简介：Genotypingbysequencing(GBS)istherecentapproachofnext-generationsequencingtechniquefordiscoveringandgenotypingsinglenucleotidepolymorphisms(SNPs)incropspecies.Genotypicvariationstudies(SNPsandinsertion-deletions/InDels)wereperformedusingfourricelinesbasedonGBSdatabyaligningtothereferencegenomeNipponbare.LocalaromaticricelandraceTulaipanjiwascrossedwithRanjit,andtwodistinctlineswereidentifiedfromtheprogenies:onelinewithawnsandaromatraitsandtheotherwithoutawnsandaroma.TotalnumberofSNPsandInDelsidentifiedwere52810and4327atreaddepth10,respectively.OutofthetotalpolymorphicSNPs/InDels,16490wereintergeneric,7812wereinsidegene,and4435wereintronic.Phylogenetically,Tulaipanjiwasclosertothereferencegenomenipponbare.Basedonrecurrentparentgenomeanalysis,outof10013alleles,92.52%wasintrogressedintoprogeny-awnfromTulaipanjiand7.48%fromRanjit,whereasprogeny-awnlesscarried89.19%allelesfromRanjitandonly10.81%allelesfromTulaipanji.Inaddition,progeny-awnwasthehighestheterozygous(83.88%)andprogeny-awnlesswastheleast(2.24%)atthisfifthgenerationofrecombinantinbredlines.TheseSNPvariationsmaybelinkedtothephenotypictraitsandcanbeutilizedincropimprovementthroughlinkagemapping.TheseresultssuggestthataddingahighdensityofSNPmarkerstoamappingorbreedingpopulationthroughGBShasagreatvaluefornumerousapplicationsinricebreedingandgeneticsresearch.