植物多倍體的遺傳及表觀遺傳

Geneticandepigeneticchangesinplantpolyploids

1.1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,2007,58:377-4062.ComaiL.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,2003,29:365-3793.OttoSP,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,pp372-4264.WendelGF.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,

47:761–755.2Introduction－

AbundanceofallopolyploidplantsPolyploidy,resultingfromeitherduplicationofasinglebutcompletegenome(autopolyploidy)orfromcombinationoftwoormoredifferentiatedgenomes(allopolyploidy),isaprominentmodeofspeciationinplants.Itisdifficulttooverstatetheimportanceofpolyploidyintheevolutionaryhistoryofplants.人類在合成多倍體方面收效甚微！6.AbundanceofallopolyploidplantsWhileestimatesvaryregardingtheproportionofangiospermsthathaveexperiencedoneormoreepisodesofchromosomedoublingatsomepointintheirevolutionaryhistory,itisatleast50%andmaybehigherthan70%;perhaps95%ofpteridophyteshaveexperiencedatleastoneepisodeofpolyploidizationintheirpast.7.8.

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

9.AbundanceofallopolyploidplantsBecausemostancientpolyploidshaveundergoneanevolutionaryprocessofchromosomalandperhapsgenic“diploidization”,theirpolyploidhistorymaybeobscuredatthecytologicalandclassicgeneticslevels.Polyploidnatureofmanyplantgenomeswasnotevidentuntiltheadventofcomparativegenomicsandwhole-genomesequencing-maize,Arabidopsis—traditionallydiploids.

10.AbundanceofallopolyploidplantsGiventheseandotherrecentexamplesfromplants,itisprobablysafetostatethattherearenobonafidediploidspeciesintheplantkingdom.11.12.ProductionofArabidopsisallotetraploids13.ProductionofArabidopsisallotetraploids14.(a)Phenotypicvariationoftheplantsafterfivegenerationsofselfing.Theplantsincludetwoparents,A.thalianaautotetraploid(At4)andA.arenosa(Aa),sixallotetraploids(S–1toS–6),andanaturalallotetraploid,A.suecica(As).15.(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).

16.

3Non-MendelianPhenomenainAllopolyploidGenomeEvolution

non-Mendelianattributes:thosenotcharacterizedbyconventionaltransmissiongenetics.Mysteriousprocessofrapidandinsomecasesdirectedstructuralchangesthatoccurinpolyploidgenomesupontheirformation;Novelintergenomicinteractionsasaconsequenceofthemergeroftwoformerlyisolatedgenomes;17.Non-MendelianPhenomenainAllopolyploidGenomeEvolution

Epigeneticmechanismsinnascentallopolyploidy,suchasnucleolardominance,genesilencingandmobileelementactivation.Thesemyriadphenomenadonotcharacterizeallpolyploidsystems,andsomenascentallopolyploidsappeartobegenomicallyquiescentinthisrespect.18.3.1RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Accordingtotheclassicalviewofallopolyploidy,themergeroftwodistinctbutrelatedgenomesshouldresultingenomicadditivitywithrespecttotheparentalspecies.Thisexpectationservesasaconvenientnullhypothesisofthepredictedgenomiccontributionstoapolyploidnucleus.19.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Naturallyoccurringpolyploidsmaynotproviderobusttestsofthehypothesis,becausetheirgenomes,andthoseoftheirdiploidprogenitors,willhavecontinuedtoevolvesincepolyploidformation,therebyobscuringinitialconditions.20.

RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Becauseofthis,insightsintotheearlieststagesofpolyploidgenomeevolutionarelikelytorequirethestudyofsyntheticexperimentalallopolyploids.RecentstudiesinBrassicaandinAegilops-Triticumdemonstratethatnascentallopolyploidsoftendonotshowgenomicadditivitywithrespecttotheirparents.21.

RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDS

Instead,theirgenomesdisplayremarkablepatternsofnon-Mendeliangenomicchangesaccompanyinghybridizationandpolyploidization--agrowingrecognitionofthedynamicandunpredictablenatureofpolyploidgenomes.22.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSThefirststudydemonstratingextensiveandrapidgenomicchangesaccompanyingpolyploidformationwasbySongetal.,whousednewlysynthesizedreciprocalsyntheticallopolyploidsinBrassicabetweenthediploidsB.rapaandB.nigraandtheotherfromB.rapaandB.oleracea.Followingcolchicine-doubling,F2individualswererecoveredfromwhichprogeniesuptotheF5generationweresynthesizedbyself-pollination.23.RAPIDGENOMICCHANGESINNEWLY

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

24.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSThislatterobservationreflectsthequantitativeconclusionthatnearlytwiceasmuchchangewasdetectedincrossesinvolvingthedistantrelativesB.rapaandB.nigraasinthemorecloselyrelatedB.rapaandB.oleracea.Thechangeswereapparentlyrandom,asindividualsfromthesameanddifferentgenerationsexhibitedagreatdegreeofvariation.25.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSLoss=fragmentspresentindiploidsandintheF2butnotinFsplants;gain=diploidparentalfragmentsabsentinF2plantsbutpresentinFsplants.A,B,andC=fragmentsspecifictoA,B,orCparentalgenomes;sharedfragments=sharedbybothdiploidparents;F2fragments=foundintheF2butnotineitherdiploidparent;novelfragments=foundonlyinFsplants.26.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSAsimilarphenomenonofunexplainedgainandlossofDNAfragmentswasdescribedfromsyntheticallopolyploidsoftheAegilops-Triticumgroup.Thewheatgroupprovidesanidealsystemtostudypolyploidgenomeevolutionbecauseseveralallopolyploidspeciesareyoung,theirdiploidprogenitorsareextant,andthephylogeneticrelationshipsamongthediploidspeciesandbetweenthediploidsandpolyploidsarereasonablywellunderstood.27.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSMoreover,allopolyploidscanbereadilysynthesizedinthelaboratorybycolchicinetreatment.Perhapsofmoresignificance,theyoung(~8,500year-old)naturalhexaploidspeciesTriticumaestivum(commonorbreadwheat),vitaltothedevelopmentandpresentsustenanceofhumancivilization,isaclassicexampleofspeciationviaallopolyploidy.28.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSAprofoundrealizationemergesfromthesestudiesonBrassicaandAegilops-Triticum,namely,thatallopolyploidycannotonlyleadtotheestablishmentofnewspeciesinasinglegeneration,ashaslongbeenrecognized,butthatintheprocesstheconstituentgenomesmaybedramaticallyandvirtuallyinstantaneouslyaltered.29.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSAtpresent,onecanonlyspeculateabouttheimmediatemorphological,physiological,andecologicalconsequencesofrapidanddirectedhybridization-inducedandpolyploidy-inducedgenomicreorganization,butthepotentialrelevancetoadaptationanddiversificationisevident.Thisissuetakesonaddedimportancewhenoneconsiderstheprevalenceofwidehybridizationandpolyploidyinplants.30.RAPIDGENOMICCHANGESINNEWLY

SYNTHESIZEDALLOPOLYPLOIDSOnequestionthatnaturallyarisesiswhethertheresultsforBrassicaandAegilops-Triticumwillturnouttobetypicaloraberrant.Italreadyisevidentthatrapidgenomicchangeisnotahallmarkofallnascentplantallopolyploids.Arecentstudyincotton(Gossypium)assayedapproximately22,000genomiclociinninesetsofsyntheticallopolyploidsusingAFLPfingerprinting,yetnearlyperfectadditivitywasfoundwithrespecttoparentalAFLPbandingprofiles.31.4Epigeneticphenomenainplantallopolyploids

Allopolyploidgenesisunderbothsyntheticandnaturalconditionsoftenisaccompaniedbyrapidandsometimesevolutionarilyconservedepigeneticchanges,includingalterationincytosinemethylationpatterns,rapidsilencinginribosomalRNAandproteincodinggenes,andde-repressionofdormanttransposableelements.Thesechangesareinter-relatedandlikelyarisefromchromatinremodelinganditseffectsonepigeneticcodesduringandsubsequenttoallopolyploidformation.32.EpigeneticphenomenainplantallopolyploidsThisepigeneticvariationmaycontributetoseveralimportantattributesofallopolyploidy,includingfunctionaldiversificationorsubfunctionalizationofduplicatedgenes,geneticandcytologicaldiploidization,andquenchingofincompatibleinter-genomicinteractionsthatarecharacteristicofallopolyploids.Likelytheevolutionarysuccessofallopolyploidyisinpartattributabletoepigeneticphenomenathatweareonlyjustbeginningtounderstand.33.4.1Methylationrepatterning

Anintegralcomponentofthedevelopmentalcontrolofgeneexpressionandthemaintenanceofgenomeintegrityinadiversearrayoforganismsisspecific,programmedcytosinemethylation.Hypermethylationusuallyisahallmarkofheterochromatinandischaracteristicofeuchromaticgenesilencing,whereashypomethylationisoftenassociatedwithactivegeneexpression.34.Methylationrepatterning

Ithasbeenrecognizedforyearsthatunusualenvironmentalstimuliandpassagethroughtissueculturemaycauseheritablechangesincytosinemethylationpatternsinplants.Asapotentialprimarygenomedefensesystem,thecytosinemethylationmachinerymayrespondtoenvironmentalorgenomicchallengesbycausingalterationsinmethylationthatarethoughttomediatephysiologicallymeaningfulresponsestothechallenge.35.Methylationrepatterning

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.36.4.2Epigeneticgenesilencing

NascentallopolyploidsoftenareassociatedwithvariationandinstabilityinphenotypesthatcannotbeaccountedforbyconventionalMendeliantransmissiongeneticsorchromosomalaberrations(Comai,2000;Comaietal.,2000).Theaffectedtraitsarediverse,includingtimingofflowering,overallplanthabit,leafmorphology,andhomeotictransformationsinfloralmorphology(Comaietal.,2000;SchranzandOsborn,2000).37.EpigeneticgenesilencingIthasbeensuggestedthattheseallopolyploidyassociatedchangesinphenotypesaretheoutcomeofalteredgeneexpressionduetovariouscauses,includingincreasedvariationindosage-regulatedgeneexpression,alteredregulatoryinteractions,andrapidgeneticandepigeneticchanges,whichareprobablyconferredbygenome-wideinteractions.38.4.3Epigeneticgenesilencing-Nucleolardominance

Nucleolardominancereferstothephenomenoninhybridsorallopolyploidswherebynucleoliform,inassociationwithribosomalRNAgenes,onchromosomesinheritedfromonlyoneofthetwoparents.Althoughthisphenomenonhadbeenintensivelystudiedsinceitsdiscoveryin1934(Navashin,1934),itsmolecularbasisisnotfullyunderstood.39.Epigeneticgenesilencing-NucleolardominancerRNAtranscriptsfromonlyoneoftheparentalgenomesweredetectableinvegetativetissuesofbothnaturalandsyntheticallopolyploids,thusindicatingrapidoccurrenceofthephenomenonaswellasitsevolutionaryconservation.rRNAgenessilencedinvegetativetissuesarederepressedinreproductiveorgans,indicatingnotonlyreversibilityofthephenomenon,butalsodifferentialpartitioningofrDNAarrayexpressionduringallotetraploidplantdevelopment.40.蕓苔屬六個栽培種之間的細胞遺傳學關系(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41.4.4Epigeneticgenesilencing-Rapidsilencingofprotein-codinggenes

Allopolyploidformationmaybeaccompaniedbyepigeneticgenesilencingthatisgenomicallyglobalandphylogeneticallywidespread.Moreover,theseepigeneticchangesmayoccurwiththeonsetofpolyploidyorccruemoreslowlyonanevolutionarytimeframe.Inatleastsomecases,rapidepigeneticmodificationsthatarisewiththeonsetofallopolyploidymaybepreservedonanevolutionarytimescalethroughmultiplespeciationevents.42.Epigeneticgenesilencing-Rapidsilencingofprotein-codinggenes

Adamsetal.(2003)usedanovelSSCPapproachtoseparatetranscriptsfromthetwohomoeologuesof40differentgenesduplicatedbyallopolyploidyincotton,theyshowedaremarkablyhighleveloftranscriptionbiaswithrespecttotheduplicatedcopies,inthat25%ofthegenesstudiedexhibitedalteredexpressioninoneormoreorgans.43.Epigeneticgenesilencing-Rapidsilencingofprotein-codinggenes

Themostrelevantandsurprisingresultwastheobservationofdevelopmentallyregulated,organ-specificgenesilencingthatinsomecaseswasreciprocal,meaningthatoneduplicatewasexpressedinoneorgan(e.g.,stamens),whileitscounterpartwasexpressedinadifferentorgan(e.g.,carpels).Moreover,thisorgan-specificpartitioningofduplicateexpressionwasalsoevidentinsyntheticallopolyploids.44.5De-repressionofdormanttransposableelements

McClintockpredictedlongagothatinterspecifichybridizationcouldpotentiallyactivatedormantTEs,whichmightcausegenomerestructuring.MobilizedTEsmostlikelycausedeleteriousinsertions,particularlyunderconditionswherebyTEslosetheirpropensitytoinsertintonon-genicheterochromaticregions,suchasintheArabidopsisddm1mutantandintissueculture.45.De-repressionofdormanttransposableelements

Itthusisconceivablethatunderdiploidconditions,e.g.,inadiploidhybrid,enhancedTEactivityislikelyaladaptive.Polyploidymaybebeneficial,becausetheharmfuleffectsofTEactivitymaybebufferedbygenomicredundancyandhenceinsertionswouldbemorelikelytobetolerated.46.6Transcriptome,Metabolome,andProteome

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

47.Transcriptome,Metabolome,andProteomeThereprogrammingoftheallopolyploidtranscriptomewastriggeredpredominantlybyinterspecifichybridizationratherthanbychromosomemultiplication.Fewstudiesintotheeffectsofpolyploidyontheproteome.InsyntheticBrassicaallopolyploids,25to38%(dependingontissue)ofproteinsdisplayedquantitativevariationfromanexpectedadditivepatternofproteinsfoundinthetwoparents,withchangesbeingrapidand,insomeinstances,nonstochastic,reproducible,andorgan-specific(lessthan1%ofchangeswerequalitative).48.Transcriptome,Metabolome,andProteomeBothcomponentsofallopolyploidycontributetotheirwidespreadoccurrence:(i)interspecifichybridizationtotriggerchangesatalllevelsfromthegenetoecologyand(ii)chromosomemultiplicationtoestablishthesechanges.Wenowfacethechallengetodeterminehowperturbationstothetranscriptome,metabolome,andproteomeinfluencethephenotypeandecology,requiringthetransferofmoleculartechnologiestoanecologicalsetting.49.7Possiblemechanismsforgeneticandepigeneticchenagesinallopolyploids50.51.52.Figure.Awheelofthemodelsforpolyploidy-depe