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Table 4 Quantitative trait loci (QTLs) detected in Basmati370/Jaya F2 population

From: Discovery and mapping of genomic regions governing economically important traits of Basmati rice

SN

Trait

QTL

C

Marker interval

LFM

RFM

LOD

A

D

PVE

1

Plant height (cm)

qPH1.1

1

RM302-RM11968

16

10.4

5.138

7.908

−0.858

15.418

2

Panicle length (cm)

qPL2.1

2

RM6318-RM263

16

9.28

3.039

0.456

1.636

0.925

3

 

qPL6.1

6

RM276-RM527

2

10.22

3.413

0.408

−1.773

0.819

4

Filled grains (no.)

qFG1.1

1

RM11968-RM14

10

19.55

3.244

31.165

−28.073

22.677

5

Chaffy grains (no.)

qCG3.1

3

RM85-RM565

20

30.2

4.284

−3.532

−13.439

0.46

6

 

qCG9.1

9

RM107-RM566

34

80

3.021

−2.71

−10.48

0.328

7

 

qCG12.1

12

RM247-RM463

34

15.23

5.211

−7.804

−15.738

2.458

8

Spikelet number (no.)

qSN3.1

3

RM5864-RM426

14

10.16

2.788

666

−1.593

0

9

 

qSN10.1

10

RM216-RM171

26

1.29

2.885

−19.354

−6.115

6.661

10

Spikelet fertility (%)

qSF9.1

9

RM107-RM566

56

58

2.562

4.208

5.35

2.202

11

 

qSF12.1

12

RM463-RM235

14

11.15

7.255

7.155

1.973

4.249

12

 

qSF12.2

12

RM17-RM19

48

66

3.441

5.987

−4.491

4.472

13

Single plant yield (g)

qSPY2.1

2

RM263-RM525

0

25.55

3.72

−2.258

3.979

4.06

14

 

qSPY9.1

9

RM107-RM566

48

66

3.154

8.397

−4.769

8.15

15

Grain length (mm)

qGL3.1

3

RM353-JL14

10

1.7

9.217

0.362

−0.125

46.065

16

 

qGL5.1

5

RM430-RM18600

6

5.2

6.603

0.217

0.031

17.468

17

Grain breadth (mm)

qGB1.1

1

RM473A-RM8278

0

34.52

6.714

−0.038

0.119

1.649

18

 

qGB5.1

5

RM430-RM18600

4

7.2

3.333

−0.106

0.052

17.149

19

 

qGB8.1

8

RM502-RM310

16

64.66

3.454

666

0.015

0

20

Length-Breadth ratio

qLB1.1

1

RM473A-RM8278

0

34.52

5.063

0.116

−0.208

3.928

21

 

qLB3.1

3

RM353-JL14

8

3.7

4.358

0.22

−0.129

22.342

22

 

qLB5.1

5

RM430-RM18600

8

3.2

4.65

0.405

−0.07

46.531

23

Grain length after cooking (mm)

qGLAC12.1

12

RM247-RM463

0

49.23

3.512

0.312

0.396

2.68

24

Elongation ratio

qER5.1

5

RM430-RM18600

4

7.2

3.711

0.136

0.067

18.931

25

Alkali spreading value

qASV6.1

6

RM276-RM527

4

8.22

26.746

−1.257

0.264

71.735

26

Amylose content (%)

qAC4.1

4

RM280-RM127

0

11.15

4.077

−0.97

0.315

15.249

27

Aroma

qARM1.1

1

RM8278-RM582

74

40

6.735

0.654

5.284

1.859

28

 

qARM2.1

2

RM138-RM475

80

32.06

7.59

−0.178

−5.332

0.133

29

 

qARM8.1

8

RM502-RM310

36

44.66

6.976

−0.23

−5.309

0.218

30

 

qARM8.2

8

RM152-RM42

18

23.56

6.132

0.968

−5.312

3.116

31

 

qARM8.3

8

RM404-RM483

8

16

4.998

2.476

0.511

20.226

32

 

qARM12.1

12

RM17-RM19

30

84

7.556

−0.589

−5.334

1.512

33

Chalkiness

qCHK4.1

4

RM564-RM348

14

28.62

3.138

2.107

−0.142

63.795

34

 

qCHK5.1

5

RM289-RM430

6

12.88

3.835

−0.809

0.359

14.533

  1. A- Additive; D- Dominance; C- Chromosome; PVE- Phenotypic variance explained by each QTL (%); Left (LFM) and right (RFM) flanking marker distance from the QTL (cM);Positive and negative values of additive effect indicates the increasing effect coming from the alleles of Basmati370 and Jaya, respectively.
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BMC Plant Biology

ISSN: 1471-2229

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