Table 1 QTLs identified for 13 yield-related traits using the high density bin map.

From: Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing

Trait

QTL

Chrom.

Bina

Beijing

Hainan

LOD

R2 (%)b

Additivec

LOD

R2 (%)

Additive

PH

qPH1

1

Bin150

71.9

92.0

45.9

70.9

91.9

39.2

 

qPH3

3

Bin407

2.6

8.8

21.6

2.8

9.3

19.0

PPL

qPPL1.1

1

Bin40

   

2.0

6.9

0.7

 

qPPL1.2

1

Bin150

   

10.0

29.9

−0.8

 

qPPL2

2

Bin298

   

2.6

8.7

0.6

 

qPPL3

3

Bin317

   

2.8

9.6

0.8

 

qPPL10

10

Bin889

   

2.5

8.3

0.6

PL

qPL1

1

Bin150

26.6

60.7

2.5

10.6

31.4

1.2

 

qPL3

3

Bin329

   

3.8

12.6

−1.7

 

qPL4

4

Bin456

2.4

8.2

−1.4

2.6

8.9

−0.9

 

qPL8

8

Bin788

2.5

8.4

1.6

2.4

8.1

1.0

 

qPL11

11

Bin969

3.1

10.2

2.4

   
 

qPL12

12

Bin1059

   

2.9

9.6

1.1

PBN

qPBN1

1

Bin99

4.0

13.0

−0.6

   
 

qPBN2

2

Bin245

7.7

23.7

−0.9

   
 

qPBN4

4

Bin462

2.9

9.6

−0.6

2.5

8.3

−0.5

 

qPBN8

8

Bin781

5.0

16.1

0.7

8.7

26.6

0.9

 

qPBN11

11

Bin950

   

2.3

7.8

1.1

SNPB

qSNPB1

1

Bin29

   

2.3

7.8

5.9

 

qSNPB2

2

Bin252

4.2

13.6

−5.1

   
 

qSNPB4.1

4

Bin463

4.0

13.0

−6.5

   
 

qSNPB4.2

4

Bin470

   

3.7

12.1

−7.3

 

qSNPB6

6

Bin647

   

2.1

7.2

−4.5

 

qSNPB7

7

Bin711

4.1

13.3

7.5

4.4

14.3

7.3

 

qSNPB8

8

Bin781

7.5

23.1

7.4

9.3

28.1

7.7

SBN

qSBN1.1

1

Bin15

2.8

9.3

−4.5

2.2

7.6

−3.0

 

qSBN1.2

1

Bin149

   

3.6

12.1

2.4

 

qSBN2

2

Bin224

2.5

8.5

−5.2

   
 

qSBN7

7

Bin711

5.8

18.4

−7.7

4.7

15.2

−5.2

 

qSBN9

9

Bin817

3.8

12.5

−4.3

3.1

10.5

−2.9

SNSB

qSNSB1.1

1

Bin15

2.9

9.7

−19.1

2.3

7.9

−12.1

 

qSNSB1.2

1

Bin149

   

2.5

8.4

7.9

 

qSNSB7

7

Bin711

5.5

17.5

−31.1

4.8

15.7

−20.7

 

qSNSB9

9

Bin817

4.8

15.5

−19.8

3.7

12.4

−12.5

SPP

qSPP1.1

1

Bin15

3.2

10.6

−19.6

2.0

6.9

−11.8

 

qSPP1.2

1

Bin149

   

3.0

10.2

9.1

 

qSPP2

2

Bin213

2.5

8.3

−18.3

   
 

qSPP7

7

Bin711

3.2

10.5

−23.6

   
 

qSPP9

9

Bin817

4.0

13.1

−17.8

2.1

7.0

−9.8

SS

qSS1

1

Bin150

6.8

22.6

0.1

   
 

qSS2

2

Bin298

2.7

9.8

−0.1

   
 

qSS3

3

Bin332

2.7

9.6

−0.1

2.5

8.9

−0.04

 

qSS4

4

Bin492

   

6.5

22.0

−0.1

 

qSS6

6

Bin635

   

3.4

12.1

−0.1

 

qSS8

8

Bin793

2.6

9.4

−0.04

   

GL

qGL1.1

1

Bin111

   

3.5

11.8

0.3

 

qGL1.2

1

Bin145

4.2

13.9

0.2

   
 

qGL3.1

3

Bin373

5.5

17.9

−0.7

6.1

19.9

−0.6

 

qGL3.2

3

Bin377

5.9

18.9

−0.7

6.2

20.1

−0.6

 

qGL10

10

Bin896

2.8

9.5

−0.3

   

GW

qGW2

2

Bin284

   

5.6

18.5

−0.04

 

qGW8

8

Bin794

   

4.5

14.9

−0.1

 

qGW11.1

11

Bin980

   

2.9

10.0

−0.04

 

qGW11.2

11

Bin983

2.3

8.0

−0.1

   
 

qGW12

12

Bin1025

   

3.2

11.0

−0.03

TGW

qTGW1.1

1

Bin38

4.1

16.2

−2.3

2.1

7.5

−1.2

 

qTGW1.2

1

Bin148

3.4

13.6

1.1

3.2

11.0

0.9

 

qTGW1.3

1

Bin162

   

3.8

13.0

1.0

 

qTGW2

2

Bin310

2.2

9.0

−1.7

5.1

17.2

−1.8

 

qTGW3

3

Bin377

2.3

9.7

−2.3

6.5

21.4

−3.0

 

qTGW10

10

Bin895

5.3

20.5

−1.8

3.5

12.1

−1.1

YYP

qYYP1

1

Bin149

6.2

23.3

3.5

   
 

qYYP2

2

Bin182

2.1

8.7

4.1

   
 

qYYP4.1

4

Bin494

   

2.1

7.7

−3.4

 

qYYP4.2

4

Bin505

   

3.1

11.1

7.0

  1. aBin overlapping with the LOD peak of the QTL.
  2. bPercentage of phenotypic variation explained by individual QTL.
  3. cAdditive effect of each QTL from O. nivara.
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