細胞遺傳學課件精編版

植物多倍體的遺傳及表觀遺傳

Geneticandepigeneticchangesinplantpolyploids

植物多倍體的遺傳及表觀遺傳

Geneticandep1主要參考文獻AdamsKL,CronnR,PercifieldR,WendelJF.Genesduplicatedbypolyploidyshowunequalcontributiontothetranscriptomeandorgan-specificreciprocalsilencing.ProcNatlAcadSciUSA,2003,100:4649~4654AdamsKL.Evolutionofduplicategeneexpressioninpolyploidyandhybridplants.JHered,2007,98:136-141ChenZJ,PikaardC.Transcriptionalanalysisofnucleolardominanceinpolyploidplants:Biasedexpression/silencingofprogenitorrRNAgenesisdevelopmentallyregulatedinBrassica.ProcNatlAcadSciUSA,1997,94:3442-3447ChenZJ.Geneticandepigeneticmechanismsforgeneexpressionandphenotypicvariationinplantpolyploids.AnnRevPlantBiol,2007,58:377-4061主要參考文獻AdamsKL,CronnR,PerComaiL.Geneticandepigeneticinteractionsinallopolyploidplants.PlantMolBiol,2000,43:387~399ComaiL.Theadvantagesanddisadvantagesofbeingpolyploidy.NatRevGenet,2005,6:836-846LeitchAR,LeitchIJ.Genomicplasticityandthediversityofpolyploidyplants.Sci,2008,320:481-483LiuB,WendelJF.Non-Mendelianphenomenainallopolyploidgenomeevolution.CurrGenomics,2002,3:489-506LiuB,WendelJF.Epigeneticphenomenaandtheevolutionofplantallopolyploids.MolPhylogenetEvol,2003,29:365-379ComaiL.GeneticandepigenetiOttoSP,WhittonJ.Polyploidyincidenceandevolution.AnnRevGenet,2000,34:401-437SoltisPS,SoltisDE.Theroleofgeneticsandgenomicattributesinthesuccessofpolyploids.ProcNatlAcadSciUSA,2000,97:7051-707SongKM,LuP,TangK,OsbornTC.RapidgenomechangeinsyntheticpolyploidsofBrassicaanditsimplicationsforpolyploidsevolution.ProcNatlAcadSciUSA,1995,92:7719-7723StuparRM,BhaskarPB,YandellBS,etal.Phenotypicandtranscriptomicchangesassociatedwithpotatoautopolyploidization.Genetics,2007,176:2055-2067TateJA,SoltisDE,SoltisPS.2007.Polyploiyinplants.In:GregoryRT(ed)TheEvolutionoftheGenome.SciencePress,Beijing,pp372-426OttoSP,WhittonJ.PolyploidyWendelGF.Genomeevolutioninpolyploids.PlantMolBiol,2000,42:225-249WangJL,TianL,LeeHS,WeiNE,JiangHM,etal.GenomewidenonadditivegeneregulationinArabidopsisallotetraploids.Genetics,2006,172:507-517YangSS,CheungF,LeeJJ,HaM,WeiNE,etal.Accumulationofgenome-specifictranscripts,transcriptionfactorsandphytohormonalregulatorsduringearlystagesoffibercelldevelopmentinallotetraploidcotton.PlantJ,2006,

47:761–75WendelGF.Genomeevolutionin2Introduction－

AbundanceofallopolyploidplantsPolyploidy,resultingfromeitherduplicationofasinglebutcompletegenome(autopolyploidy)orfromcombinationoftwoormoredifferentiatedgenomes(allopolyploidy),isaprominentmodeofspeciationinplants.Itisdifficulttooverstatetheimportanceofpolyploidyintheevolutionaryhistoryofplants.人類在合成多倍體方面收效甚微！2Introduction－

AbundanceofaAbundanceofallopolyploidplantsWhileestimatesvaryregardingtheproportionofangiospermsthathaveexperiencedoneormoreepisodesofchromosomedoublingatsomepointintheirevolutionaryhistory,itisatleast50%andmaybehigherthan70%;perhaps95%ofpteridophyteshaveexperiencedatleastoneepisodeofpolyploidizationintheirpast.Abundanceofallopolyploidpla細胞遺傳學課件精編版

Typicalpolyploidcrops,wheat,oat,coffee,potato,canola,soybean,sugarcane,tobacco,cotton

Typicalpolyploidcrops,wheaAbundanceofallopolyploidplantsBecausemostancientpolyploidshaveundergoneanevolutionaryprocessofchromosomalandperhapsgenic“diploidization”,theirpolyploidhistorymaybeobscuredatthecytologicalandclassicgeneticslevels.Polyploidnatureofmanyplantgenomeswasnotevidentuntiltheadventofcomparativegenomicsandwhole-genomesequencing-maize,Arabidopsis—traditionallydiploids.

AbundanceofallopolyploidplaAbundanceofallopolyploidplantsGiventheseandotherrecentexamplesfromplants,itisprobablysafetostatethattherearenobonafidediploidspeciesintheplantkingdom.Abundanceofallopolyploidpla細胞遺傳學課件精編版ProductionofArabidopsisallotetraploidsProductionofArabidopsisalloProductionofArabidopsisallotetraploidsProductionofArabidopsisallo(a)Phenotypicvariationoftheplantsafterfivegenerationsofselfing.Theplantsincludetwoparents,A.thalianaautotetraploid(At4)andA.arenosa(Aa),sixallotetraploids(S–1toS–6),andanaturalallotetraploid,A.suecica(As).(a)Phenotypicvariationofth(b)Epigeneticsilencinginresynthesizedallopolyploids.A.suecica(As,whiteflower),naturalallotetraploid.A.thaliana(notshown)andA.arenosa(Aa),havewhiteandpinkflowers.Theflowercolorsin3rdgeneration(S3–1,2,and3)segregatefromallwhite(S3–1)toallpink(S3–3).Variegatedflowercolors(S3–2).

(b)Epigeneticsilencinginre

3Non-MendelianPhenomenainAllopolyploidGenomeEvolution

non-Mendelianattributes:thosenotcharacterizedbyconventionaltransmissiongenetics.Mysteriousprocessofrapidandinsomecasesdirectedstructuralchangesthatoccurinpolyploidgenomesupontheirformation;Novelintergenomicinteractionsasaconsequenceofthemergeroftwoformerlyisolatedgenomes;

3Non-MendelianPhenomenainNon-MendelianPhenomenainAllopolyploidGenomeEvolution

Epigeneticmechanismsinnascentallopolyploidy,suchasnucleolardominance,genesilencingandmobileelementactivation.Thesemyriadphenomenadonotcharacterizeallpolyploidsystems,andsomenascentallopolyploidsappeartobegenomicallyquiescentinthisrespect.Non-MendelianPhenomenainAll3.1RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Accordingtotheclassicalviewofallopolyploidy,themergeroftwodistinctbutrelatedgenomesshouldresultingenomicadditivitywithrespecttotheparentalspecies.Thisexpectationservesasaconvenientnullhypothesisofthepredictedgenomiccontributionstoapolyploidnucleus.3.1RAPIDGENOMICCHANGESINNRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Naturallyoccurringpolyploidsmaynotproviderobusttestsofthehypothesis,becausetheirgenomes,andthoseoftheirdiploidprogenitors,willhavecontinuedtoevolvesincepolyploidformation,therebyobscuringinitialconditions.RAPIDGENOMICCHANGESINNEWLY

RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Becauseofthis,insightsintotheearlieststagesofpolyploidgenomeevolutionarelikelytorequirethestudyofsyntheticexperimentalallopolyploids.RecentstudiesinBrassicaandinAegilops-Triticumdemonstratethatnascentallopolyploidsoftendonotshowgenomicadditivitywithrespecttotheirparents.

RAPIDGENOMICCHANGESINNEWL

RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Instead,theirgenomesdisplayremarkablepatternsofnon-Mendeliangenomicchangesaccompanyinghybridizationandpolyploidization--agrowingrecognitionofthedynamicandunpredictablenatureofpolyploidgenomes.

RAPIDGENOMICCHANGESINNEWLRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSThefirststudydemonstratingextensiveandrapidgenomicchangesaccompanyingpolyploidformationwasbySongetal.,whousednewlysynthesizedreciprocalsyntheticallopolyploidsinBrassicabetweenthediploidsB.rapaandB.nigraandtheotherfromB.rapaandB.oleracea.Followingcolchicine-doubling,F2individualswererecoveredfromwhichprogeniesuptotheF5generationweresynthesizedbyself-pollination.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSSouthernhybridizationanalysisusing89nuclearprobescorrespondingtocDNAs,known-functiongenes,andanonymousgenomicclonesrevealedahighfrequencyofunexpectedfragmentprofilesineachgeneration.Thesegenomicchangesincludedlossofparentalfragments,recoveryofparentalfragmentsintheF5thatwerenotdetectedintheF2,andthefrequentappearanceofnovelfragments,especiallyinallopolyploidsinvolvingB.rapaandB.nigra.

RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSThislatterobservationreflectsthequantitativeconclusionthatnearlytwiceasmuchchangewasdetectedincrossesinvolvingthedistantrelativesB.rapaandB.nigraasinthemorecloselyrelatedB.rapaandB.oleracea.Thechangeswereapparentlyrandom,asindividualsfromthesameanddifferentgenerationsexhibitedagreatdegreeofvariation.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSLoss=fragmentspresentindiploidsandintheF2butnotinFsplants;gain=diploidparentalfragmentsabsentinF2plantsbutpresentinFsplants.A,B,andC=fragmentsspecifictoA,B,orCparentalgenomes;sharedfragments=sharedbybothdiploidparents;F2fragments=foundintheF2butnotineitherdiploidparent;novelfragments=foundonlyinFsplants.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSAsimilarphenomenonofunexplainedgainandlossofDNAfragmentswasdescribedfromsyntheticallopolyploidsoftheAegilops-Triticumgroup.Thewheatgroupprovidesanidealsystemtostudypolyploidgenomeevolutionbecauseseveralallopolyploidspeciesareyoung,theirdiploidprogenitorsareextant,andthephylogeneticrelationshipsamongthediploidspeciesandbetweenthediploidsandpolyploidsarereasonablywellunderstood.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSMoreover,allopolyploidscanbereadilysynthesizedinthelaboratorybycolchicinetreatment.Perhapsofmoresignificance,theyoung(~8,500year-old)naturalhexaploidspeciesTriticumaestivum(commonorbreadwheat),vitaltothedevelopmentandpresentsustenanceofhumancivilization,isaclassicexampleofspeciationviaallopolyploidy.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSAprofoundrealizationemergesfromthesestudieson

BrassicaandAegilops-Triticum,namely,thatallopolyploidy

cannotonlyleadtotheestablishmentofnewspeciesina

single

generation,ashaslongbeenrecognized,but

thatintheprocesstheconstituentgenomesmaybe

dramaticallyandvirtuallyinstantaneouslyaltered.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSAt

present,onecanonlyspeculateabouttheimmediate

morphological,physiological,andecologicalconsequences

ofrapidanddirectedhybridization-inducedandpolyploidy-induced

genomicreorganization,butthe

potentialrelevance

toadaptationanddiversificationisevident.Thisissuetakesonaddedimportancewhenone

considerstheprevalenceofwidehybridizationand

polyploidyinplants.RAPIDGENOMICCHANGESINNEWLYRAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSOnequestionthatnaturallyarisesiswhethertheresultsforBrassicaandAegilops-Triticumwillturnouttobetypicaloraberrant.Italreadyisevidentthatrapidgenomicchangeisnotahallmarkofallnascentplantallopolyploids.Arecentstudyincotton(Gossypium)assayedapproximately22,000genomiclociinninesetsofsyntheticallopolyploidsusingAFLPfingerprinting,yetnearlyperfectadditivitywasfoundwithrespecttoparentalAFLPbandingprofiles.RAPIDGENOMICCHANGESINNEWLY4Epigeneticphenomenainplantallopolyploids

Allopolyploidgenesisunderbothsyntheticandnaturalconditionsoftenisaccompaniedbyrapidandsometimesevolutionarilyconservedepigeneticchanges,includingalterationincytosinemethylationpatterns,rapidsilencinginribosomalRNAandproteincodinggenes,andde-repressionofdormanttransposableelements.Thesechangesareinter-relatedandlikelyarisefromchromatinremodelinganditseffectsonepigeneticcodesduringandsubsequenttoallopolyploidformation.4EpigeneticphenomenainplaEpigeneticphenomenainplantallopolyploidsThisepigeneticvariationmaycontributetoseveralimportantattributesofallopolyploidy,includingfunctionaldiversificationorsubfunctionalizationofduplicatedgenes,geneticandcytologicaldiploidization,andquenchingofincompatibleinter-genomicinteractionsthatarecharacteristicofallopolyploids.Likelytheevolutionarysuccessofallopolyploidyisinpartattributabletoepigeneticphenomenathatweareonlyjustbeginningtounderstand.Epigeneticphenomenainplant4.1Methylationrepatterning

Anintegralcomponentofthedevelopmentalcontrolofgeneexpressionandthemaintenanceofgenomeintegrityinadiversearrayoforganismsisspecific,programmedcytosinemethylation.Hypermethylationusuallyisahallmarkofheterochromatinandischaracteristicofeuchromaticgenesilencing,whereashypomethylationisoftenassociatedwithactivegeneexpression.4.1Methylationrepatterning

AMethylationrepatterning

Ithasbeenrecognizedforyearsthatunusualenvironmentalstimuliandpassagethroughtissueculturemaycauseheritablechangesincytosinemethylationpatternsinplants.Asapotentialprimarygenomedefensesystem,thecytosinemethylationmachinerymayrespondtoenvironmentalorgenomicchallengesbycausingalterationsinmethylationthatarethoughttomediatephysiologicallymeaningfulresponsestothechallenge.Methylationrepatterning

IthaMethylationrepatterning

Allopolyploidy,byunitingdivergentgenomesintoonenucleus,mayconstitutesuchachallenge,or‘‘genomicshock’’(sensuMcClintock,1984).Thissuggestionissupportedbyexperimentalevidence,whichshowsthatinseveralnascentallopolyploidplants,includingBrassica(Songetal.,1995),wheat(Kashkushetal.,2002;Liuetal.,1998a;Shakedetal.,2001)andArabidopsis(Comaietal.,2000;LeeandChen,2001;Madlungetal.,2002),allopolyploidformationleadstoheritablyre-patternedcytosineDNAmethylation.Methylationrepatterning

Allop4.2Epigeneticgenesilencing

NascentallopolyploidsoftenareassociatedwithvariationandinstabilityinphenotypesthatcannotbeaccountedforbyconventionalMendeliantransmissiongeneticsorchromosomalaberrations(Comai,2000;Comaietal.,2000).Theaffectedtraitsarediverse,includingtimingofflowering,overallplanthabit,leafmorphology,andhomeotictransformationsinfloralmorphology(Comaietal.,2000;SchranzandOsborn,2000).4.2Epigeneticgenesilencing

EpigeneticgenesilencingIthasbeensuggestedthattheseallopolyploidyassociatedchangesinphenotypesaretheoutcomeofalteredgeneexpressionduetovariouscauses,includingincreasedvariationindosage-regulatedgeneexpression,alteredregulatoryinteractions,andrapidgeneticandepigeneticchanges,whichareprobablyconferredbygenome-wideinteractions.EpigeneticgenesilencingItha4.3Epigeneticgenesilencing-Nucleolardominance

Nucleolardominancereferstothephenomenoninhybridsorallopolyploidswherebynucleoliform,inassociationwithribosomalRNAgenes,onchromosomesinheritedfromonlyoneofthetwoparents.Althoughthisphenomenonhadbeenintensivelystudiedsinceitsdiscoveryin1934(Navashin,1934),itsmolecularbasisisnotfullyunderstood.4.3Epigeneticgenesilencing-Epigeneticgenesilencing-NucleolardominancerRNAtranscriptsfromonlyoneoftheparentalgenomesweredetectableinvegetativetissuesofbothnaturalandsyntheticallopolyploids,thusindicatingrapidoccurrenceofthephenomenonaswellasitsevolutionaryconservation.rRNAgenessilencedinvegetativetissuesarederepressedinreproductiveorgans,indicatingnotonlyreversibilityofthephenomenon,butalsodifferentialpartitioningofrDNAarrayexpressionduringallotetraploidplantdevelopment.Epigeneticgenesilencing-Nucl蕓苔屬六個栽培種之間的細胞遺傳學關(guān)系(U,1935).四倍體中核仁顯性(nucleolardominance)的梯度為B.nigra>B.rapa>B.oleracea.PNAS,1997,94:3442黑芥埃芥甘藍甘藍型油菜白菜型油菜芥菜型油菜蕓苔屬六個栽培種之間的細胞遺傳學關(guān)系(U,1935).4.4Epigeneticgenesilencing-Rapidsilencingofprotein-codinggenes

Allopolyploidformationmaybeaccompaniedbyepigeneticgenesilencingthatisgenomicallyglobalandphylogeneticallywidespread.Moreover,theseepigeneticchangesmayoccurwiththeonsetofpolyploidyorccruemoreslowlyonanevolutionarytimeframe.Inatleastsomecases,rapidepigeneticmodificationsthatarisewiththeonsetofallopolyploidymaybepreservedonanevolutionarytimescalethroughmultiplespeciationevents.4.4Epigeneticgenesilencing-Epigeneticgenesilencing-Rapidsilencingofprotein-codinggenes

Adamsetal.(2003)usedanovelSSCPapproachtoseparatetranscriptsfromthetwohomoeologuesof40differentgenesduplicatedbyallopolyploidyincotton,theyshowedaremarkablyhighleveloftranscriptionbiaswithrespecttotheduplicatedcopies,inthat25%ofthegenesstudiedexhibitedalteredexpressioninoneormoreorgans.Epigeneticgenesilencing-RapiEpigeneticgenesilencing-Rapidsilencingofprotein-codinggenes

Themostrelevantandsurprisingresultwastheobservationofdevelopmentallyregulated,organ-specificgenesilencingthatinsomecaseswasreciprocal,meaningthatoneduplicatewasexpressedinoneorgan(e.g.,stamens),whileitscounterpartwasexpressedinadifferentorgan(e.g.,carpels).Moreover,thisorgan-specificpartitioningofduplicateexpressionwasalsoevidentinsyntheticallopolyploids.Epigeneticgenesilencing-Rapi5De-repressionofdormanttransposableelements

McClintockpredictedlongagothatinterspecifichybridizationcouldpotentiallyactivatedormantTEs,whichmightcausegenomerestructuring.MobilizedTEsmostlikelycausedeleteriousinsertions,particularlyunderconditionswherebyTEslosetheirpropensitytoinsertintonon-genicheterochromaticregions,suchasintheArabidopsisddm1mutantandintissueculture.5De-repressionofdormanttraDe-repressionofdormanttransposableelements

Itthusisconceivablethatunderdiploidconditions,e.g.,inadiploidhybrid,enhancedTEactivityislikelyaladaptive.Polyploidymaybebeneficial,becausetheharmfuleffectsofTEactivitymaybebufferedbygenomicredundancyandhenceinsertionswouldbemorelikelytobetolerated.De-repressionofdormanttrans6Transcriptome,Metabolome,andProteome

Genomicplasticityhasdownstreameffectsonthetranscriptome,proteome,andmetabolomethatcangeneratephenotypicvariationinpolyploidsexceedingthatfoundintheparents.Atthetranscriptomelevel,studiesonnaturalandsyntheticpolyploidshavedemonstratedgenomewidenonadditive,nonrandomchangesingeneregulation(e.g.,silencingandup-anddown-regulation),manyofwhichweretissueand/orspecies-specific.

6Transcriptome,Metabolome,aTranscriptome,Metabolome,andProteomeThereprogrammingoftheallopolyploidtranscriptomewastriggeredpredominantlybyinterspecifichybridizationratherthanbychromosomemultiplication.Fewstudiesintotheeffectsofpolyploidyontheproteome.InsyntheticBrassicaallopolyploids,25to38%(dependingontissue)ofproteinsdisplayedquantitativevariationfromanexpectedadditivepatternofproteinsfoundinthetwoparents,withchangesbeingrapidand,insomeinstances,nonstochastic,reproducible,andorgan-specific(lessthan1%ofchangeswerequalitative).Transcriptome,Metabolome,andTranscriptome,Metabolome,andProteomeBothcomponentsofallopolyploidycontributetotheirwidespreadoccurrence:(i)interspecifichybridizationtotriggerchangesatalllevelsfromthegenetoecologyand(ii)chromosomemultiplicationtoestablishthesechanges.Wenowfacethechallengetodeterminehowperturbationstothetranscriptome,metabolome,andproteomeinfluencethephenotypeandecology,requiringthetransferofmoleculartechnologiestoanecologicalsetting.Transcriptome,Metabolome,and7Possiblemechanismsforgeneticandepigeneticchenagesinallopolyploids7Possiblemechanismsforgene細胞遺傳學課件精編版細胞遺