.4

8

2.67

2.66

2.53

2.67

†‡

 

qKSL6-b

6

Lca223

3.22

6.1

2.4

3.8

2.59

2.60

2.64

2.70

†

 

qKSL7

7

Lca436

3.88

6.1

2.8

4.6

2.68

2.67

2.58

2.58

†

 

qKSL16

16

LcaE22

2.29

6.1

1.7

2.9

2.67

2.63

2.57

2.63

†

 

qKSL21-a

21

Lca349

3.26

6.1

2.4

4.2

2.69

2.65

2.58

2.59

†

 

qKSL21-b

21

Lca421

3.24

6.1

2.4

6

2.63

2.71

2.56

2.61

†‡

  1. For each QTL detected, the linkage group maximum LOD score, and percentage of the phenotypic variance explained (PVE) are indicated. The genome-wide LOD significance thresholds are 4.5 body weight, and 6.1 for total length and body length. Mean phenotypic values of each trait were also calculated for those progeny with the alternate alleles at the most closely linked microsatellite markers, inherited from the male parent (m1 or m2), alleles inherited from the female parent (f1 or f2). *: Significant QTL; †: Significant effect within male alleles, ‡: Significant effect within female alleles; and § Significant interaction between alleles from male and female.