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Table 2 The significant SNPs detected in a GWAS for five chlorophyll parameters and associated QTLs and genes

From: Chlorophyll fluorescence analysis in diverse rice varieties reveals the positive correlation between the seedlings salt tolerance and photosynthetic efficiency

Trait

SNP ID

Chr.

Position (IRGSP-1.0)

Statistical model

P-value

Known QTL

Known gene

 

NPQ

id1003509

1

4,209,827

All - P

4.17E-07

QKr1.1 [28]; qRNC-1, qRRNC4, qRKC1, qRRKC1, qRNa/K1–1, qRRNa/K1–1 [29]

  

F0

id1004960

1

6,508,269

IND - K

2.17E-04

qRL-1, qNAUP-1b [30]

  

qL

id1016791

1

28,594,265

All - P + K

7.95E-05

qNAUP-1a, qFWSH-1 [30]; QKr1.2, Qnar/Kr1 [28]

  
 

id1016825

1

28,599,615

All - K

8.10E-04

   

NPQ

id1024223

1

38,162,791

All - P

4.95E-05

   

ΦPSII

id1026852

1

41,787,616

All - P

3.99E-05

qSH1–3 [31]

Ygl8 (LOC_Os01g73450, Zhu et al. [32])

 
 

id1027309

1

42,134,803

All - K

2.20E-04

   

NPQ

id1026852

1

41,787,616

All - P

4.67E-06

qSH1–3 [31]

  

F0

id1027269

1

42,082,183

All - K

1.01E-04

qSH1–3 [31]

  
    

JPN - K

7.39E-04

   
 

id1027563

1

42,339,408

All - P

7.63E-06

qSH1–3 [31]

  
    

All - P + K

1.53E-04

   

qL

id1027309

1

42,134,803

All - P

4.26E-05

qSH1–3 [31]

  
    

All - K

5.44E-04

   

Fm

id1027821

1

42,581,986

All - P

1.55E-05

qSH1–3 [31]

  

ΦPSII

id2001842

2

3,253,759

All - P

7.78E-05

   
    

All - K

3.05E-04

   
    

All - P + K

2.35E-04

   

qL

id2001842

2

3,253,759

All - K

7.90E-04

qSST2 [33]

  

NPQ

id2006687

2

16,648,368

All - P

4.10E-05

qPL-2 [30]; QSsst2b, QDss2b [34]

  

NPQ

id2007192

2

17,927,911

All - P

5.81E-05

qPL-2 [30]; QSsst2b, QDss2b [34]

  

F0

id2008158

2

20,817,846

All - P

7.91E-05

QDss2a, QSkc2, QKna2 [34]

  
    

All - K

2.06E-04

   
    

All - P + K

1.41E-04

   

NPQ

id2008679

2

21,812,170

All - P

5.36E-05

QDss2a, QSkc2, QKna2 [34]

  

F0

id2010410

2

24,565,561

All - P + K

2.62E-04

QDss2a, QSkc2, QKna2 [34]; qRRNa/K1–2 [29]

  
 

id2010572

2

24,696,197

All - P

1.25E-05

   
 

id2010581

2

24,713,963

All - K

5.03E-04

   

NPQ

id2010932

2

25,236,351

All - P

5.50E-05

QDss2a, QSkc2, QKna2 [34]; qRRNa/K1–2 [29]

  

Fm

id4000429

4

686,361

All - P

1.90E-05

   
    

All - K

7.32E-04

   

qL

id4002349

4

5,526,924

IND - K

3.61E-04

qRL4 [30]

  

Fm

id4002319

4

5,487,935

IND - K

5.13E-04

   

F0

id5001540

5

2,773,921

All - P

1.70E-06

QKs5 [28]

OsNHX3 (LOC_Os05g05610, Fukuda et al. [35])

 
 

id5001584

5

2,825,199

All - K

9.66E-05

   
    

All - P + K

6.82E-06

   
    

JPN - K

3.06E-04

   

Fm

id5001738

5

3,064,389

IND - K

2.25E-05

QSst5, QDss5a, QDss5b [34]

  

NPQ

   

IND - K

7.46E-04

   

qL

id5012588

5

26,473,167

All - P

3.40E-06

qRL-5, qDWRO-5a, qDWRO-5b [30]; qSST5 [33]

OsCBL4 (LOC_Os05g45810, Martinez-Atienza et al. [36])

 
    

All - K

5.61E-04

   
    

All - P + K

4.95E-04

   

ΦPSII

id6002261

6

2,930,916

All - P

8.97E-07

   
    

All - P + K

4.12E-05

   
 

id6002494

6

3,113,730

All - K

6.48E-05

   
    

IND - K

8.00E-04

   

Fm

id6002261

6

2,930,916

All - P

2.77E-05

   
    

All - K

5.39E-04

   
    

All - P + K

4.79E-04

   

qL

id6002261

6

2,930,916

All - P

3.90E-05

   
    

All - P + K

5.85E-04

   
 

id6002286

6

2,974,286

All - K

3.95E-04

   

NPQ

id6002389

6

3,042,568

All - P

2.10E-06

   
    

All - P + K

4.59E-04

   

NPQ

id6005326

6

8,187,911

All - P

1.31E-08

qDRW6 [31]

  
    

All - K

3.98E-04

   
    

All - P + K

2.35E-04

   

NPQ

id6006336

6

10,184,310

All - P

3.32E-05

qDRW6 [31]

  
    

All - K

1.70E-04

   
    

All - P + K

1.83E-04

   
    

JPN - K

2.29E-04

   

NPQ

id7000336

7

1,865,306

All - P

3.43E-05

   

F0

id7003938

7

22,819,640

All - P

2.00E-05

QSkc7; [34] qSST7 [33]

  

qL

id10000081

10

407,964

JPN - K

6.21E-04

   

ΦPSII

id10003594

10

13,662,830

All - K

5.63E-04

   
    

All - P + K

4.98E-04

   
    

JPN - K

3.21E-04

   

Fm

id10003623

10

13,782,039

All - P

3.03E-05

   

Fm

id10006610

10

20,943,116

All - P

1.43E-06

   

NPQ

id11008520

11

22,516,795

All - P

6.39E-06

qSNC11 [37]

  

Fm

id11008950

11

23,178,265

All - P

4.04E-06

qSNC11 [37]

  

Fm

id12001261

12

3,059,845

All - K

4.65E-05

   
    

All - P

1.30E-06

   
    

JPN - K

5.35E-05

   
 

id12001332

12

3,223,671

All - P + K

6.34E-05

   

NPQ

id12001256

12

3,027,442

All - P

1.23E-05

   

qL

id12001769

12

4,044,980

All - P + K

6.57E-04

qRRNC12 [29]

  

ΦPSII

id12004053

12

10,470,139

All - P

5.14E-06

qRRNC12 [29]; qSUR12, qSES12, qCNL12 [38]

  
    

All - K

3.54E-04

   

ΦPSII

id12007270

12

21,906,089

All - P

1.48E-04

QSst12, QDss12 [34]; qSUR12, qSES12, qCNL12 [38]

  

ΦPSII

id12008292

12

23,734,278

All - P

2.45E-05

qSH12.1, qSH12.2, qDSW12.1 [31]; qSUR12, qSES12, qCNL12 [38]

  
    

All - K

4.67E-04

   

qL

id12008234

12

23,663,599

All - P

5.21E-05

qSH12.1, qSH12.2, qDSW12.1 [31]; qSUR12, qSES12, qCNL12 [38]

  
    

All - K

8.73E-04

   

ΦPSII

id12010084

12

27,378,310

All - P

1.65E-05

qSUR12, qSES12, qCNL12 [38]

  
    

All - K

1.76E-04

   
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BMC Plant Biology

ISSN: 1471-2229

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