QTLmappingforsevenqualitytraitswasconductedbyusing254recombinantinbredlines(RIL)derivedfromajaponica-japonicaricecrossofXiushui79/CBao.Theseventraitsinvestigatedweregrainlength(GL),grainlengthtowidthratio(LWR),chalkgrainrate(CGR),chalkinessdegree(CD),gelatinizationtemperature(GT),amylosecontent(AC)andgelconsistency(GC)ofheadrice.ThreemappingmethodsemployedwerecompositeintervalmappinginQTLMapper2.0softwarebasedonmixedlinearmodel(MCIM),inclusivecompositeintervalmappinginQTLIciMapping3.0softwarebasedonstepwiseregressionlinearmodel(ICIM)andmultipleintervalmappingwithregressionforwardselectioninWindowsQTLCartographer2.5basedonmultipleregressionanalysis(MIMR).ResultsshowedthatfiveQTLswithadditiveeffect(A-QTLs)weredetectedbyallthethreemethodssimultaneously,twobytwomethodssimultaneously,and23byonlyonemethod.FiveA-QTLsweredetectedbyMCIM,ninebyICIMand28byMIMR.ThecontributionratesofsingleA-QTLrangedfrom0.89%to38.07%.AlltheQTLswithepistaticeffect(E-QTLs)detectedbyMIMRwerenotdetectedbytheothertwomethods.FourteenpairsofE-QTLsweredetectedbybothMCIMandICIM,and142pairsofE-QTLsweredetectedbyonlyonemethod.Twenty-fivepairsofE-QTLsweredetectedbyMCIM,141pairsbyICIMandfourpairsbyMIMR.ThecontributionratesofsinglepairofE-QTLwerefrom2.60%to23.78%.IntheXiu-BaoRILpopulation,epistaticeffectplayedamajorroleinthevariationofGLandCD,andadditiveeffectwasthedominantinthevariationofLWR,whilebothepistaticeffectandadditiveeffecthadequalimportanceinthevariationofCGR,AC,GTandGC.QTLsdetectedbytwoormoremethodssimultaneouslywerehighlyreliable,andcouldbeappliedtoimprovethequalitytraitsinjaponicahybridrice.
