Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed 英文参考文献.docVIP

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Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed 英文参考文献.doc

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Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed 英文参考文献

DiscoveryofPodShatter-ResistantAssociatedSNPsby DeepSequencingofaRepresentativeLibraryFollowed byBulkSegregantAnalysisinRapeseed ZhiyongHu.,WeiHua.,ShunmouHuang,HongliYang,GaomiaoZhan,XinfaWang,GuihuaLiu, HanzhongWang* KeyLaboratoryofBiologyandGeneticImprovementofOilCrops,MinistryofAgriculture,OilCropsResearchInstituteoftheChineseAcademyofAgriculturalSciences, Wuhan,Hubei,People’sRepublicofChina Abstract Background:Singlenucleotidepolymorphisms(SNPs)areanimportantclassofgeneticmarkerfortargetgenemapping.As of yet, there is no rapid and effective method to identify SNPs linked with agronomic traits in rapeseed and other crop species. Methodology/Principal Findings: We demonstrate a novel method for identifying SNP markers in rapeseed by deep sequencing a representative library and performing bulk segregant analysis. With this method, SNPs associated with rapeseed pod shatter-resistance were discovered. Firstly, a reduced representation of the rapeseed genome was used. Genomic fragments ranging from 450–550bp were prepared from the susceptible bulk (ten F2 plants with the silique shatteringresistanceindex,SSRI,0.10)andtheresistancebulk(tenF2plantswithSSRI.0.90),andalsoSolexasequencing- produced90bpreads.Approximately50millionofthesesequencereadswereassembledintocontigstoadepthof20-fold coverage.Secondly,60,396‘simpleSNPs’wereidentified,andthestatisticalsignificancewasevaluatedusingFisher’sexact test.Therewere70associatedSNPswhose–log10pvalueover16wereselectedtobefurtheranalyzed.Thedistributionof theseSNPsappearedatightcluster,whichconsistedof14associatedSNPswithina396kbregiononchromosomeA09. Ourevidenceindicatesthatthisregioncontainsamajorquantitativetraitlocus(QTL).Finally,twoassociatedSNPsfromthis regionweremappedonamajorQTLregion. Conclusions/Significance: 70associatedSNPswerediscoveredandamajorQTLforrapeseedpodshatter-resistancewas foundonchromosomeA09usingournovelmethod.TheassociatedSNPmarkerswereusedformappingoftheQTL,and maybeusefulforimprovingpodshatter-resi