细胞遗传学课件精编版

植物多倍体的遗传及表观遗传

Geneticandepigeneticchangesinplantpolyploids

植物多倍体的遗传及表观遗传

Geneticandep1主要参考文献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主要参考文献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.人类在合成多倍体方面收效甚微！2Introduction－

AbundanceofaAbundanceofallopolyploidplantsWhileestimatesvaryregardingtheproportionofangiospermsthathaveexperiencedoneormoreepisodesofchromosomedoublingatsomepointintheirevolutionaryhistory,itisatleast50%andmaybehigherthan70%;perhaps95%ofpteridophyteshaveexperiencedatleastoneepisodeofpolyploidizationintheirpast.Abundanceofallopolyploidpla细胞遗传学课件精编版

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

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

AbundanceofallopolyploidplaAbundanceofallopolyploidplantsGiventheseandotherrecentexamplesfromplants,itisprobablysafetostatethattherearenobonafidediploidspeciesintheplantkingdom.Abundanceofallopolyploidpla细胞遗传学课件精编版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芸苔属六个栽培种之间的细胞遗传学关系(U,1935).四倍体中核仁显性(nucleolardominance)的梯度为B.nigra>B.rapa>B.oleracea.PNAS,1997,94:3442黑芥埃芥甘蓝甘蓝型油菜白菜型油菜芥菜型油菜芸苔属六个栽培种之间的细胞遗传学关系(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细胞遗传学课件精编版细胞遗