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Table 6 Epistasis and epistasis by environment interaction on yield and P use efficiency traits

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

Trait QTL Chr Interval Position a QTL Chr Interval Position a aa b h 2(aa)% c aae d h 2(aae)% e
BIOM   2 BIN292-BIN293 74.8   6 BIN962-BIN963 128.4 −51.91** 10.2   
   3 BIN375-BIN376 28.2   6 BIN891-BIN892 52.2 −26.30** 2.6   
   3 BIN413-BIN414 76.2   4 BIN562-BIN563 8.2 −29.30** 3.2   
   3 BIN413-BIN414 76.2   3 BIN483-BIN484 125.3 −26.12** 2.6   
   7 BIN990-BIN991 26.4   11 BIN1515-BIN1516 104.2 29.65** 3.3 19.36* (aae4) 0.5
HI qBIOM1 1 BIN30-BIN31 24.9   6 BIN862-BIN863 29.6 −1.23** 4.3   
   1 BIN80-BIN81 78.6   3 BIN435-BIN436 92.3 1.24** 4.4   
   2 BIN242-BIN243 17.7   2 BIN337-BIN338 162.0 −1.81** 9.3   
   6 BIN909-BIN910 75.3   10 BIN1328-BIN1329 22.4 0.99** 2.8   
Yield   3 BIN530-BIN531 177.2   4 BIN580-BIN581 14.7 −26.25** 5.2   
   5 BIN694-BIN695 5.3   10 BIN1321-BIN1322 16.8 −21.15** 3.4   
   12 BIN1572-BIN1573 49.2 qPUEg12 12 BIN1612-BIN1613 99.1 −23.47** 4.2   
PUP qPUP1 1 BIN46-BIN47 36.1 qPUP7 7 BIN1007-BIN1008 55.0 0.07** 2.3   
   2 BIN241-BIN242 17.5   8 BIN1169-BIN1170 111.4 0.11** 5.8   
  qPUP10 10 BIN1348-BIN1349 37.7   12 BIN1613-BIN1614 104.3 0.04* 0.9   
PHI qPHI1,qHI1,qstrPUE1-1 1 BIN59-BIN60 63.4 qPHI11 11 BIN1392-BIN1393 2.2 0.58 0.4 1.19* (aae4) 0.5
   2 BIN218-BIN219 0   5 BIN815-BIN816 113.3 −1.65** 3.1   
   3 BIN490-BIN491 129.7   9 BIN1290-BIN1291 104.7 2.18** 5.5   
   5 BIN691-BIN692 3.0   11 BIN1405-BIN1406 17.9 −1.49** 2.6   
strPUE   5 BIN692-BIN693 4.3   10 BIN1354-BIN1355 43.5 −25.93** 4.3   
PUEg   1 BIN28-BIN29 23.9   8 BIN1163-BIN1164 106.4 −8.42** 5.4   
PTE qPTE1-2 1 BIN160-BIN161 140.7 qPTE2, qPHI2 2 BIN310-BIN311 88.0 0.84 0.42 2.00* (aae4) 0.8
   3 BIN451-BIN452 97.4   8 BIN1085-BIN1086 35.8 −2.34** 3.30   
   10 BIN1299-BIN1300 3.4   12 BIN1549-BIN1550 38.5 2.49** 3.72   
  1. aPosition (cM) denotes the genetic distance in centiMorgan between the QTL and the first marker on the relevant chromosome.
  2. bAdditive by additive effect, a negative value means that recombinant alleles from the two parents increase the phenotypic score, a positive value means that two alleles from an identical parent increase the phenotypic score.
  3. cPhenotypic variation explained by an epistatic effect.
  4. dEpistasis by environment interaction, e1 and e2 represent low P in 2008 and 2009, e3 and e4 represent normal P in 2008 and 2009, respectively.
  5. ePhenotypic variation explained by an epistasis by environment interaction.
  6. * and **Indicate significance at P = 0.05 and P = 0.01, respectively.