GenomicsAbioticStressOct.ppt

GenomicsandAbioticStress,Oct11,2012,Outline,Introductiongenome269(5223):496-512.,2000年12月拟南芥Arabidopsisthaliana第一个植物基因组序列,遗传图谱、物理图谱建立,全基因组为125Mb。基因组测序区段覆盖了全基因组的115.4Mb,共含有25498个基因。,GenomeSequencing,2001年2月人类基因组人类基因组共有30亿个碱基对,预测编码基因31000个,比最初预测的10万个编码基因数大大减少。,GenomeSequencing,2002年4月，水稻基因组,GenomeSequencing,RelativeGenomeSizes,PlantGenomesCanBeLargerThanTheHumanGenome,GenomeSequencing,NewSequencingTechnologiesnextgenerationsequencing(NGS),IlluminaHiSeqABISOLiDRoche454,NGS:Highthroughtput,lowcost,Sequencingtechnologies-NGS,Sequencers,SangerSequencing:1977,Metzkeretal.2010NatureReviews|Genetics,Sequencingtechnologies-NGS,NGSapplications,NGSapplications,BRIEFINGSINBIOINFORMATICS.2010VOL11.NO5.499,NGSapplications,Agriculture,LivestockBreeding,andBioprocessinggrowdisease-,insect-,anddrought-resistantcropsbreedhealthier,moreproductive,disease-resistantfarmanimalsgrowmorenutritiousproducedevelopbiopesticidesincorporateediblevaccinesincorporatedintofoodproducts,U.S.DepartmentofEnergyGenomePrograms,GenomicsandItsImpactonScienceandSociety,2003,AnticipatedBenefitsofGenomeResearch-农业领域,NGSapplications,AnticipatedBenefitsofGenomeResearch人类健康,U.S.DepartmentofEnergyGenomePrograms,GenomicsandItsImpactonScienceandSociety,2003,HumanhealthandMedicineimproveddiagnosisofdiseaseearlierdetectionofgeneticpredispositionstodiseasegenetherapyandcontrolsystemsfordrugspersonalized,customdrugs,NGSapplications,AnticipatedBenefitsofGenomeResearch-微生物应用,MicrobialGenomicsrapidlydetectandtreatpathogens(disease-causingmicrobes)inclinicalpracticedevelopnewenergysources(biofuels)monitorenvironmentstodetectpollutantsprotectcitizenryfrombiologicalandchemicalwarfarecleanuptoxicwastesafelyandefficiently,U.S.DepartmentofEnergyGenomePrograms,GenomicsandItsImpactonScienceandSociety,2003,NGSapplications,Applicationsofgenomicsincropimprovement,DiscoveryofmolecularmarkerspopulationgeneticsHighthroughputgenotyping(GBS)germplasmdiversityGenomicresourceandvariationQTLmapping(GWAS,Mappingbysequencing)mappingIdentificationofcandidategenesgenediscoveryTransgenicbreeding,MarkerassistedbreedingbreedingGenomeselectionEvolutionofcrops(domesticationandselection)evolution,NGSapplications,ImprovementsNeeded,J.S.Boyer“PlantProductivityandEnvironment,”Science,Vol.218,October29,1982pp.443-448.,Cropgenomicsandabioticstress,HowtoImproveCrops,Genomicsallowstheidentificationofthegenesandgenenetworksresponsibleforhardiness,Cropgenomicsandabioticstress,AcidicAlstress,Droughtstress,Salt-affectedbarrenlandinnorthIndia,Saltstress,30,LinkageDisequilibrium(LD),Linkagedisequilibrium:thenon-randomassociationofallelesatlinkedloci.Ameasureofthetendencyofsomeallelestobeinheritedtogetheronhaplotypesdescendedfromancestralchromosomes.IfwegenotypethefirstSNP,weknowwhattheallelesareatthesecondSNP.,IntroducingGWASgenome-wideassociationstudies,Genotype:pairofalleles(onepaternal,onematernal)atalocusGenotypeforthisindividualisGTHaplotype:sequenceofallelesalongasinglechromosomeGenotypesforthisindividual(vertical):CAandTTHaplotypes(horizontal):CTandAT,GenotypesandHaplotypes,IntroducingGWAS,2007ScientificBreakthroughoftheYear,Individual1Individual2Individual3Individual4,GWAS-SNPs,UsingSNPstoTrackPredispositiontoDiseaseandotherGeneticTraits,Gibson2:467;PLoSGenet.2011Aug;7(8):e1002221,GWASofAltoleranceinRice,Phenotyping,GWASofAltoleranceinRice,Manhattanplot,GWASofAltoleranceinRice,GWASofAltoleranceinRice,Nrat1Nrampaluminumtransporter1,Nramp(naturalresistance-associatedmacrophageprotein)family,Nrat1transportstrivalentAlion,KnockoutofNrat1resultedindecreasedAluptake,andenhancedAlsensitivity,apriorstepoffinalAldetoxificationthroughsequestrationofAlintovacuoles.,ProcNatlAcadSciUSA.2010,107(43):18381-5.,GWASofAltoleranceinRice,HaplotypeanalysisoftheNrat1generegion,GWASofAltoleranceinRice,GWASofAltoleranceinRice,Summary,Subpopulationstructureexplained57%ofthephenotypicvariation,andthemeanAltoleranceinJaponicawastwicethatofIndica.Forty-eightregionsassociatedwithAltolerancewereidentifiedbyGWAanalysis,mostofwhichweresubpopulation-specific.Fouroftheseregionsco-localizedwithaprioricandidategenes,ThreeregionscorrespondingtoinducedAl-sensitivericemutants(ART1,STAR2,Nrat1)wereidentified.HaplotypeanalysisaroundtheNrat1geneidentifiedsusceptibleandtoleranthaplotypesexplaining40%oftheAltolerancevariationwithintheaussubpopulationSequenceanalysisofNrat1identifiedatrioofnon-synonymousmutationspredictiveofAlsensitivityinourdiversitypanel.,Naturalmutation,GWASofAltoleranceinRice,ComparativeGenomics,InsightsintosalttolerancefromthegenomeofThellungiellasalsuginea盐芥基因组PNAS2012,134-foldcoveragetosevenchromosomeswithacodingcapacityofatleast28,457genes.Geneticbasisunderlyingplantabioticstresstolerance.Comparativegenomicsandexperimentalanalysesidentifiedgenesrelatedtocationtransport,abscisicacidsignaling,andwaxproductionprominentinT.salsugineaaspossiblecontributorstoitssuccessinstressfulenvironments.通过比较基因组学和定量表达分析显示，更强的离子转运、更多的叶表面蜡质、和更快的ABA响应等过程使得盐芥具有更好的高盐耐受性。,ComparativeGenomics,EvolutionaryRelationshipofmajorcrops,Jacksonetal.2011.NewPhytologist191:91592591,PhylogeneticandEvolutionaryAnalysis,Muchisstillunknown!,Futuredirection,FunctionalGenomics,ThePlantJournal(2010)61,10411052,Futuredirection,Geneexpressionnetwork,Blackedgesrepresenttherelationofgenesunderstressfactor1Blueedgesrepresenttherelationofgenesunderstressfactor2,Theyellowdottedgenesaretheonestoleranttobothstressfactors.,Futuredirection,SystemsBiology,Futuredirection,WhatsNext