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Table 4 Identified QTL in Gal1056, Oria6 and GxO maps

From: Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification

Trait

Time-point

Map

Total var.

LG

LOD

Sig.

Var.

Add. Eff.

Position (cM)

CI1LOD(cM)

CI 2LOD(cM)

QTL id

An

2

Oria6

23

4

2.7

**ch

10

+

91.4

77.1-107.4

69.7-112.4

AnS2LG4m

    

6

2

*ch

7.1

-

18.5

5-44.5

0-79.5

AnS2LG6m

    

9

2.4

**ch

8.7

+

61.8

40-79.8

30-113.8

AnS2LG9m

 

3

Oria6

 

12

1.5

*ch

12

-

30.6

0-41

0-66.6

An_S3LG12m

gsw

1

Gal1056

18.7

7_1

1.9

**ch

7.4

+

0.0

0-25

0-27

gsw S1LG7_1f

    

12

2.1

*ch

8

+

132.2

119-145.2

95.1-152.1

gsw S1LG12f

  

GxO

37.8

7

3.5

**ch

10.7

 

37.5

27-47

5-65

gsw S1LG7i

    

10

4.1

**ch

12.5

 

16.1

5-40

5-55

gsw S1LG10i

    

12

3.9

**ch

12

 

114.5

103.1-125.5

90-131.6

gsw S1LG12i

 

2

Gal1056

 

5

2.4

**ch

10.1

+

86.4

52.9-112.3

36.7-121.6

gsw S2LG5f

  

GxO

24.1

5

3.9

**ch

14.4

 

68.7

61.9-79.7

48.3-85.7

gsw S2LG5i

    

11

2.8

*ch

10

 

50.1

32.6-55.1

10-75

gsw S2LG11i

WUEi

1

Gal1056

15

7_1

1.2

*ch

4.7

-

6.0

0-27

0-27

WUEiS1LG7_1f

    

12

2.0

*ch

7.8

-

132.2

118-141.2

83.1-152.1

WUEiS1LG12f

  

Oria6

 

3_2

1.06

*ch

4.6

+

0

0-18.4

0-18.4

WUEiS1LG3_2m

 

2

Gal1056

 

5

2.1

*ch

9

-

103.3

87.4-116.3

13-130.6

WUEiS2LG5f

  

GxO

 

5

3

*ch

12.7

 

68.7

49.9-76.2

42.1-115.7

WUEiS2LG5i

δ13C

1

Gal1056

 

6

2.3

*ch

9.7

+

34.3

22-56.4

11-79.8

δ13C S1LG6f

  

GxO

 

6

3.2

*ch

13.4

 

33.2

21.2-45.2

8-55.4

δ13C S1LG6i

SLA

1

Gal1056

16.2

5

1.9

*ch

7.5

+

53.4

29.4-86.4

0-130.6

SLAS1LG5f

    

12

2.2

*ch

8.8

-

10.1

0-38.1

0-58.2

SLAS1LG12f

  

GxO

 

7

3.1

*ch

13.1

 

12.9

0-53.8

0-76.1

SLAS1LG7i

 

2

Gal1056

18.6

5

2.5

**ch

9.7

+

46.9

20-72

3-96.9

SLAS2LG5f

    

12

2.6

**ch

9.8

-

10.1

0-34.1

0-51.1

SLAS2LG12f

 

3

Gal1056

16.8

5

2.5

**ch

9.7

+

46.9

17.5-55.9

12-83.9

SLAS3LG5f

    

7_1

2.2

**ch

8.5

+

0.0

0-8

0-25

SLAS3LG7_1f

  

GxO

 

7

3.1

*ch

13.1

 

44.8

29.6-87.7

0-101.5

SLAS3LG7i

Fv'Fm'

1

Gal1056

 

7_2

2.9

*gw

12.1

-

5.5

0-35

0-54.4

Fv’Fm’S1LG7_2f

  

Oria6

18

6

1.9

*ch

7.4

+

122.4

114.7-122.4

0-122.4

Fv’Fm’S1LG6m1

    

6

2.7

**ch

10.3

-

62.7

37.5-96.7

25.5-104.7

Fv’Fm’S1LG6m2

  

GxO

28.2

3_2

3.5

**ch

12

 

0

0-3

0-8

Fv’Fm’S1LG3_2i

    

7

3.7

**ch

12.9

 

90.3

67-120

40-145.3

Fv’Fm’S1LG7i

 

2

Gal1056

22.9

2_1

1.9

*ch

7

-

0.0

0-11

0-100.3

Fv’Fm’S2LG2_1f

    

5

2.7

**ch

10

+

86.5

71.9-99.4

20.5-114.4

Fv’Fm’S2LG5f

    

12

2.1

*ch

7.5

+

152.1

130.6-152.1

75.2-152.1

Fv’Fm’S2LG12f

  

Oria6

32.7

1_2

2.6

**ch

8.2

-

45.1

30.2-66.1

24.5-67.8

Fv’Fm’S2LG1_2m

    

3_1

3.3

**gw

10.8

+

18.6

2-22.6

0-26.6

Fv’Fm’S2LG3_1m

    

6

2

*ch

6.4

-

62.7

38.3-85.7

0-101.7

Fv’Fm’S2LG6m

    

12

1.7

*ch

5.4

-

30.6

0-41.6

0-66.6

Fv’Fm’S2LG12m

  

GxO

44

6

4.1

**ch

11.4

 

59.3

55-77

50-95

Fv’Fm’S2LG6i

    

7

7

**gw

20.9

 

54.8

50-66

48-70

Fv’Fm’S2LG7i

    

9

3.6

*ch

9.6

 

71.3

65-80

60-85

Fv’Fm’S2LG9i

    

12

4.7

**gw

13.2

 

83.3

80-95

77-110

Fv’Fm’S2LG12i

 

3

Oria6

 

6

2.1

*ch

9

-

34.3

0-43.3

0-68.7

Fv’Fm’S3LG6m

  

GxO

29.1

6

3.7

**ch

13.3

 

54.8

0-80

0-124.8

Fv’Fm’S3LG6i

    

7

4.5

*gw

15.6

 

63.7

55.8-71.6

54.5-81.6

Fv’Fm’S3LG7i

ΦPSII

1

Gal1056

20.1

2_2

1.8

*ch

6.8

-

85.2

69.9-95.5

0-95.5

ΦPSII S1LG2_2f

    

4_1

2.7

**ch

10.1

+

3.3

0-22.3

0-34.3

ΦPSII S1LG4_1f

    

7_2

1.8

*ch

6.5

-

37.4

23.8-60.4

0-88.8

ΦPSII S1LG7_2f

  

Oria6

 

8_2

2.7

**ch

11.3

-

79

74.1-79

60.8-79

ΦPSII S1LG8_2m

 

2

GxO

 

7

2.9

*ch

12.3

 

37.5

24.6-62.8

16.5-62.8

ΦPSII S2LG7i

 

3

Gal1056

 

8

1.8

*ch

7.8

-

99.6

78.5-110

0-124.5

ΦPSII S3LG8f

  

Oria6

15.1

4

2

*ch

7.9

+

20.5

10.5-30.5

0-56.5

ΦPSII S3LG4m

    

12

1.9

*ch

7.3

-

12.7

0-30.7

0-66.5

ΦPSII S3LG12m

  

GxO

 

7

2.9

*ch

12.2

 

63.7

48.8-67.1

24.6-71.2

ΦPSII S3LG7i

  1. Columns stand for trait names [An = net photosynthetic rate (μmol CO2m-2 s-1); gsw = stomatal conductance to water vapour (molH2Om-2 s-1); WUEi = intrinsic water use efficiency (μmol CO2 molH2O-1); δ13C = isotopic composition of 13C (‰); SLA = specific leaf area (m2Kg-1), Fv’Fm’ = maximum efficiency of PSII under light conditions; ΦPSII = quantum yield], time-points of measurements (1st stands for well watered, 2nd and 3rd for seven and 14 days without watering), genetic map where the QTL was identified, total phenotypic variance explained (%) for all detected QTL for a given trait in a given time-point of measurements, linkage group, maximum LOD score for mapped markers, level of significance (* <0.05, ** < 0.01, ch stands for chromosome and gw for genome wide level), total phenotypic variance explained for each QTL (%), sign of the additive effect, position of the marker with the maximum LOD score, one LOD confidence interval, two LOD confidence interval and QTL identification name.