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Rice

Table 3 Results of QTL Analysis for 14 Traits Identified in the Four Experiments for the IR64 × Azucena Populations

From: Genetic Analysis of Water Use Efficiency in Rice (Oryza sativa L.) at the Leaf Level

QTLa

Chr

Marker interval flanking peakb

Position cM (confidence interval)

Pop

QTL clusterc

LOD score thresholdd

LOD score

R 2e

a f

ANOVA

Δ13C4.1_E2

4

RM280–RM567

131.2 (122.3–134.7)

DH

4-C

3.25

4.21

0.13

−0.138

–g

Δ13C4.1_E3

4

RM518–RM261

17.7 (11.7–29.2)

RIL

4-A

3.11

3.08

0.08

0.137

–h

Δ13C 4.1_E4

4

RM307–RM185

27.2 (24.1–31.2)

RIL

4-A

3.17

5.23

0.11

0.193

–i

Δ13C 4.2_E3

4

RM252–RM241

89.1 (85.9–93.1)

RIL

4-B

3.11

3.73

0.08

−0.140

–j

Δ13C4.2_E4

4

RM317–RM349

124.5 (118.5–127.7)

RIL

4-C

3.17

4.51

0.11

−0.190

–g

Δ 13 C5.1_E1

5

RZ67

108.3

DH

5-A

3.30

1.89

0.10

0.175

–i

Δ13C 5.1_E2

5

RM459–RM161

87.8 (81.9–92.9)

DH

5-A

3.25

5.71

0.19

0.165

–g

Δ13C 5.1_E3

5

RM440–RM188

113.3 (103.0–119.3)

RIL

5-A

3.11

5.76

0.15

0.186

–i

Δ13C 5.1_E4

5

RM440–RM188

107.0 (101.0–119.3)

RIL

5-A

3.17

5.07

0.13

0.202

–g

Δ13C8.1_E1

8

RM547–RM72

54.4 (49.7–58.4)

DH

8-A

3.3

3.38

0.15

0.207

–i

Δ 13 C8.1_E4

8

RM342b

77.24

RIL

8-A

3.17

3.05

0.06

0.138

–g

%N1.1_E3

1

RM431–RM165

209.8 (204.1–213.8)

RIL

1-C

3.11

7.09

0.20

−0.157

–i

%N1.1_E4

1

RM165–RM14

224.0 (209.8–230.0)

RIL

1-C

3.19

3.26

0.09

−0.105

–j

%N2.1_E1

2

RM492–RM452

62.8 (60.5–68.5)

DH

2-B

3.42

3.74

0.19

0.117

–g

%N2.1_E2

2

RG437–RM492

61.5 (60.5–71.3)

DH

2-B

3.11

4.90

0.15

0.129

–g

%N5.1_E3

5

RM440–RM188

105.0 (101.0–117.3)

RIL

5-A

3.11

5.65

0.18

0.147

–i

%N10.1_E2

10

RG257–RM467

35.7 (29.7–47.0)

DH

10-A

3.11

3.96

0.13

0.114

–j

%N11.1_E2

11

RM116–RM441

43.0 (40.0–49.0)

DH

11-A

3.11

3.59

0.11

0.102

–g

SLA1.1_E3

1

RM431–RM165

207.8 (204.1–213.8)

RIL

1-C

3.17

3.19

0.06

−0.510

–j

SLA4.1_E4

4

RM518–RM261

17.2 (13.7–25.2)

RIL

4-A

3.21

5.30

0.15

−1.046

–g

SLA5.1_E1

5

RM459–RM161

86.5 (81.9–89.8)

DH

5-A

3.42

5.27

0.19

−1.008

–j

SLA5.1_E2

5

RM459–RM161

87.8 (81.9–89.8)

DH

5-A

3.30

6.30

0.23

−0.963

–i

SLA5.1_E3

5

RM440–RM188

97.0 (94.2–101.0)

RIL

5-A

3.17

7.15

0.16

−0.800

–i

SLA9.1_E3

9

RM257–RM242

62.0 (60.4–64.0)

RIL

9-A

3.17

6.07

0.13

0.730

–g

SLA12.1_E3

12

RM309–RM7018

71.9 (69.5–81.8)

RIL

12-A

3.17

3.59

0.07

−0.530

–h

SB1.1_E1

1

RG331–RM568

206.1 (205.6–206.1)

DH

1-C

3.45

6.45

0.29

0.249

–i

SB1.1_E2

1

RG331–RM568

206.1 (205.6–206.1)

DH

1-C

3.33

7.33

0.22

0.194

–i

SB11.1_E2

11

RM167–RG118

34.1 (31.6–38.4)

DH

11-A

3.33

4.30

0.13

−0.159

–j

SB12.1_E2

12

RG901–RM270

90.5 (84.7–98.2)

DH

12-B

3.33

4.50

0.12

0.147

–j

LW2.1_E3

2

RM475–RM5430

79.2 (73.9–83.6)

RIL

2-D

3.05

3.80

0.08

0.403

–g

LW2.1_E4

2

RM452–RM324

39.0 (32.7–43.0)

RIL

2-B

3.05

3.40

0.06

0.435

 

LW4.1_E2

4

RG214–RG143

118.3 (112.3–122.3)

DH

4-C

3.38

7.30

0.21

0.454

–g

LW4.1_E3

4

RM307–RM185

25.2 (24.1–27.2)

RIL

4-A

3.02

7.77

0.18

−0.607

–i

LW4.1_E4

4

RM307–RM185

25.2 (24.1–27.1)

RIL

4-A

3.05

15.91

0.31

−1.014

–i

LW4.2_E4

4

RM317–RM349

122.5 (118.5–127.8)

RIL

4-C

3.05

5.32

0.12

0.624

–j

LW5.1_E4

5

RM163–RM440

92.2 (88.2–107.0)

RIL

5-A

3.05

3.46

0.07

−0.469

–h

LW12.1_E2

12

RM17–RG181

110.5 (92.2–112.5)

DH

12-B

3.38

4.52

0.12

0.348

–g

LL1.1_E3

1

RM472–RM431

204.1 (199.8–213.8)

RIL

1-C

3.17

3.20

0.08

1.082

–j

LL1.1_E4

1

RM472–RM431

206.1 (202.1–211.8)

RIL

1-C

3.05

5.81

0.13

3.311

–g

LL2.1_E2

2

RM497–RM6

163.3 (159.3–168.4)

DH

2-E

3.15

6.74

0.17

−1.578

–g

LL2.1_E4

2

RM250–RM166

125.7 (115.1–129.4)

RIL

2-E

3.05

3.45

0.07

−2.430

–j

LL3.1_E2

3

RM514–RM570

236.0 (228.3–244.4)

DH

3-C

3.15

3.96

0.10

1.218

–g

LL3.1_E3

3

RM143–RM514

200.5 (190.5–203.2)

RIL

3-C

3.17

3.56

0.09

2.320

–i

LL3.1_E4

3

RM143–RM514

194.5 (186.5–200.5)

RIL

3-C

3.05

5.64

0.14

3.391

–i

LL12.1_E3

12

RM6123–RM17

114.0 (106.0–114.0)

RIL

12-B

3.17

5.27

0.13

2.586

–g

LL12.1_E4

12

RM6123–RM17

110.0 (104.0–114.0)

RIL

12-B

3.05

4.41

0.11

2.999

–g

TN1.1_E2

1

RM472–RM431

190.9 (187.3–198.9)

DH

1-C

3.23

5.13

0.17

1.082

–j

TN2.1_E3

2

RM263–RM526

91.7 (83.7–94.0)

RIL

2-D

3.22

3.45

0.08

−0.663

–g

TN2.1_E4

2

RM550–RM465C

45.6 (39.0–47.6)

RIL

2-B

3.11

4.87

0.09

−1.177

–i

TN2.2_E4

2

RM5651–RM106

81.6 (79.1–85.6)

RIL

2-D

3.11

4.11

0.08

−1.086

–i

TN8.1_E3

8

RM433–RM281

128.9 (124.9–132.9)

RIL

8-B

3.22

6.53

0.17

−1.000

–i

TN8.1_E4

8

RM433–RM281

130.9 (126.9–132.9)

RIL

8-B

3.11

5.93

0.14

−1.507

–i

LF1.1_E2

1

RM543–RM302

153.0 (146.8–155.0)

DH

1-B

3.29

4.42

0.12

0.223

–h

LF1.1_E4

1

RM200–RM319

177.1 (173.1–180.8)

RIL

1-B

3.08

4.33

0.07

0.226

–i

LF2.1_E4

2

RM561–RM341

57.1 (51.3–63.9)

RIL

2-C

3.08

3.59

0.06

0.200

–i

LF3.1_E2

3

RM156–RM411

134.6 (128.4–136.6)

DH

3-A

3.29

5.56

0.13

−0.233

–i

LF5.1_E2

5

CDO105–RZ649

78.9 (76.9–89.8)

DH

5-A

3.29

8.03

0.28

0.335

–i

LF5.1_E4

5

RM163–RM440

101.0 (97.0–107.0)

RIL

5-A

3.08

9.55

0.22

0.388

–i

LF11.1_E4

11

RM332–RM167

14.0 (9.8–18.0)

RIL

11-A

3.08

3.49

0.06

0.196

–i

LE3.1_E2

3

RM168–RM520

190.7 (179.2–202.8)

DH

3-B

3.22

4.28

0.17

0.231

–j

LE4.1_E4

4

RM518–RM261

17.7 (13.7–27.2)

RIL

4-A

3.20

3.84

0.10

0.201

–j

LE5.1_E4

5

RM440–RM188

111.2 (105.0–119.3)

RIL

5-A

3.20

3.87

0.08

−0.178

–g

LE6.1_E2

6

RM528–RM30

129.9 (129.2–139.6)

DH

6-A

3.22

5.32

0.16

−0.227

–g

LE6.1_E4

6

RM275–RM30

86.5 (80.5–102.5)

RIL

6-A

3.20

3.59

0.09

−0.193

–j

A/m24.1_E3

4

RM518–RM261

19.7 (13.7–24.1)

RIL

4-A

3.17

4.37

0.14

1.019

–i

A/m24.1_E4

4

RM518–RM261

19.7 (17.7–24.1)

RIL

4-A

3.09

8.17

0.16

1.290

–i

Ci/Ca1.1_E4

1

RM265–RM315

184.6 (180.3–190.6)

RIL

1-C

3.15

3.28

0.07

2.536

–g

Ci/Ca2.1_E3 f

2

RM423

16.2

RIL

2-A

3.20

2.77

0.08

−3.077

–j

Ci/Ca2.1_E4

2

RM423–RM555

18.3 (11.3–22.7)

RIL

2-A

3.15

3.47

0.08

−2.704

–g

Ci/Ca4.1_E4 f

4

RM518

15.7

RIL

4-A

3.15

2.69

0.08

2.600

–j

SCO1.1_E4

1

RM034–RM246

133.5 (129.5–140.5)

RIL

1-A

3.03

4.47

0.13

0.039

–g

SCO4.1_E4

4

RM518–RM261

17.7 (15.7–27.2)

RIL

4-A

3.03

8.32

0.19

0.048

–i

lABA4.1_E4

4

RM307–RM185

25.2 (24.1–29.2)

RIL

4-A

3.02

3.11

0.07

−0.070

–j

lABA12.1_E3

12

RM270–RM235

100.4 (94.4–108.0)

RIL

12-B

3.02

4.09

0.13

0.130

–j

  1. Loci indicated in italics represent potential QTL detected only by single marker analysis
  2. DH doubled haploid population, RIL recombinant inbred lines
  3. aQTL nomenclature is as described in “Results” section, “QTL identification”
  4. bMarker interval indicates the interval in which the QTL peak is found. Confidence interval = peak LOD scores minus 1
  5. cQTL cluster indicates chromosomal regions shared by several QTLs based on marker comparison between the two populations used in this study
  6. dLOD score threshold has been calculated with 1,000 permutations
  7. e R 2: variance explained by the QTL
  8. fAdditive effect (increasing allele effect) provided by Azucena
  9. gSignificance at the 0.1% level by single marker analysis
  10. hSignificance at the 5% by single marker analysis
  11. iSignificance at the 0.01% level by single marker analysis
  12. jSignificance at the 1% level by single marker analysis
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