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Table 5 Yield and yield related QTLs detected in Pusa1266 × Jaya RIL population across three locations in India

From: QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativaL.)

Sl.No

QTL

Chr

Flanking Marker interval

Peak point

Increasing effect

New Delhi

Karnal

Aduthurai

      

LOD

R2

LOD

R2

LOD

R2

Days to 50% flowering

           

1

qDFF1-1

1

RM302-RM212

223.3

Jaya

-

-

-

-

3.58**

0.04

2

qDFF2-1

2

RM3732-RM7144

0.0

Jaya

-

-

-

-

3.44**

0.04

3

qDFF3-1

3

GNMS1289-RM5474

24.1

Jaya

16.2**

0.18

20.3**

0.25

-

-

4

qDFF6-1

6

RM190-GNMS3878

61.4

Pusa1266

14.3**

0.25

7.59**

0.1

5.96**

0.11

5

qDFF7-1

7

RM214-RM70

126

Jaya

-

-

5.95**

0.15

-

-

6

qDFF8-1

8

RM25-GNMS2765

92

Pusa1266

22.9**

0.42

16**

0.41

5.89**

0.07

7

qDFF11-1

11

GNMS3575-HV11-13

19.9

Pusa1266

-

-

-

-

4.14**

0.07

Plant height

           

8

qPHT1-1

1

GNMS114-GNMS3879

54.2

Pusa1266

3.72**

0.05

4.23**

0.06

-

-

9

qPHT2-1

2

RM1178-RM1211

45.3

Jaya

-

-

-

-

3.96**

0.05

10

qPHT3-1

3

GNMS1289-RM569

16.01

Jaya

-

-

-

-

7.62**

0.11

11

qPHT3-2

3

RM15283-RM251

171.01

Jaya

3.59**

0.1

-

-

-

-

12

qPHT3-3

3

RM6266-RM168

276.1

Jaya

-

-

3.04*

0.07

-

-

13

qPHT4-1

4

RM551-RM16569

10.01

Jaya

3.44*

0.07

-

-

-

-

14

qPHT4-2

4

RM16553-RM307

29.1

Jaya

4.89**

0.06

4.05**

0.05

-

-

15

qPHT4-3

4

RM5709-RM1112

183.8

Pusa1266

4.35**

0.09

4.81**

0.09

-

-

16

qPHT7-1

7

HV7-02-RM5711

12.01

Pusa1266

-

-

3.83**

0.11

-

-

17

qPHT7-2

7

RM560-RM336

203.7

Jaya

-

-

-

-

3.65*

0.06

18

qPHT7-3

7

RM429-RM3555

263.8

Pusa1266

-

-

3.43*

0.05

-

-

19

qPHT8-1

8

RM25-GNMS2765

82.01

Pusa1266

3.09*

0.04

-

-

-

-

20

qPHT12-1

12

RM1261-GNMS3766

88.31

Jaya

-

-

-

-

4.56**

0.14

Panicle length

           

21

qPL1-1

1

RM1282-RM220

15.41

Pusa1266

3*

0.07

-

-

-

-

22

qPL2-1

2

RM3732-RM324

32.91

Jaya

-

-

6.7**

0.08

-

-

23

qPL2-2

2

RM1178-RM1211

41.3

Jaya

-

-

6.17**

0.08

4.87**

0.07

24

qPL2-3

2

RM262-GNMS3876

107.4

Jaya

7.74**

0.1

-

-

-

-

25

qPL3-1

3

RM569-RM5474

22.11

Jaya

3.22*

0.05

-

-

9.06**

0.12

26

qPL3-2

3

RM3766-RM157A

66.9

Jaya

3.57*

0.05

3.96**

0.06

-

-

27

qPL3-3

3

RM7-GNMS1140

112.9

Jaya

5.95**

0.22

-

-

-

-

28

qPL3-4

3

RM15283-RM3698

217.2

Jaya

5.18**

0.22

-

-

-

-

29

qPL3-5

3

RM16-RM168

256.1

Jaya

-

-

3.37*

0.04

-

-

30

qPL7-1

7

RM429-RM3555

263.8

Pusa1266

-

-

3.87**

0.05

-

-

31

qPL11-1

11

RM1812-HV11-13

9.9

Pusa1266

-

-

-

-

3.52*

0.04

32

qPL11-2

11

GNMS3235-RM144

160.3

Jaya

-

-

3.7**

0.05

-

-

Panicles per plant

           

33

qPPP3-1

3

RM7-GNMS1140

142.9

Pusa1266

3.02**

0.04

-

-

-

-

34

qPPP4-1

4

RM273-GNMS1539

154.11

Jaya

5.73**

0.13

4.81**

0.09

-

-

35

qPPP4-2

4

RM3276-RM1112

187.8

Jaya

7.11**

0.10

5.18**

0.08

9.74**

0.19

36

qPPP12-1

12

RM1103-RM17

194

Jaya

-

-

3.16*

0.06

-

-

Flag leaf length

           

37

qFLL1-1

1

RM220-GNMS114

32.01

Jaya

-

-

3.75**

0.04

-

-

38

qFLL1-2

1

GNMS3879-RM493

69.91

Jaya

3.3*

0.10

-

-

-

-

39

qFLL2-1

2

RM324-RM1211

45.31

Jaya

3.03*

0.04

3.73**

0.05

-

-

40

qFLL3-1

3

GNMS1289-RM5474

26.11

Jaya

-

-

-

-

5.93**

0.1

41

qFLL3-2

3

RM157A-RM1256

73.01

Jaya

-

-

3.02*

0.04

-

-

42

qFLL3-3

3

GNMS3875-RM7

91.11

Jaya

-

-

3.07*

0.04

-

-

43

qFLL3-4

3

GS3-RM15283

148.4

Pusa1266

-

-

-

-

2.99*

0.04

44

qFLL4-1

4

RM1112-RM315

260

Jaya

-

-

3.52**

0.07

3.05*

0.22

45

qFLL6-1

6

RM190-RM204

63.4

Pusa1266

7.92**

0.12

2.92*

0.07

-

-

46

qFLL7-1

7

RM70-RM1135

163.5

Pusa1266

-

-

4.73**

0.13

-

-

47

qFLL7-2

7

RM429-RM3555

261.8

Pusa1266

3.3*

0.05

-

-

-

-

48

qFLL8-1

8

RM25-GNMS2765

82.01

Pusa1266

6.79**

0.08

-

-

-

-

49

qFLL10-1

10

RM474-RM222

0.0

Pusa1266

-

-

-

-

3.11*

0.04

50

qFLL12-1

12

RM1261-GNMS3766

68.31

Jaya

2.9*

0.03

-

-

-

-

Flag leaf width

           

51

qFLW1-1

1

RM5389-RM6141

269.1

Pusa1266

4.22**

0.07

-

-

-

-

52

qFLW2-1

2

RM3732-RM7144

0.0

Jaya

-

-

-

-

4.26**

0.04

53

qFLW3-1

3

GNMS1289-RM569

6.01

Jaya

-

-

-

-

4.02**

0.05

54

qFLW3-2

3

RM55-RM570

363.9

Pusa1266

-

-

3.1*

0.04

3.44**

0.18

55

qFLW4-1

4

RM307-RM401

32.81

Jaya

3.82**

0.04

-

-

-

-

56

qFLW4-2

4

RM3276-RM5709

170.01

Pusa1266

40**

0.44

46.5**

0.53

25.9**

0.33

57

qFLW6-1

6

RM204-GNMS3878

66.31

Pusa1266

2.87*

0.02

-

-

-

-

58

qFLW7-1

7

RM336-RM1132

214.01

Jaya

2.89*

0.03

-

-

-

-

59

qFLW8-1

8

RM25-GNMS2765

82.01

Pusa1266

2.92*

0.02

-

-

-

-

Spikelets per panicle

           

60

qSPP1-1

1

RM220-GNMS114

34.01

Jaya

-

-

3.15*

0.04

-

-

61

qSPP1-2

1

RM5389-RM5310

255.1

Pusa1266

3.31*

0.11

-

-

-

-

62

qSPP2-1

2

RM324-RM1211

45.31

Jaya

-

-

-

-

4.56**

0.05

63

qSPP3-1

3

GNMS1289-RM5474

10.01

Jaya

-

-

-

-

4.18**

0.07

64

qSPP3-2

3

GNMS1140-RM15283

154.4

Pusa1266

-

-

-

-

11.4**

0.15

65

qSPP3-3

3

RM3698-RM168

251.01

Pusa1266

3.39*

0.04

-

-

-

-

66

qSPP4-1

4

RM3276-RM5709

170.01

Pusa1266

6.58**

0.09

13.8**

0.16

9.42**

0.13

67

qSPP6-1

6

RM204-GNMS3878

96.31

Pusa1266

3.42*

0.3

-

-

-

-

68

qSPP7-1

7

RM70-RM432

165.5

Pusa1266

3.53*

0.09

11.4**

0.21

-

-

69

qSPP7-2

7

RM560-RM336

201.71

Pusa1266

3.93**

0.07

6.25**

0.09

-

-

70

qSPP12-1

12

RM1261-GNMS3766

76.31

Jaya

3.02*

0.07

-

-

4.35**

0.08

71

qSPP12-2

12

GNMS3781-HV12-41

149.31

Jaya

-

-

4.03**

0.05

-

-

Filled grains per panicle

           

72

qFGP2-1

2

RM1211-RM561

45.91

Jaya

-

-

-

-

4.04**

0.05

73

qFGP3-1

3

GNMS1289-RM569

10.01

Jaya

-

-

-

-

3.53**

0.06

74

qFGP3-2

3

GNMS1140-GS3

147.11

Jaya

3.43*

0.05

2.89*

0.03

-

-

75

qFGP4-1

4

RM241-GNMS1539

158.11

Pusa1266

7.5**

0.15

12.8**

0.21

-

-

76

qFGP4-2

4

RM3276-RM5709

172.0

Pusa1266

9.38**

0.15

15.3**

0.22

8.17**

0.12

77

 

7

RM70-RM1135

169.51

Pusa1266

-

-

6.32**

0.13

-

-

78

qFGP12-1

12

RM1261-GNMS3766

74.31

Jaya

-

-

-

-

4.11**

0.07

Per cent sterility

           

79

qPSTE3-1

3

RM7-GS3

145.11

Pusa1266

14.24**

0.18

10.00**

0.18

7.85**

0.18

80

qPSTE11-1

11

RM206-GNMS3600

90.0

Pusa1266

-

-

2.8*

0.03

-

-

1000 grain weight

           

81

qTGW3-1

3

GNMS1289-RM5474

26.11

Jaya

-

-

-

-

8.08**

0.13

82

qTGW3-2

3

RM3766-RM157A

64.91

Jaya

-

-

3.33*

0.05

-

-

83

qTGW3-3

3

GNMS1140-RM15283

145.11

Pusa1266

-

-

5.23**

0.06

-

-

84

qTGW3-4

3

RM3698-RM16

243.71

Pusa1266

-

-

-

-

5.42**

0.07

85

qTGW3-5

3

RM6266-RM168

262.11

Pusa1266

-

-

-

-

6.08**

0.1

86

qTGW4-1

4

RM3276-RM1112

174.01

Jaya

-

-

4.76**

0.07

3.81**

0.05

87

qTGW5-1

5

GNMS1776-RM413

78.51

Jaya

-

-

4.93**

0.18

5.11**

0.2

88

qTGW5-2

5

GNMS1826-HV5-39

226.41

Jaya

4.78**

0.09

3.22*

0.26

-

-

89

qTGW6-1

6

RM6273-RM204

57.41

Jaya

12.9**

0.25

6.39**

0.14

6.42**

0.16

90

qTGW9-1

9

RM278-RM160

107.91

Pusa1266

-

-

2.92*

0.04

-

-

91

qTGW11-1

11

HV11-13-RM202

38.71

Jaya

-

-

2.83*

0.05

-

-

92

qTGW12-1

12

RM1261--GNMS3781

132.01

Pusa1266

-

-

2.77*

0.07

-

-

93

qTGW12-2

12

RM1103-RM17

186.31

Pusa1266

4.23**

0.1

7.22**

0.18

3.03*

0.07

Yield per plant

           

94

qYLD2-1

2

RM3732-RM7144

4.01

Jaya

-

-

-

-

3.24*

0.05

95

qYLD3-1

3

RM16-RM168

255.01

Pusa1266

-

-

-

-

3.6*

0.04

96

qYLD4-1

4

RM1112-RM315

23.11

Jaya

-

-

-

-

3.28*

0.16

97

qYLD9-1

9

RM160-RM201

124.51

Jaya

6.88**

0.11

-

-

-

-

98

qYLD11-1

11

GNMS3600-GNMS3235

135.01

Jaya

-

-

-

-

4.51**

0.05

Spikelet setting density

           

99

qSSD1-1

1

GNMS3879-RM493

63.91

Jaya

3.37**

0.07

-

-

-

-

100

qSSD1-2

1

RM5389-RM5310

255.11

Pusa1266

2.82*

0.09

-

-

-

-

101

qSSD3-1

3

RM3766-RM157A

66.91

Pusa1266

2.95*

0.04

-

-

-

-

102

qSSD3-2

3

RM1256-GNMS3875

76.51

Pusa1266

3.32*

0.04

-

-

-

-

103

qSSD3-3

3

GS3-RM15283

154.41

Pusa1266

-

-

-

-

11.7**

0.16

104

qSSD4-1

4

RM273-GNMS1539

152.11

Pusa1266

10.2**

0.2

15**

0.23

10.2**

0.17

105

qSSD4-2

4

RM3276-RM5709

170.01

Pusa1266

11.4**

0.14

16.3**

0.19

12.4**

0.17

106

qSSD6-1

6

RM204-GNMS3878

92.31

Pusa1266

3.71**

0.25

3.44**

0.1

-

-

107

qSSD7-1

7

RM70-RM1135

161.51

Pusa1266

-

-

10.2**

0.19

3.95*

0.09

108

qSSD7-2

7

RM560-RM336

203.71

Pusa1266

4.96**

0.08

7.23**

0.10

-

-

109

qSSD7-3

7

RM1132-RM429

246.01

Pusa1266

-

-

3.48**

0.05

-

-

110

qSSD8-1

8

GNMS2825-GNMS2921

248.01

Jaya

-

-

-

-

2.99*

0.22

111

qSSD11-1

11

RM21-206

82.11

Pusa1266

-

-

2.87*

0.03

-

-

112

qSSD12-1

12

GNMS3725-RM1261

60.61

Jaya

-

-

-

-

3.75*

0.06

  1. *Significance at 5%; **Significance at 1%.
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