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Table 4 Candidate QTLs and their interactions with environment for yield and P use efficiency traits determined by multi-environment combined analysis

From: Identification of quantitative trait loci for phosphorus use efficiency traits in rice using a high density SNP map

Trait

QTL

Chr a

Interval b

Position

(cM) c

a d

h 2(a)% e

ae f

h 2(ae)% g

Individual environment h

BIOM

qBIOM1

1

BIN31-BIN32

26.1

−47.65**

8.6

  

e1,e3

 

qBIOM2

2

BIN244-BIN245

32.4

−21.46**

1.7

−19.55* (ae4)

0.5

 
 

qBIOM7

7

BIN1008-BIN1009

59.2

45.50**

7.8

17.35* (ae4)

0.4

e2,e4

 

qBIOM10

10

BIN1342-BIN1343

34.0

56.95**

12.3

  

e1,e3

 

qBIOM11

11

BIN1497-BIN1498

92.4

31.02**

3.6

  

e1,e2

HI

qHI1

1

BIN59-BIN60

62.9

1.85**

9.7

  

e4

 

qHI2

2

BIN302-BIN303

79.6

−1.08**

3.4

   
 

qHI11

11

BIN1398-BIN1399

5.9

1.60**

7.4

0.93* (ae4)

0.8

e4

Yield

qYield2

2

BIN302-BIN303

79.6

−32.75**

8.1

  

e1,e2,e4

 

qYield11

11

BIN1401-BIN1402

15.2

20.18**

3.1

   

PUP

qPUP1

1

BIN46-BIN47

36.1

−0.10**

4.7

  

e1,e3

 

qPUP7

7

BIN1007-BIN1008

55.0

0.09**

3.4

  

e2

 

qPUP10

10

BIN1348-BIN1349

37.7

0.11**

5.5

  

e1,e2,e3

PHI

qPHI1

1

BIN59-BIN60

63.4

3.71**

15.8

  

e2,e4

 

qPHI2

2

BIN310-BIN311

99.0

−4.18**

20.0

   
 

qPHI6

6

BIN838-BIN839

9.0

−1.49**

2. 6

  

e1,e3

 

qPHI11

11

BIN1392-BIN1393

2.2

1.96**

4.4

1.24* (ae4)

0.6

e4

gPUE

qgPUE4

4

BIN680-BIN681

106.6

−3.83**

1.4

   

strPUE

qstrPUE1-1

1

BIN60-BIN61

63.9

24.67**

3.9

   
 

qstrPUE1-2

1

BIN177-BIN178

150.8

27.62**

4.9

  

e1,e3,e4

 

qstrPUE2

2

BIN302-BIN303

79.6

−31.30**

6.3

  

e2,e3,e4

PUEb

qPUEb2

2

BIN253-BIN254

39.5

−11.36**

6.4

  

e3

PUEg

qPUEg1

1

BIN143-BIN144

135.9

6.84**

3.6

   
 

qPUEg2

2

BIN302-BIN303

79.6

−13.27**

13.4

  

e4

 

qPUEg6

6

BIN946-BIN947

112.7

−7.37**

4.1

   
 

qPUEg11

11

BIN1395-BIN1396

5.2

7.62**

4.4

−4.82* (ae2)

0.6

e2,e4

 

qPUEg12

12

BIN1612-BIN1613

100.1

9.63**

7.1

−5.14* (ae2)

0.7

e2

PT

qPT2

2

BIN294-BIN295

75.7

−0.09**

4.6

  

e4

 

qPT5

5

BIN709-BIN710

13.9

−0.09**

4.9

  

e1,e2,e4

 

qPT8

8

BIN1130-BIN1131

56.3

−0.09**

5.0

  

e2,e4

PTE

qPTE1-1

1

BIN33-BIN34

30.1

3.26**

6.4

  

e4

 

qPTE1-2

1

BIN160-BIN161

140.7

2.59**

4.0

  

e4

 

qPTE2

2

BIN310-BIN311

88.0

−4.04**

9.9

−1.92* (ae4)

0.7

 
 

qPTE5

5

BIN708-BIN709

13.4

−2.71**

4.4

  

e1,e2

 

qPTE8

8

BIN1131-BIN1132

56.5

−3.45**

7.2

   
 

qPTE12

12

BIN1618-BIN1619

109.3

1.91**

2.2

  

e2,e4

  1. See Table 1 for abbreviations.
  2. aChromosome the QTL is located on.
  3. bThe underlined marker is closer to the QTL.
  4. cPosition (cM) denotes the genetic distance in centiMorgan between the QTL and the first marker on the relevant chromosome.
  5. dAdditive effect, a negative value indicates that the Zhenshan 97 allele increases phenotypic score.
  6. ePhenotypic variation explained by an additive effect.
  7. fAdditive by environment interaction effect, e1 and e2 represent low P in 2008 and 2009, e3 and e4 represent normal P in 2008 and 2009, respectively.
  8. gPhenotypic variation explained by an additive by environment interaction.
  9. hThe individual environment in which a QTL for the identical trait was detected by individual environment analysis and located in the same or neighboring region listed in the fourth column.
  10. * and **Indicate significance at P = 0.05 and P = 0.01, respectively.