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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.