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Table 3 Genome-wide significant association signals of GP in the after-ripened seeds using LMM method

From: Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.)

Pop

Signals

Lead SNPb

Chr

Position

P value

Contr%

Known gene

Dis (kb)

QTL

Reference

Whole

ARS1.1ca

sf0131727984

1

31727984

1E-09

0.3

GA2ox3

66

  
 

ARS1.2

sf0138588391

1

38588391

6E-09

29.3

  

qSD1

[79]

 

ARS2.1

sf0206686399

2

6686399

4.1E-09

0.1

OsHPL2

−56

qSD2

[32]

 

ARS5.1

sf0523494718

5

23494718

1.5E-09

9.1

EXP4

−60

  
 

ARS6.1

sf0611491573

6

11491573

1E-10

0.5

  

qSD6

[79]

 

ARS6.2

sf0620628649

6

20628649

1.3E-09

2.4

    
 

ARS7.1

sf0720587413

7

20587413

1E-10

1.8

    
 

ARS8.1

sf0807777822

8

7777822

2.6E-08

0.7

    
 

ARS9.1

sf0905593232

9

5593232

7.3E-10

1.6

    
 

ARS9.2

sf0914236447

9

14236447

3.7E-08

3.9

    
 

ARS10.1

sf1019156688

10

19156688

2.4E-10

0.6

    
 

ARS11.1

sf1101407923

11

1407923

2.5E-08

0.1

  

qDOR11–1

[80]

 

ARS11.2a

sf1114328194

11

14328194

5.6E-10

1.2

    
 

ARS12.1

sf1207745486

12

7745486

1.1E-10

2.9

OsMADS13

52

  

Aus

ARS1.1ca

sf0131706848

1

31706848

8.4E-08

0.7

GA2ox3

87

  
 

ARS2.2

sf0226365962

2

26365962

6.2E-09

27.3

AP59

50

  
 

ARS8.2

sf0804981132

8

4981132

2.6E-07

40.1

    
 

ARS11.3

sf1103208304

11

3208304

1.7E-07

9.5

OsAsr1

66

qDOR11–1

[80]

Indica

ARS1.3

sf0137198693

1

37198693

9.8E-09

1.7

OsABI5

23

qSD.1

[31]

 

ARS2.3

sf0201212724

2

1212724

8.6E-09

2.0

    
 

ARS3c

sf0332024688

3

32024688

1.7E-08

9.3

OSH43

−61

qDOR3–3

[80]

 

ARS4.1

sf0403783716

4

3783716

1.6E-10

30.2

    
 

ARS6.3

sf0613057982

6

13057982

9.8E-11

7.0

Pid3

−1

  
 

ARS7.2

sf0726194419

7

26194419

4.6E-09

8.4

    
 

ARS10.2

sf1018639995

10

18639995

7.2E-08

0.9

    
 

ARS11.4

sf1119110821

11

19110821

5.7E-08

8.0

  

qDOR11–3

[80]

 

ARS11.5

sf1126973978

11

26973978

1.5E-08

1.1

  

qDOR11–6

[80]

 

ARS12.2

sf1214076931

12

14076931

5.7E-10

5.4

    

Japonica

ARS2.4

sf0232512303

2

32512303

2E-07

6.6

    
 

ARS3

sf0331989391

3

31989391

5.2E-08

0.7

OSH43

−26

qDOR3–3

[80]

 

ARS4.2

sf0421860784

4

21860784

3.9E-09

36.6

OsCLC-1

25

  
 

ARS5.2a

sf0510583389

5

10583389

3.5E-09

2.1

    
 

ARS6.4

sf0619595095

6

19595095

3.1E-09

4.2

    
 

ARS7.3

sf0708015120

7

8015120

2.3E-09

4.3

  

qSD7–1

[79]

 

ARS8.3

sf0803353408

8

3353408

1.3E-08

8.3

OsLHY

11

  
 

ARS9.3

sf0922932869

9

22932869

6.1E-09

2.5

    
 

ARS11.6

sf1122384837

11

22384837

2E-07

8.7

  

qDOR11–4

[80]

 

ARS12.3

sf1223239793

12

23239793

6E-08

0.5

OsBOR1

−20

qSD12

[79]

  1. ARS signals for germination percentage in after-ripened seeds, followed by the chromosome and the signal number in the chromosome, Lead SNPs ID the first two digits after sf indicate the chromosome number followed by the position on chromosome, Contr contribution to the phenotype variance, Dis the distance from known gene locus to the lead SNP with negative sign representing upstream
  2. acommonly detected signals in FHS and ARS
  3. bfor more information see Additional file 7
  4. cCommonly detected signals between subpopulations
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BMC Genomic Data

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