Table 2

Summary of QTL based on a skeleton map derived from the 2846 loci data set.

Trait, QTL number and QTL interaction

Chrom.

QTL peak position

2-LOD confidence interval

Morphological and/or cloned genes within 2 LOD conf. interval

LOD

Additive effect

R2*

LOD threshold

MIM R2**

H2


Final leaf number

3.0

0.47

0.87

1

1H

158

(154-158)

6.9

-0.9

0.17

2

4H

118

(117-120)

VRN-H2

4.6

0.7

0.10

3

5H

157

(154-161)

VRN-H1

3.5

-0.7

0.09

4

7H

29

(26-36)

3.6

0.7

0.08

Plant height

3.1

0.82

0.94

1

1H

131

(120-136)

7.1

-6.7

0.06

2

2H

156

(155-158)

ZEO1

32.1

-22.8

0.67

3

3H

51

(43-60)

6.1

6.3

0.05

4

6H

100

(74-104)

6.0

5.7

0.05

Spike number

2.9

0.50

0.63

1

2H

99

(95-102)

VRS1

13.3

3.5

0.38

    2

    5H

    43

    2.4

    -1.3

    0.05

    3

    6H

    80

    2.7

    1.3

    0.06

Spike length

3.1

0.93

0.98

1

1H

158

(152-158)

6.7

-0.5

0.00

2

2H

156

(155-159)

ZEO1

45.8

-3.0

0.81

3

3H

20

(13-23)

5.0

-0.5

0.04

4

5H

138

(137-144)

3.8

-0.3

0.02

5

6H

95

(93-100)

4.5

0.4

0.02

1 × 2

0.5

0.05

Floret number

3.0

0.87

0.97

1

1H

156

(150-158)

9.4

-5.8

0.06

2

2H

99

(97-101)

VRS1

40.3

-21.6

0.79

    3

    3H

    36

    2.9

    -2.9

    0.01

4

4H

120

(112-127)

VRN-H2

3.6

3.3

0.02

5

6H

91

(73-103)

4.6

3.7

0.02

Grain number

3.0

0.74

0.92

1

1H

151

(142-156)

3.9

-4.9

0.01

2

2H

99

(99-101)

VRS1

20.1

-12.3

0.46

3

2H

156

(150-163)

ZEO1

10.4

-7.3

0.18

1 × 2

2.9

0.04

2 × 3

3.4

0.05

Hundred grain weight

2.9

0.66

0.78

1

2H

99

(97-101)

VRS1

19.9

0.5

0.53

2

6H

60

(54-61)

3.5

-0.1

0.04

3

7H

103

(96-111)

4.2

0.2

0.05

Grain yield

3.1

0.29

0.49

1

1H

157

(153-158)

4.4

-2.9

0.11

2

2H

160

(150-165)

ZEO1

8.1

-4,1

0.23


***Proportion of phenotypic the variance explained by individual QTL

**R2 of the multi-locus model that includes QTL and their significant interactions calculated with MIM

The QTLs in italics and underlined showed a trend in the RAD-only map but did not reach the LOD threshold.

Chutimanitsakun et al. BMC Genomics 2011 12:4   doi:10.1186/1471-2164-12-4

Open Data