Rapid Genomic Characterization of the Genus Vitis 英文参考文献.docVIP

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Rapid Genomic Characterization of the Genus Vitis 英文参考文献.doc

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Rapid Genomic Characterization of the Genus Vitis 英文参考文献

RapidGenomicCharacterizationoftheGenusVitis SeanMyles1.,Jer-MingChia2.,BonnieHurwitz2,CharlesSimon3,4,GanYuanZhong3,4 ,Edward Buckler1,4*,DoreenWare2,4 * 1InstituteforGenomicDiversity,CornellUniversity,Ithaca,NewYork,UnitedStatesofAmerica,2ColdSpringHarborLaboratory,ColdSpringHarbor,NewYork,United StatesofAmerica,3NewYorkStateAgriculturalExperimentStation,Geneva,NewYork,UnitedStatesofAmerica,4UnitedStatesDepartmentofAgriculture,Agricultural ResearchService,Ithaca,NewYork,UnitedStatesofAmerica Abstract Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvementbyfacilitatingthegeneticmappingofagriculturallyimportantphenotypes.Thefirststepinoptimizingthe design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessmentofthepopulationstructureandpatternoflinkagedisequilibrium(LD)inthespeciesofinterest.Inthepresent study,weprovidesuchanassessmentforthegrapevine(genusVitis),theworld’smosteconomicallyimportantfruitcrop. Reducedrepresentationlibraries(RRLs)from17grapeDNAsamples(10cultivatedV.viniferaand7wildVitisspecies)were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundredsofthousandsofSNPsandvalidatedasubsetoftheseSNPsona9Kgenotypingarray.Wedemonstratethatthe9K SNParrayprovidessufficientresolutiontodistinguishamongV.viniferacultivars,betweenV.viniferaandwildVitisspecies, andevenamongdiversewildVitisspecies.WeshowthatthereissubstantialsharingofpolymorphismbetweenV.vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographicoriginsusingprincipalcomponentsanalysis(PCA).LevelsofLDinthedomesticatedgrapevinearelowevenat shortranges,butLDpersistsabovebackgroundlevelsto3kb.Whilegenotypingarraysareusefulforassessingpopulation structureandthedecayofLDacrosslargenumbersofsamples,wesuggestthatwhole-genomesequencingwill