Table 5 MiRNA promoters with significantly differentially methylated status between ovules of two rice lines
MiRNA NameLog2 Fold-ChangeMethylation LevelP-valueSignificance
osa-miR1425-3p−3.044394119Hypo-methylation3.3523E−06**
osa-miR1425-5p−3.087462841Hypo-methylation2.0804E−06**
osa-miR1432-3p1.874469118Hyper-methylation0.026893*
osa-miR1432-3p1.044394119Hyper-methylation0.00027986**
osa-miR1432-5p1.736965594Hyper-methylation0.044044*
osa-miR14351.169925001Hyper-methylation0.039095*
osa-miR156i3Hyper-methylation0.016686*
osa-miR159d−2.807354922Hypo-methylation0.0034877**
osa-miR160c-3p−1.144389909Hypo-methylation0.0052627**
osa-miR160c-5p−1.10433666Hypo-methylation0.0061281**
osa-miR166b-3p1.502500341Hyper-methylation0.016861*
osa-miR166b-5p1.736965594Hyper-methylation0.0044014**
osa-miR166c-3p−3.169925001Hypo-methylation0.013607*
osa-miR166d-3p−3Hypo-methylation0.022957*
osa-miR166d-5p−3Hypo-methylation0.022957*
osa-miR166e-3p1.584962501Hyper-methylation0.0059267**
osa-miR166e-5p1.584962501Hyper-methylation0.0059267**
osa-miR167b−1.125530882Hypo-methylation0.037497*
osa-miR167f−1.263034406Hypo-methylation0.022275*
osa-miR169g2Hyper-methylation0.0055546**
osa-miR169o2.321928095Hyper-methylation0.017365*
osa-miR169r-3p1.807354922Hyper-methylation0.014604*
osa-miR169r-5p1.378511623Hyper-methylation0.048778*
osa-miR171c-3p2.700439718Hyper-methylation0.0035233**
osa-miR171c-5p2.584962501Hyper-methylation0.0060011**
osa-miR171d-3p−2.321928095Hypo-methylation0.025026*
osa-miR171d-5p−3.321928095Hypo-methylation0.0080917**
osa-miR172a1.415037499Hyper-methylation0.0016432**
osa-miR1846c-3p−1.044394119Hypo-methylation0.022017*
osa-miR1846c-5p−1.044394119Hypo-methylation0.022017*
osa-miR1848−1.754887502Hypo-methylation0.0019694**
osa-miR1850.21.321928095Hyper-methylation0.039814*
osa-miR1850.31.321928095Hyper-methylation0.039814*
osa-miR18591.584962501Hyper-methylation0.037516*
osa-miR2096-3p−2.402098444Hypo-methylation0.000011225**
osa-miR2100-3p1.192645078Hyper-methylation0.048544*
osa-miR2100-5p−3.169925001Hypo-methylation0.013607*
osa-miR2275a2.129283017Hyper-methylation0.000021442**
osa-miR2863b1.736965594Hyper-methylation0.044044*
osa-miR2873a2.906890596Hyper-methylation0.001213**
osa-miR2907c−1Hypo-methylation0.0018074**
osa-miR29191.286881148Hyper-methylation0.00004735**
osa-miR2932−1.584962501Hypo-methylation0.011048*
osa-miR319a-3p.2-3p−1.169925001Hypo-methylation0.022704*
osa-miR319a-3p.2-3p−1.169925001Hypo-methylation0.022704*
osa-miR396b-3p−1.584962501Hypo-methylation0.0065944**
osa-miR396b-5p−1.222392421Hypo-methylation0.016184*
osa-miR396c-3p−2.584962501Hypo-methylation0.0093555**
osa-miR396d−1.201633861Hypo-methylation0.031607*
osa-miR3981-3p1.137503524Hyper-methylation0.025448*
osa-miR3981-5p1.070389328Hyper-methylation0.036884*
osa-miR399c−1.485426827Hypo-methylation0.047871*
osa-miR399g−1.247927513Hypo-methylation0.043997*
osa-miR399j−2.169925001Hypo-methylation0.040849*
osa-miR415−1.700439718Hypo-methylation0.035614*
osa-miR439c−1.502500341Hypo-methylation0.0018721**
osa-miR439d−1.874469118Hypo-methylation0.00003647**
osa-miR5071−1.321928095Hypo-methylation0.030533*
osa-miR5071−2.321928095Hypo-methylation0.025026*
osa-miR51451.395928676Hyper-methylation0.000096668**
osa-miR5162−1.440572591Hypo-methylation0.024287*
osa-miR5339−4.058893689Hypo-methylation2.731E−10**
osa-miR54892.201633861Hyper-methylation0.00045157**
osa-miR5491−2.584962501Hypo-methylation0.001458**
osa-miR5504−1.874469118Hypo-methylation0.039005*
osa-miR55212.222392421Hyper-methylation1.8915E−06**
osa-miR5527−1.029747343Hypo-methylation0.0058305**
osa-miR5533−1.807354922Hypo-methylation0.0013048**
osa-miR5534b1.184424571Hyper-methylation0.014149*
osa-miR55354Hyper-methylation0.00019844**
osa-miR5788−1Hypo-methylation0.0066162**
osa-miR57891.906890596Hyper-methylation0.0090287**
osa-miR5791−1.157541277Hypo-methylation0.01925*
osa-miR5810−2.187627003Hypo-methylation0.000011529**
osa-miR5811−1.874469118Hypo-methylation0.039005*
osa-miR5816−1.222392421Hypo-methylation0.007174**
osa-miR5822−1Hypo-methylation0.0091971**
osa-miR62513.321928095Hyper-methylation0.005432**
osa-miR812b1.807354922Hyper-methylation0.0027809**
osa-miR812c1.362570079Hyper-methylation0.021442*
osa-miR812e−2.099535674Hypo-methylation0.00025097**
osa-miR812j3.392317423Hyper-methylation0.000049436**
osa-miR812s−1.362570079Hypo-methylation0.035634*
osa-miR821a1.169925001Hyper-methylation0.039095*
  • In this study, the significantly differentially methylated miRNA gene promoters between fsv1 and Gui99 were labeled with “**” and “*.” **, |fold change log2| > 1 and P-value <0.01; *, |fold change log2| > 1 and 0.01 < P-value <0.05.