Saltstressisamajorprobleminmostofthericegrowingareasintheworld.AmajorQTLSaltolassociatedwithsalttoleranceattheseedlingstagehasbeenmappedonchromosome1inrice.ThisstudyaimedtocharacterizethehaplotypepersityatSaltolandadditionalQTLsassociatedwithsalttolerance.Salttoleranceattheseedlingstagewasassessedin54ricegenotypesinthescaleof1to9scoreatEC=10dSm-1undercontrolledenvironmentalconditions.SevennewbreedinglinesincludingthreeKMR3/O.rufipogonintrogressionlinesshowedsimilarsalttolerantabilityasFL478andcanbegoodsourcesofnewgenes/allelesforsalttolerance.Simplesequencerepeat(SSR)markerRM289showedonlytwoallelesandRM8094showedsevenalleles.Polymorphicinformationcontentvaluevariedfrom0.55forRM289to0.99forRM8094andRM493.Basedon14SSRmarkers,the54lineswereclearlyseparatedintotwomajorclusters.FourteenhaplotypeswereidentifiedbasedonSaltollinkedmarkerswithFL478asthereference.AllelesofRM8094andRM3412candiscriminatebetweenthesalttolerantandsusceptiblegenotypesclearlyandhencecanbeusefulinmarker-assistedselectionattheseedlingstage.OthermarkersRM10720onchromosome1andRM149andRM264onchromosome8canalsodistinguishtolerantandsusceptiblelinesbutwithlesserstringency.
