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DNAAFLPX11112M.A.SaghaiMaroof311(430070)2(DepartmentofCropandSoilEnvironmentalSciences,VirginiaPolytechnicInstituteandStateUniversity,VA24061,USA)3(DepartmentofVegetableCrops,UniversityofCalifornia,Davis,CA91616,USA)(OryzasativaL.ssp.indica)(O.rufipogonGriff)F2RFLP,DNAAFLP28DNA172AFLP28DNA6,22Cornell172AFLP2522812200PCRRFLP,612SSR,AFLP,RFLP,DISTRIBUTIONOFSIMPLESEQUENCEREPEATANDAFLPMARKERSINMOLECULARLINKAGEMAPOFRICEX1XIONGLi2Zhong1WANGShi2Ping1LIUKe2De1DAIXian2Kai2M.A.SAGHAIMAROOF3HUJin-Guo1ZHANGQi2Fa1(NationalKeyLaboratoryofCropGeneticImprovement,HuazhongAgriculturalUniversity,Wuhan430070)2(DepartmentofCropandSoilEnvironmentalSciences,VirginiaPolytechnicInstituteandStateUniversity,VA24061,USA)3(DepartmentofVegetableCrops,UniversityofCalifornia,Davis,CA91616,USA)AbstractSSR(simplesequencerepeat)andAFLP(amplifiedfragmentlengthpolymorphism)arePCR2basedmolecularmarkersdevelopedinrecentyears.Inthisstudy,theauthorsanalyzedthepolymorphisms,inheritanceanddistributionofSSRandAFLPmarkersusinganF2populationfromacrossbetweencultivarAijiaoNante(OryzasativaL.ssp.indica)andanaccessionofthecom2monwildrice(O.rufipogonGriff).Atotalof200newmarkerswereobtainedincluding28SSRand172AFLPmarkers.Sixofthe28SSRmarkersweredevelopedbyNationalKeyLaboratoryofCropGeneticImprovement(NKLCGI)usingDNAsequencesfromGenBankandtheother22werefromdatapublishedpreviously.The172AFLPmarkerswerefromatotal228polymorphicbandsamplifiedusing25selectedprimercombinations.Mappingofthe200newmarkersusingNKLCGISpreviouslydevelopedRFLPmapbasedonthesameF2populationresolvedthesemarkerstoall12ricechromosomes.IntegrationoftheSSRandAFLPmarkersintotheRFLPmapresultedinahighdensitymolecularlinkagemapcontaining612polymorphicloci.XSupportedbyagrantfromtheChineseRiceGenomeProgramandtheRockefellerFoundation.:1997210231:19982012121998,40(7):605614ActaBotanicaSinicaKeywordsSSR,AFLP,RFLP,Genomemapping,,(RFLP),(PCR),DNA(RAPD)[1](STS)[2]DNA(,SSR)[3](AFLP)[4],[5][6][7][8,9],[10],,F2400RFLP[11],PCR,DNAAFLP,F2,RFLP,1111DNA(OryzasativaL.ssp.indica)(O.rufipogon)(P16)F2[11],CTAB[12]DNARFLP172F2F1DNAAFLP112:GenBankDNA,Primer;29,10WuTanksley[13],19(RM1RM19)Panaud[14]WuTanksley[13]Yang[15](multiplexPCR)1.3AFLPAFLPVos[4]EcoRMse,ZabeauVos[16],E+AM+AM+C36EcoR(E1:E+AAA,E2:E+AAG,E3:E+AAT,E4:E+AAC,E5:E+ACA,E6:E+ACC)11Mse(M1:M+AAA,M2:M+AAG,M3:M+AAT,M4:M+AAC,M5:M+CAG,M6:M+CAC,M7:M+CGA,M8:M+CGT,M9:M+CTG,M10:M+CTT,M11:M+CCT),(bp)(606402),F1,AFLP,,,,D,B;,C,A1.4SSRAFLPRFLP,Mapmaker/EXP3.0[17]group(LOD6.0),orderrippleLOD3.0map(MacintoshMapmaker2.0),(cM)Kosambi[18]LOD3.0(AFLP)RFLP(20cM),,,2211SSRGenBank,28,22(6)12,6(1);8;2,6267(1),RMD(RM#)(1),29,22(75.9%),[13,14](1)212AFLP2.2.1AFLP,6625AFLP3070,52.6(70400bp),,20(2),9.1,17.4%(r=0.884)2.2.2AFLP228,109,11922849(21.5%)(P0.05)31LOD6.0,172AFLP12,LOD56AFLPLOD3.0AFLP7:DNAAFLP607112Table112SSRmarkersdevelopedusingsequencesfromGenBankdatabaseMarkerPrimersequence1)RepeatunitChromosomelocationAccessionRelatedgenesRMD152GCAAACTCCAAAGTCCAAA(T)n2D10676Ricep2SINE12r7gene52ATAGAGGCTGGTGTAACGTGTGRMD252GGTCTTCTTGGGATGCAGAG(TA)n7L103462amylasegene52CATTGGAGCATGTGTCATTTRMD352TATTGCTTTACCCGCGAGAC(TA)nD13099Ricemitochondrial52GAATCCGCCATTTCAGCTACDNAfortRNA2ArgRMD42)52GACAAATAGCCACCCACACC(TC)n6D10677Riceglucosyl52TTTCCAGCCCAACACCTTACTransferasegeneRMD752ATCTCCGTCAGAATCAAGCG(GA)n2D16340RFLPmarker52GCTTCCAAGGACCCCATCRMD852TTTCCAGCCGTGACCCTAAT(TA)nD13112Ricemitochondrial52GCCTCCACCTCCTCCTCCTCDNAfortRNAsRMD952AGCCTCTTCGGCTACTGCG(GGC)nD14776RFLPmarker(G295)52GGCGTTCATGTTCCCGACRMD1152AACGTGTTCGACCCATTCTC(GGA)nM8093916.9kDheatshockprotein52TCACCTCCTCCTTCTTGACGRMD1452AATGTTCAGATGGGAGGGTG(AAT)n6RG213FRFLPmarker52CATCGCTTAATGGTTTATCTCGRMD1552GCTCCTCATTGCTGTCTCCA(TCC)nD10838Starchbranchingenzymegene52TACCGCTGATTACCCTCGICRMD2152TGCATCTTTCATTGCTCGTT(AATT)n6D10677Riceglucosyltransferasegene52ACCCCTGGATGTGTTTCTCTRMD2252ATGGACGTCGTCATACGCTC(TTCC)n2D10397RicemRNAforhistone52CAGAAGCCAACACAAAGCAGH4(T127)1)Theupperrowisforwardprimer,thelowerrowisreverseprimer;2)BothRMD4andRMD21weregeneratedfromD10677,butRMD4ismonomorphicinthepopulationusedhere.,60%AFLP;LOD2.0,AFLP,6000cMRFLP,LOD3.0(104AFLP54RFLP13DNA),16LOD3.0AFLP(1),6121973cM,RFLP(412RFLP)273cM(3)2.2.3AFLP,172AFLP1612Fig.1Thegeneticlinkagemapcontaining612markersbasedontheF2populationofacrossbetweenAijiaoNante(Oryzasativa)andP16(O.rufipogon)MarkerswithticksaretheonesmappedatLOD3.0.ThosethatareinparenthesesandplacedonthesidesofthechromosomesaretheonesplacedintheirmostlikelyintervalswithLOD3.0.AfewRFLPmarkersaremappedtochromosomallocationsdifferentfromwheretheyappearedinpreviouslypublishedmaps[15,16]andareindicatedbyparenthesesgivingtheoriginalchromosomalloca2tions.SSRmarkerswereinboldface.RFLPandmicrosatellitemarkersinthegrayregionsofsomechromosomesaretheonesshowingsegregationdistortion.AFLPmarkerswithsegregationdistortionweremarkedbyasterisk(3).CentromereoneachchromosomewasindicatedwithblackbasedontheresultofSinghetal[21].7:DNAAFLP611225AFLPTable2Comparisonoftheamplificationefficiencyof25primercombinationsPrimerTotalPolymorphicPolymorphism(