Table 3

Summary of QTL based on RAD-only map constructed with 436 RAD and nine morphological loci.

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

2.8

0.41

0.87

1

1H

175

(170-175)

6.2

-0.9

0.18

2

4H

123

(120-123)

VRN-H2

2.9

0.6

0.08

3

5H

154

(148-156)

VRN-H1

2.8

-0.6

0.07

    4

    7H

    27

    2.7

    0.6

    0.07

Plant height

2.8

0.78

0.94

1

1H

144

(133-158)

6.5

-6.5

0.06

2

2H

122

(119-128)

ZEO1

31.0

-21.7

0.64

3

3H

57

(51-73)

5.6

6.0

0.05

4

6H

112

(103-121)

5.7

5.9

0.05

Spike number

2.7

0.56

0.63

1

2H

57

(50-64)

VRS1

11.4

3.6

0.40

2

5H

9

(2-24)

3.8

-1.8

0.06

3

6H

91

(85-98)

3.6

1.2

0.05

1 × 2

-1.5

0.06

Spike length

2.9

0.92

0.98

1

1H

175

(158-175)

4.9

-0.5

0.00

2

2H

122

(120-127)

ZEO1

42.9

-3.1

0.82

3

3H

20

(7-34)

5.1

-0.5

0.04

    4

    5H

    105

    2.4

    -0.2

    0.01

    5

    6H

    106

    2.7

    0.3

    0.02

1 × 2

0.4

0.04

Floret number

2.8

0.89

0.97

1

1H

175

(157-1175)

7.5

-5.3

0.05

2

2H

57

(54-61)

VRS1

38.6

-21.4

0.77

3

3H

39

(30-45)

3.2

-3.2

0.02

4

4H

123

(117-123)

3.1

3.2

0.02

5

6H

103

(66-120)

4.8

3.9

0.03

Grain number

3.0

0.75

0.92

1

1H

169

(162-174)

3.8

-5.0

0.01

2

2H

56

(53-62)

VRS1

18.7

-12.4

0.47

3

2H

122

(116-130)

ZEO1

10.3

-7.2

0.18

1 × 2

2.9

0.04

2 × 3

3.3

0.05

Hundred grain weight

2.8

0.66

0.78

1

2H

57

(54-62)

VRS1

19.8

0.5

0.54

2

6H

66

(56-70)

3.5

-0.1

0.04

3

7H

104

(86-130)

3.9

0.2

0.05

Gain yield

2.8

0.30

0.49

1

1H

175

(170-175)

3.5

-2.8

0.11

2

2H

122

(112-131)

ZEO1

6.2

-3.7

0.19


*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 italic and underlined showed a trend in the full 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