细胞遗传学精课件

植物多倍体的遗传及表观遗传 Genetic and epigenetic changes in plant polyploids 1.1 主要参考文献Adams KL,Cronn R,Percifield R,Wendel JF.Genes duplicated by polyploidy show unequal contribution to the transcriptome and organ-specific reciprocal silencing.Proc Natl Acad Sci USA,2003,100:46494654Adams KL.Evolution of duplicate gene expression in polyploidy and hybrid plants.J Hered,2007,98:136-141Chen ZJ,Pikaard C.Transcriptional analysis of nucleolar dominance in polyploid plants:Biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica.Proc Natl Acad Sci USA,1997,94:3442-3447Chen ZJ.Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids.Ann Rev Plant Biol,2007,58:377-4062.Comai L.Genetic and epigenetic interactions in allopolyploid plants.Plant Mol Biol,2000,43:387399Comai L.The advantages and disadvantages of being polyploidy.Nat Rev Genet,2005,6:836-846Leitch AR,Leitch IJ.Genomic plasticity and the diversity of polyploidy plants.Sci,2008,320:481-483Liu B,Wendel JF.Non-Mendelian phenomena in allopolyploid genome evolution.Curr Genomics,2002,3:489-506Liu B,Wendel JF.Epigenetic phenomena and the evolution of plant allopolyploids.Mol Phylogenet Evol,2003,29:365-3793.Otto SP,Whitton J.Polyploidy incidence and evolution.Ann Rev Genet,2000,34:401-437Soltis PS,Soltis DE.The role of genetics and genomic attributes in the success of polyploids.Proc Natl Acad Sci USA,2000,97:7051-707 Song KM,Lu P,Tang K,Osborn TC.Rapid genome change in synthetic polyploids of Brassica and its implications for polyploids evolution.Proc Natl Acad Sci USA,1995,92:7719-7723 Stupar RM,Bhaskar PB,Yandell BS,et al.Phenotypic and transcriptomic changes associated with potato autopolyploidization.Genetics,2007,176:2055-2067Tate JA,Soltis DE,Soltis PS.2007.Polyploiy in plants.In:Gregory RT(ed)The Evolution of the Genome.Science Press,Beijing,pp372-4264.Wendel GF.Genome evolution in polyploids.Plant Mol Biol,2000,42:225-249 Wang JL,Tian L,Lee HS,Wei NE,Jiang HM,et al.Genomewide nonadditive gene regulation in Arabidopsis allotetraploids.Genetics,2006,172:507-517Yang SS,Cheung F,Lee JJ,Ha M,Wei NE,et al.Accumulation of genome-specific transcripts,transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton.Plant J,2006,47:76175 5.2 IntroductionAbundance of allopolyploid plantsPolyploidy,resulting from either duplication of a single but complete genome(autopolyploidy)or from combination of two or more differentiated genomes(allopolyploidy),is a prominent mode of speciation in plants.It is difficult to overstate the importance of polyploidy in the evolutionary history of plants.人类在合成多倍体方面收效甚微！6.Abundance of allopolyploid plantsWhile estimates vary regarding the proportion of angiosperms that have experienced one or more episodes of chromosome doubling at some point in their evolutionary history,it is at least 50%and may be higher than 70%;perhaps 95%of pteridophytes have experienced at least one episode of polyploidization in their past.7.8.Typical polyploid crops,wheat,oat,coffee,potato,canola,soybean,sugarcane,tobacco,cotton9.Abundance of allopolyploid plantsBecause most ancient polyploids have undergone an evolutionary process of chromosomal and perhaps genic“diploidization”,their polyploid history may be obscured at the cytological and classic genetics levels.Polyploid nature of many plant genomes was not evident until the advent of comparative genomics and whole-genome sequencing-maize,Arabidopsis traditionally diploids.10.Abundance of allopolyploid plantsGiven these and other recent examples from plants,it is probably safe to state that there are no bona fide diploid species in the plant kingdom.11.12.Production of Arabidopsis allotetraploids13.Production of Arabidopsis allotetraploids14.(a)Phenotypic variation of the plants after five generations of selfing.The plants include two parents,A.thaliana autotetraploid(At4)and A.arenosa(Aa),six allotetraploids(S1 to S6),and a natural allotetraploid,A.suecica(As).15.(b)Epigenetic silencing in resynthesized allopolyploids.A.suecica(As,white flower),natural allotetraploid.A.thaliana(not shown)and A.arenosa(Aa),have white and pink flowers.The flower colors in 3rd generation(S31,2,and 3)segregate from all white(S31)to all pink(S33).Variegated flower colors(S32).16.3 Non-Mendelian Phenomena in Allopolyploid Genome Evolutionnon-Mendelian attributes:those not characterized by conventional transmission genetics.Mysterious process of rapid and in some cases directed structural changes that occur in polyploid genomes upon their formation;Novel intergenomic interactions as a consequence of the merger of two formerly isolated genomes;17.Non-Mendelian Phenomena in Allopolyploid Genome EvolutionEpigenetic mechanisms in nascent allopolyploidy,such as nucleolar dominance,gene silencing and mobile element activation.These myriad phenomena do not characterize all polyploid systems,and some nascent allopolyploids appear to be genomically quiescent in this respect.18.3.1 RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSAccording to the classical view of allopolyploidy,the merger of two distinct but related genomes should result in genomic additivity with respect to the parental species.This expectation serves as a convenient null hypothesis of the predicted genomic contributions to a polyploid nucleus.19.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSNaturally occurring polyploids may not provide robust tests of the hypothesis,because their genomes,and those of their diploid progenitors,will have continued to evolve since polyploid formation,thereby obscuring initial conditions.20.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSBecause of this,insights into the earliest stages of polyploid genome evolution are likely to require the study of synthetic experimental allopolyploids.Recent studies in Brassica and in Aegilops-Triticum demonstrate that nascent allopolyploids often do not show genomic additivity with respect to their parents.21.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSInstead,their genomes display remarkable patterns of non-Mendelian genomic changes accompanying hybridization and polyploidization-a growing recognition of the dynamic and unpredictable nature of polyploid genomes.22.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSThe first study demonstrating extensive and rapidgenomic changes accompanying polyploid formation was by Song et al.,who used newly synthesized reciprocal synthetic allopolyploids in Brassica between the diploids B.rapa and B.nigra and the other from B.rapa and B.oleracea.Following colchicine-doubling,F2 individuals were recovered from which progenies up to the F5 generation were synthesized by self-pollination.23.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSSouthern hybridization analysis using 89 nuclear probes corresponding to cDNAs,known-function genes,and anonymous genomic clones revealed a high frequency of unexpected fragment profiles in each generation.These genomic changes included loss of parental fragments,recovery of parental fragments in the F5 that were not detected in the F2,and the frequent appearance of novel fragments,especially in allopolyploids involving B.rapa and B.nigra.24.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSThis latter observation reflects the quantitative conclusion that nearly twice as much change was detected in crosses involving the distant relatives B.rapa and B.nigra as in the more closely related B.rapa and B.oleracea.The changes were apparently random,as individuals from the same and different generations exhibited a great degree of variation.25.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSLoss=fragments present in diploids and in the F2 but not in Fs plants;gain=diploid parental fragments absent in F2 plants but present in Fs plants.A,B,and C=fragments specific to A,B,or C parental genomes;shared fragments=shared by both diploid parents;F2 fragments=found in the F2 but not in either diploid parent;novel fragments=found only in Fs plants.26.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSA similar phenomenon of unexplained gain and loss of DNA fragments was described from synthetic allopolyploids of the Aegilops-Triticum group.The wheat group provides an ideal system to study polyploid genome evolution because several allopolyploid species are young,their diploid progenitors are extant,and the phylogenetic relationships among the diploid species and between the diploids and polyploids are reasonably well understood.27.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSMoreover,allopolyploids can be readily synthesized in the laboratory by colchicine treatment.Perhaps of more significance,the young(8,500 year-old)natural hexaploid species Triticum aestivum(common or bread wheat),vital to the development and present sustenance of human civilization,is a classic example of speciation via allopolyploidy.28.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSA profound realization emerges from these studies on Brassica and Aegilops-Triticum,namely,that allopolyploidy can not only lead to the establishment of new species in a single generation,as has long been recognized,but that in the process the constituent genomes may be dramatically and virtually instantaneously altered.29.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSAt present,one can only speculate about the immediate morphological,physiological,and ecological consequences of rapid and directed hybridization-induced and polyploidy-induced genomic reorganization,but the potential relevance to adaptation and diversification is evident.This issue takes on added importance when one considers the prevalence of wide hybridization and polyploidy in plants.30.RAPID GENOMIC CHANGES IN NEWLYSYNTHESIZED ALLOPOLYPLOIDSOne question that naturally arises is whether the results for Brassica and Aegilops-Triticum will turn out to be typical or aberrant.It already is evident that rapid genomic change is not a hallmark of all nascent plant allopolyploids.A recent study in cotton(Gossypium)assayed approximately 22,000 genomic loci in nine sets of synthetic allopolyploids using AFLP fingerprinting,yet nearly perfect additivity was found with respect to parental AFLP banding profiles.31.4 Epigenetic phenomena in plant allopolyploidsAllopolyploid genesis under both synthetic and natural conditions often is accompanied by rapid and sometimes evolutionarily conserved epigenetic changes,including alteration in cytosine methylation patterns,rapid silencing in ribosomal RNA and protein coding genes,and de-repression of dormant transposable elements.These changes are inter-related and likely arise from chromatin remodeling and its effects on epigenetic codes during and subsequent to allopolyploid formation.32.Epigenetic phenomena in plant allopolyploidsThis epigenetic variation may contribute to several important attributes of allopolyploidy,including functional diversification or subfunctionalization of duplicated genes,genetic and cytological diploidization,and quenching of incompatible inter-genomic interactions that are characteristic of allopolyploids.Likely the evolutionary success of allopolyploidy is in part attributable to epigenetic phenomena that we are only just beginning to understand.33.4.1 Methylation repatterningAn integral component of the developmental control of gene expression and the maintenance of genome integrity in a diverse array of organisms is specific,programmed cytosine methylation.Hypermethylation usually is a hallmark of heterochromatin and is characteristic of euchromatic gene silencing,whereas hypomethylation is often associated with active gene expression.34.Methylation repatterningIt has been recognized for years that unusual environmental stimuli and passage through tissue culture may cause heritable changes in cytosine methylation patterns in plants.As a potential primary genome defense system,the cytosine methylation machinery may respond to environmental or genomic challenges by causing alterations in methylation that are thought to mediate physiologically meaningful responses to the challenge.35.Methylation repatterningAllopolyploidy,by uniting divergent genomes into one nucleus,may constitute such a challenge,or genomic shock(sensu McClintock,1984).This suggestion is supported by experimental evidence,which shows that in several nascent allopolyploid plants,including Brassica(Song et al.,1995),wheat(Kashkush et al.,2002;Liu et al.,1998a;Shaked et al.,2001)and Arabidopsis(Comai et al.,2000;Lee and Chen,2001;Madlung et al.,2002),allopolyploid formation leads to heritably re-patterned cytosine DNA methylation.36.4.2 Epigenetic gene silencingNascent allopolyploids often are associated with variation and instability in phenotypes that cannot be accounted for by conventional Mendelian transmission genetics or chromosomal aberrations(Comai,2000;Comai et al.,2000).The affected traits are diverse,including timing of flowering,overall plant habit,leaf morphology,and homeotic transformations in floral morphology(Comai et al.,2000;Schranz and Osborn,2000).37.Epigenetic gene silencingIt has been suggested that these allopolyploidy associated changes in phenotypes are the outcome of altered gene expression due to various causes,including increased variation in dosage-regulated gene expression,altered regulatory interactions,and rapid genetic and epigenetic changes,which are probably conferred by genome-wide interactions.38.4.3 Epigenetic gene silencing-Nucleolar dominanceNucleolar dominance refers to the phenomenon in hybrids or allopolyploids whereby nucleoli form,in association with ribosomal RNA genes,on chromosomes inherited from only one of the two parents.Although this phenomenon had been intensively studied since its discovery in 1934(Navashin,1934),its molecular basis is not fully understood.39.Epigenetic gene silencing-Nucleolar dominancerRNA transcripts from only one of the parental genomes were detectable in vegetative tissues of both natural and synthetic allopolyploids,thus indicating rapid occurrence of the phenomenon as well as its evolutionary conservation.rRNA genes silenced in vegetative tissues are derepressed in reproductive organs,indicating not only reversibility of the phenomenon,but also differential partitioning of rDNA array expression during allotetraploid plant development.40.芸苔属六个栽培种之芸苔属六个栽培种之间间的的细细胞胞遗传遗传学关系学关系(U,1935).四倍体中核仁四倍体中核仁显显性性(nucleolar dominance)的梯度的梯度为为 B.nigraB.rapaB.oleracea.PNAS,1997,94:3442黑芥黑芥埃芥埃芥甘甘蓝蓝甘甘蓝蓝型油菜型油菜白菜型油菜白菜型油菜芥菜型油菜芥菜型油菜41.4.4 Epigenetic gene silencing-Rapid silencing of protein-coding genesAllopolyploid formation may be accompanied by epigenetic gene silencing that is genomically global and phylogenetically widespread.Moreover,these epigenetic changes may occur with the onset of polyploidy or ccrue more slowly on an evolutionary time frame.In at least some cases,rapid epigenetic modifications that arise with the onset of allopolyploidy may be preserved on an evolutionary timescale through multiple speciation events.42.Epigenetic gene silencing-Rapid silencing of protein-coding genesAdams et al.(2003)used a novel SSCP approach to separate transcripts from the two homoeologues of 40 different genes duplicated by allopolyploidy in cotton,they showed a remarkably high level of transcription bias with respect to the duplicated copies,in that 25%of the genes studied exhibited altered expression in one or more organs.43.Epigenetic gene silencing-Rapid silencing of protein-coding genesThe most relevant and surprising result was the observation of developmentally regulated,organ-specific gene silencing that in some cases was reciprocal,meaning that one duplicate was expressed in one organ(e.g.,stamens),while its counterpart was expressed in a different organ(e.g.,carpels).Moreover,this organ-specific partitioning of duplicate expression was also evident in synthetic allopolyploids.44.5 De-repression of dormant transposable elementsMcClintock predicted long ago that interspecific hybridization could potentially activate dormant TEs,which might cause genome restructuring.Mobilized TEs most likely cause deleterious insertions,particularly under conditions whereby TEs lose their propensity to insert into non-genic heterochromatic regions,such as in the Arabidopsis ddm1 mutant and in tissue culture.45.De-repression of dormant transposable elementsIt thus is conceivable that under diploid conditions,e.g.,in a diploid hybrid,enhanced TE activity is likely aladaptive.Polyploidy may be beneficial,because the harmful effects of TE activity may be buffered by genomic redundancy and hence insertions would be more likely to be tolerated.46.6 Transcriptome,Metabolome,and ProteomeGenomic plasticity has downstream effects on the transcriptome,proteome,and metabolome that can generate phenotypic variation in polyploids exceeding that found in the parents.At the transcriptome level,studies on natural and synthetic polyploids have demonstrated genomewide nonadditive,nonrandom changes in gene regulation(e.g.,silencing and up-and down-regulation),many of which were tissue and/or species-specific.47.Transcriptome,Metabolome,and ProteomeThe reprogramming of the allopolyploid transcriptome was triggered predominantly by interspecific hybridization rather than by chromosome multiplication.Few studies into the effects of polyploidy on the proteome.In synthetic Brassica allopolyploids,25 to 38%(depending on tissue)of proteins displayed quantitative variation from an expected additive pattern of proteins found in the two parents,with changes being rapid and,in some instances,nonstochastic,reproducible,and organ-specific(less than 1%of changes were qualitative).48.Transcriptome,Metabolome,and ProteomeBoth components of allopolyploidy contribute to their widespread occurrence:(i)interspecific hybridization to trigger changes at all levels from the gene to ecology and(ii)chromosome multiplication to establish these changes.We now face the challenge to determine how perturbations to the transcriptome,metabolome,and proteome influence the phenotype and ecology,requiring the transfer of molecular technologies to an ecological setting.49.7 Possible mechanisms for genetic and epigenetic chenages in allopolyploids50.51.52.Figure.A wheel of the models for polyploidy-dependent genomic rearrangements and gene regulation.Eight types of observed changes(bold-type fonts)and their underlying mechanisms(italicized fonts)were arranged circularly around an allotetraploid cell(center).The changes may be mediated by genetic(DNA sequence-dependent,top and red),epigenetic(DNA sequence-independent,bottom and green)mechanisms or both(middle and light blue).The distinctions among some of the classified changes and underlying mechanisms may not be very clear.53.Additional research is needed in order to provide experimental data for these models.Note that a polyploid organism may experience some but not all changes listed in the diagram.For instance,genomic sequence rearrangements were predominately detected in Brassica and wheat allopolyploids but not in Arabidopsis and cotton allopolyploids.The thickness of arrows may correspond to an arbitrarily level of the changes that have been documented in the polyploids.54.8 Conclusions and Future ProspectsIn angiosperms,allopolyploidy triggers a new steady state for the transcriptome,metabolome,and proteome networks and perhaps enhances network robustness and/or increases network complexity.It is genomic plasticity that enables step changes in the steady state,equipping newly originated polyploid individuals with novel biochemical pathways and transgressive characters and allowing them to exploit new niches and/or outcompete diploid parents.55.FUTURE ISSUESAddressing the following questions is essential to illuminate new insights into molecula