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Table 5 Location, significance and effect of QTLs detected for phenology, berry size and seed content

From: Berry and phenology-related traits in grapevine (Vitis viniferaL.): From Quantitative Trait Loci to underlying genes

Trait

QTL position

LOD

LOD threshold

% var

KW sig

 

LG

Map

Peak (cM)

Nearest marker

cM

Interval

 

α = 0.20

α = 0.05

  

FT

1

Ia

54.7

VVIS21

44.7

43.1–66.6

2.3, 3.2, 4.3

2.0

2.8

6.3, 11.7, 8.6

1, 1, 2

  

Ib

88.2

mCTGeACC1

 

83.0–88.9

2.1, 4.7, 3.1

2.0

2.8

6.3, 11.5, 6.5

0, 3, 3

 

1

Ca

54.4

VVIS21

44.4

44.3–65.0

2.3, 3.8, 4.6

2.2

3.2

7.8, 13.9, 9.1

1, 1, 2

  

Cb

87.5

mCTGeACC1

 

82.8-b

-, 4.8, 3.1

2.2

3.2

-, 11.7, 6.6

-, 3, 3

 

1

BPa

35.4

VVIS21

25.4

24.3–46.4

2.3, 3.1, 4.2

2.1

3.0

6.2, 11.4, 8.4

1, 1, 2

  

BPb

67.3

mCTGeACC1

 

62.2–68.0

2.1, 4.7, 3.1

2.1

3.0

6.3, 11.5, 6.6

0, 3, 3

 

2

I

35.0

VVIB23

 

31.9–36.5

3.4, 3.5, 8.2

2.0

2.9

9.1, 7.3, 16.1

3, 4, 7

 

2

C

62.6

VVIB23

 

59.5–64.0

3.3, 3.6, 8.4

2.2

2.9

9.0, 7.7, 16.4

3, 4, 7

 

2

BP

60.2

VVIB23

 

55.1–61.5

3.4, 3.5, 8.1

2.0

2.9

9.2, 7.4, 16.1

3, 4, 7

 

6

I

5.0

VVIN31

t

t-9.5

4.1, 7.4, 6.8

1.8

2.6

13.8, 20.5, 15.5

3, 7, 5

 

6

C

5.0

VVIN31

t

t-9.5

3.9, 7.2, 6.8

1.9

2.7

13.4, 19.9, 15.4

3, 7, 5

 

6

BP

5.0

VVIN31

t

t-9.2

4.1, 7.4, 6.9

1.9

2.8

13.9, 20.8, 15.6

3, 7, 5

VT

2

I

30.1

VVIO55

 

27.0–31.9

3.5, 3.0, 5.6

2.3

3.5

6.6, 5.9, 12.6

0, 3, 1

 

2

C

55.0

VMC2C10.1

 

52.0–55.2

3.5, 2.9, 5.6

2.6

4.0

6.6, 5.8, 12.6

0, 1, 1

 

2

BP

52.5

VMC2C10.1

 

48.1–53.4

3.5, 2.9, 5.6

2.0

2.7

6.6, 5.8, 12.6

0, 1, 1

 

6

I

17.6

VMC4G6

 

13.4–18.0

4.6, 4.9, -

1.6

2.4

9.0, 9.8, -

3, 4, -

 

6

C

17.6

VMC4G6

 

13.5–17.9

4.8, 4.9, -

1.8

2.6

9.3, 9.9, -

3, 4, -

 

6

BP

17.4

VMC4G6

 

13.4–17.7

4.8, 4.9, -

1.9

2.7

9.3, 9.9, -

3, 4, -

 

16

I

17.8

VMC1E11

 

15.6–20.6

13.7, 9.7, 11.3

1.8

2.5

31.6, 21.1, 29.1

7, 7, 7

 

16

C

16.9

VMC1E11

18.0

15.2–20.5

15.1, 9.6, 11.9

1.9

2.7

38.0, 24.1, 45.4

7, 7, 7

 

16

BP

17.8

VMC1E11

 

14.3–17.8

14.0, 9.7, 11.5

1.5

2.2

32.1, 21.2, 29.1

7, 7, 7

VP

2

I

19.0

mCTGeACC2

 

3.6–20.2

13.6, 15.4, 7.0

2.1

3.9

41.8, 38.0, 44.2

7, 7, 7

 

2

C

40.9

colour

 

40.2–45.9

14.0, 16.4, -

3.0

4.4

40.0, 39.8, -

7, 7, -

 

2

BP

40.5

colour

 

39.8–44.4

13.9, 16.4, 4.3

2.0

2.7

38.9, 39.6, 15.8

7, 7, 7

R

6

I

19.6

VMC4H5

 

18.4–20.8

4.1, 3.5, -

1.7

2.5

17.2, 10.2, -

5, 2, -

 

6

C

19.7

VMC4H5

 

18.5–21.0

4.1, 3.5, -

1.9

2.7

17.2, 10.2, -

5, 2, -

 

6

BP

19.6

VMC4H5

 

18.3–20.8

4.1, 3.5, -

1.9

2.7

17.2, 10.2, -

5, 2, -

F-V

2

I

24.0

VMC5G7

24.2

20.4–24.8

7.7, 6.4, 5.7

2.5

3.9

18.7, 14.0, 12.6

6, 6, 4

 

2

C

51.2

VMC5G7

51.4

47.1–51.8

7.7, 6.4, 5.8

2.8

4.1

18.4, 13.8, 12.7

6, 6, 4

 

2

BP

45.5

VMC5G7

48.9

40.4–49.4

8.0, 6.5, 5.8

1.9

2.8

21.4, 15.6, 12.7

6, 6, 4

 

6

I

17.6

VMC4G6

 

13.3–18.0

3.9, 4.0, -

1.7

2.5

8.5, 8.2, -

1, 1, -

 

6

C

17.6

VMC4G6

 

13.3–18.0

3.9, 4.0, -

1.8

2.6

8.5, 8.2, -

1, 1, -

 

6

BP

17.4

VMC4G6

 

13.3–17.8

3.9, 4.0, -

1.9

2.6

8.5, 8.2, -

1, 1, -

 

16

I

17.8

VMC1E11

 

15.8–19.1

7.9, 7.3, 11.4

1.8

2.6

18.7, 15.5, 27.8

7, 7, 7

 

16

C

18.0

VMC1E11

 

15.8–19.3

8.7, 7.2, 11.8

1.9

2.6

23.0, 15.4, 37.2

7, 7, 7

 

16

BP

17.8

VMC1E11

 

15.0–17.8

7.9, 7.2, 11.4

1.4

2.2

18.7, 15.4, 27.8

7, 7, 7

F-R

6

I

19.6

VMC4H5

 

18.3–21.0

3.6, 3.1, -

1.7

2.6

15.3, 9.1, -

4, 2, -

 

6

C

19.7

VMC4H5

 

18.3–21.2

3.6, 3.1, -

1.8

2.5

15.3, 9.1, -

4, 2, -

 

6

BP

19.6

VMC4H5

 

18.1–21.0

3.6, 3.1, -

1.9

2.6

15.3, 9.1, -

4, 2, -

V-R

2

I

35.0

VVIB23#

 

29.9–35.7

3.3, 6.6, 6.0

2.0

3.0

15.4, 18.0, 20.7

2, 7, 7

 

2

C

62.6

VVIB23#

 

57.3–63.3

3.4, 6.5, 5.9

2.2

3.1

14.6, 17.8, 19.9

2, 7, 7

 

2

BP

60.2

VVIB23#

 

55.1–60.8

3.7, 6.6, 6.2

2.0

2.8

15.9, 18.1, 21.7

2, 7, 7

 

12*

I

18.7

VMC2H4

23.8

7.8–29.5

3.2, -, 2.6

2.0

2.8

16.7, -, 10.4

3, -, 1

 

12*

C

21.9

VMC2H4

 

21.4–28.5

3.3, -, 2.8

1.9

2.7

13.5, -, 9.0

3, -, 3

 

12*

BP

18.8

PHEA-sscp

 

16.3–19.2

3.5, -, 2.5

1.9

2.6

16.8, -, 9.1

0, -,0

MBW

1

C

18.9

mCACeATC4

 

t-19.5

3.2, 2.6, 5.4

2.2

3.1

10.7, 4.7, 17.5

1, 2, 4

 

1

BP

t

mCACeATC4

 

t-0.9

-, 2.4, 3.7

2.0

2.8

-, 4.6, 9.1

-, 2, 4

 

12

C

29.8

mCTGeAAG5

 

22.8–29.8

3.4, 3.2, 3.9

1.9

2.8

8.4, 5.6, 8.8

2, 2, 6

 

12

BP

28.5

mCTGeAAG5

 

20.6–28.6

2.4, 3.2, 3.7

1.9

2.8

5.1, 5.7, 8.0

1, 2, 6

 

18

C

81.9

SdI

 

74.5–81.9

14.2, 19.4, 11.5

2.5

3.3

41.7, 43.1, 32.6

7, 7, 7

 

18

BP

17.4

SdI

 

13.8–17.4

11.8, 18.3, 9.9

1.9

2.6

29.6, 40.8, 27.2

7, 7, 7

MSN

2

I

35.0

VVIB23

 

31.6–35.6

6.2, 8.5, -

1.9

2.6

19.6, 22.9, -

7, 7, -

 

2

C

62.6

VVIB23

 

60.8–63.0

6.3, 8.5, -

2.1

2.9

19.9, 22.9, -

7, 7, -

 

2

BP

60.2

VVIB23

 

58.7–60.7

6.3, 8.5, -

2.0

2.7

19.8, 22.9, -

7, 7, -

% SDM

18

BP

17.4

SdI

 

13.1–17.5

65.9, 61.7, 59.2

2.1

3.6

90.0, 86.5, 91.4

7, 7, 7

MSFW

6*

BP

42.3

mCACeACA4

 

39.4–48.3

3.4, -, 4.2

1.9

2.7

5.3, -, 13.2

0, -, 4

 

6

C

47.2

mCTCeACA1

 

37.4–48.3

4.3, 2.1, 5.8

1.8

2.5

11.3, 3.5, 21.4

1, 1, 4

 

10

I

43.3

mCTAeAAG10

 

39.0–53.0

2.6, 3.3, -

2.0

2.7

9.4, 10.0, -

0, 0, -

 

10

C

47.2

mCTAeAAG10#

 

46.9–55.6

4.4, 6.4, '-

2.3

3.0

36.3, 13.4, -

2, 0, -

 

10

BP

50.0

mCTGeATT18

50.6

44.8–55.7

2.9, 4.2, 2.2

2.0

2.7

7.7, 12.1, 9.8

2, 3, 0

 

13

I

62.6

mCATeATG9#

b

42.5–b

3.5, 3.9, -

1.9

2.7

14.6, 14.2, -

1, 3, -

 

13

C

b

mCATeATG9#

 

52.0–b

3.8, 4.4, -

2.3

3.0

8.8, 15.7, -

0, 3, -

 

13

BP

25.5

VMC3D12#

 

25.1–29.8

3.3, 3.4, -

1.7

2.4

7.2, 7.8, -

1, 2, -

 

15

I

5.8

mCACeACA10#

 

5.5–13.5

2.1, 2.6, 3.5

1.9

2.6

7.5, 6.7, 13.0

0, 0, 5

 

18

C

80.1

SdI

81.9

65.0–82.0

10.7, 5.5, 6.4

2.4

3.2

27.5, 15.8, 25.7

7, 4, 6

 

18

BP

17.4

SdI

 

8.7–17.7

10.3, 3.9, 5.9

1.9

2.7

26.3, 13.8, 24.8

7, 4, 6

MSDW

2*

I

35.0

VVIB23

 

29.8–36.7

3.3, -, 2.9

1.8

2.6

10.5, -, 10.8

6, -, 2

 

2*

C

62.6

VVIB23

 

60.4–63.2

8.9, -, 2.3

2.2

8.0

4.6, -, 3.7

6, -, 2

 

15

I

5.8

mCACaACA10#

 

5.2–12.3

-, 2.9, 2.2

1.8

2.6

-, 10.8, 8.2

-, 0, 2

 

15

C

5.7

mCACeACA10#

 

5.5–9.4

-, 2.2, 3.2

1.8

2.8

-, 3.1, 5.4

-, 0, 2

 

18

C

80.1

SdI

81.9

72.0–81.4

55.5, 27.5, 19.8

2.2

3.4

73.8, 57.1, 49.3

7, 7, 7

 

18

BP

15.0

SdI

17.4

12.9–17.4

54.5, 25.6, 19.0

2.0

2.8

75.0, 62.1, 49.4

7, 7, 7

  1. LG = linkage group; Map = map in which the QTL was identified (I for Italia, C for consensus, BP for Big Perlon); Peak = QTL position as estimated by the cM distance of the local LOD maximum from the top of the linkage group, with 't' for top and 'b' for bottom of linkage group; Nearest marker = marker nearest to the QTL position; Interval = 1-LOD confidence interval of QTL position in cM; # = LOD peak position and confidence interval were not exactly the same in different years; LOD = LOD value at QTL position; LOD threshold = chromosome wide LOD threshold for type I error rates of 20% and 5%; %var = proportion of the total phenotypic variance explained by the QTL; KW = Kruskal-Wallis significance level, given by the P value (1 = 0.1, 2 = 0.05, 3 = 0.01; 4 = 0.005; 5 = 0.001; 6 = 0.0005; 7 = 0.0001). Complete data are referred to 2003 (2002 in case of QTL lack in 2003, as indicated by an asterisk), yearly details (year 2002, 2003 and 2004 are respectively in first, second and third position) are given for LOD scores, percentage of explained variance and Kruskal-Wallis significance, which represent the most variable data
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