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1、lettersGenome-widepatternsofgeneticvariationamongelitemaizeinbredlinesJinshengLai1,2,7,RuiqiangLi3,7,XunXu3,7,WeiweiJin2,7,MingliangXu2,7,HainanZhao1,2,ZhongkaiXiang1,2,WeibinSong1,2,KaiYing4,MeiZhang1,2,YinpingJiao1,2,PeixiangNi3,JianguoZhang3,DongLi3,
2、XiaosenGuo3,KaixiongYe3,MinJian3,BoWang3,HuisongZheng3,HuiqingLiang3,XiuqingZhang3,ShoucaiWang2,ShaojiangChen2,JianshengLi2,YanFu4,NathanMSpringer5,HuanmingYang3,JianWang3,JingruiDai2,PatrickSSchnable4&JunWang3,6Wehaveresequencedagroupofsixelitemaizeinb
3、redlines,parentsofthecommercialhybrid(ZD958)thatiscurrentlythemostincludingtheparentsofthemostproductivecommercialwidelygrowninChina.Inbredline178isthefemaleparentofanotherhybridinChina.Thiseffortuncoveredmorethan ,000,000hybrid(ND108)thatisalsowidelyg
4、rowninChina.Inbredline478isaSNPs,30,000indelpolymorphismsand 0 low-sequence-parentandinbredline5003isagrandparentofZheng58(Fig.1).diversitychromosomalintervalsinthemaizegenome.Resequencingyielded1.26billion75-bppaired-endreads,whichWealsoidentifiedsev
5、eralhundredcompletegenesthatcomprised83.7Gbofhigh-qualityrawdata.Sequencereadswereshowpresence/absencevariationamongtheseresequencedalignedtothemaizereferencegenomeusingSOAPsoftwarev2.18lines.Wediscussthepotentialrolesofcomplementationof(ref.10).Intotal
6、,weachievedaneffectivedepthof×32.4coverage,withpresence/absencevariationsandotherdeleteriousmutationsanaverageof×5.4foreachinbredline(SupplementaryTable1).incontributingtoheterosis.High-densitySNPandindelWeuseduniquereadsinnon-repeatregionstodetectSNPsa
7、ndpolymorphismmarkersreportedhereareexpectedtobeaindelpolymorphisms(IDPs).SNPswerecalledwithSOAPsnp11usingvaluableresourceforfuturegeneticstudiesandthemolecularaconservativequalityfilterpipeline(OnlineMethods).Weidentifiedbreedingofthisimportantcrop.1,2
8、72,134SNPsinnon-repeatregions,with468,966inthe32,540high-confidencemaizegenes(the‘filteredgeneset’)and130,053Themaizegenomeislargeandcomplex1–4.ItsgeneticvariationhasSNPsincodingregions.Wealsoidentified30,178indelsrangingbeenchar
