Table 5 Genomic positions of QTLs identified in stagnant flooding with its QTL cluster and comparison to the QTLs identified in control irrigated condition in this study and previously published QTLs

qGY3.1

(Xiao et al. 1996); dth3.1: (Moncada et al. 2001); qtl3.1: (Bernier et al. 2007); qPH3.1, qFLW3.1, qGW3.1: this study under SF; qDTF3.1: this study under SF and control

qGY5.1

qYl-5: (Cho et al. 2003); qGW5.1: this study under SF and control; qHI5.1: this study under SF

qGY6.1

qDTY6.1: (Venuprasad et al. 2012)

qGW1.1

GW1-2: (Yu et al. 2008); qGW1.1: this study under control

qGW2.1

tgw2: (Yoon et al. 2006); qHI2.1, qLSL ₃ 2.1: this study under SF

qGW3.1

QKw3a: (Li et al. 1997); qPH3.1, qFLW3.1, qGY3.1: this study under SF; qDTF3.1: this study under SF and control

qGW5.1

gw-5: (Lu et al. 1997); qGW5.1: this study under control qHI5.1 and qGY5.1: this study under SF

qGW10.1

QKw10: (Li et al. 1997)

qGW10.2

(Ishimaru 2003); gw10.1: (Thomson et al. 2003)

qHI2.1

qGW2.1 and qLSL ₃ 2.1: this study under SF

qHI5.1

qGW5.1: this study SF and control; qGY5.1: this study under SF

qHI7.1

none

qHI7.2

qPL7.1 and qFLW7.1: this study under SF

qSR1.1

none

qSR6.1

qSER6.1: this study under SF and control

qPL7.1

(Mei et al. 2003); qHI7.2, qFLW7.1: this study under SF

qPL9.1

qPL-9: (Cho et al. 2003); pl9.1: (Septiningsih et al. 2003); pl9.1: (Thomson et al. 2003); (Marri et al. 2005); (Li et al. 2006); qPL9.1: this study under control

qPH3.1

(Li et al. 1997); qPh3a: (Li et al. 2003); qGY3.1, qFLW3.1, qGW3.1: this study under SF; qDTF3.1: this study under SF and control

qPH5.1

(Mei et al. 2003); ph5.1: (Moncada et al. 2001); ph5.1: (Thomson et al. 2003); qPH5.1: this study under control; qLSL ₁ 5.1, qLSI2-5.1, qLSI3-5.1, qSER5.1, qFLL5.1 and qDTF5.1: this study under SF and control

qPH6.1

ph6: (Xiao et al. 1996); qPH2-6-1: (Cui et al. 2004); qLSL ₂ 6.1: this study under SF

qSER5.1

qSER5.1: this study under control; qPH5.1, qLSL ₁ 5.1, qLSI ₂ 5.1, qLSI ₃ 5.1, qSER5.1, qFLL5.1, and DTF5.1: this study under SF and control

qSER6.1

qSR6.1: this study under SF and control

qLSL ₁ 5.1

qLSL ₁ 5.1: this study under control; qPH5.1, qLSL ₂ 5.1; qLSL ₃ 5.1, qSER5.1, qFLL5.1, and DTF5.1: this study under SF and control

qLSL ₂ 5.1

qLSL ₂ 5.1: this study undercontrol; qPH5.1, qLSL ₁ 5.1 and qLSL ₃ 5.1, qSER5.1, qFLL5: this study under SF and control; DTF5.1: this study under SF

qLSL ₂ 6.1

qPH6.1: this study under SF

qLSL ₃ 2.1

qHI2.1 and qGW2.1: this study under SF

qLSL ₃ 5.1

qLSL ₃ 5.1: this study under control; qPH5.1, qLSL ₁ 5.1, qLSL ₂ 5.1, qSER5.1, and qFLL5.1: this study under SF and control; DTF5.1: under SF

qFLL4.1

(Mei et al. 2005)

qFLL5.1

QFll7: (Bing et al. 2006); (Yan et al. 2003); qFLL5.1: this study under irrigated; qPH5.1, qLSI1-5.1, qLSL ₂ 5.1, qLSL ₃ 5.1, qSER5.1: this study under SF and control; DTF5.1: this study under SF

qFLL6.1

(Mei et al. 2005); qDTF6.1: this study under SF and control

qFLL9.1

fll9: (Yan et al. 1999); qPL9.1: this study under SF and control

qFLW3.1

qPH3.1, qGW3.1, qGY3.1: this study under SF; qDTF3.1: this study SF and control

qFLW7.1

qHI7.2, qPL7.1: this study under SF

qDTF1.1

qDTH-1: (Cho et al. 2003); QHd1b: (Li et al. 2003); (Mei et al. 2003); qFLL6.1 : this study under SF

qDTF3.1

(Albar et al. 1998); dth3.1: (Moncada et al. 2001); qHD-3-1: (Takeuchi et al. 2001); qHDD3-1: (Hittalmani et al. 2003); QHd3a: (Li et al. 2003); (Mei et al. 2003); qEMF3: (Hirabayashi et al. 2014); qDTF3.1: this study under control; qGW3.1, qFLW3.1, qPH3.1, qGY3.1: this study under SF

qDTF5.1

(Li et al. 1998); QHd5b: (Li et al. 2003); qPH5.1, qLSL ₁ 5.1, qLSL ₂ 5.1, qLSL ₃ 5.1, qSER5.1, and qFLL5.1: this study under SF and control

qDTF6.1

QHd6b: (Li et al. 2003); (Mei et al. 2003); qDTF6.1: this study under control; qFLL6.1: this study under SF

qDTF10.1

(Price et al. 1997); (Li et al. 1998); qDTF10.1:this study under control