the causes and molecular consequences of polyploidy in...

19
Ann. N.Y. Acad. Sci. ISSN 0077-8923 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES Issue: The Year in Evolutionary Biology The causes and molecular consequences of polyploidy in flowering plants Gaurav D. Moghe 1,2 and Shin-Han Shiu 1,2,3 1 Programs in Genetics, 2 Quantitative Biology, and 3 Department of Plant Biology, Michigan State University, East Lansing, Michigan Address for correspondence: Shin-Han Shiu, Department of Plant Biology, Michigan State University, 2265 Molecular Plant Sciences Building, East Lansing, MI 48824. [email protected] Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploid species, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century, a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In this review, we summarize our current understanding of the causes and molecular consequences of polyploidization in angiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areas where further research may provide a better understanding of polyploidy. Keywords: whole-genome duplication; plants; adaptation; expression divergence; fractionation; molecular conse- quences of polyploidy Introduction Polyploidization results in multiplication of the genome and an increase in gene content that fre- quently leads to morphological and physiological differences between polyploids and their diploid progenitors. 1 Polyploidy is widespread among flow- ering plants 2,3 and has been postulated as an answer to Darwin’s “abominable mystery” regarding the causes behind the rapid acceleration in the diversifi- cation of angiosperms. 4,5 It is also a major route for origination of new genes via gene duplication and subsequent diversification. 6,7 Although we have a fairly good understanding about the extent of poly- ploidy in eukaryotes 8–10 and the modes of diversifi- cation of duplicate genes derived from polyploidy, 11 there is still a considerable debate about whether polyploidy indeed confers an evolutionary advan- tage to the organism and if it does, whether it con- tributes to speciation. In addition, although the pri- mary pathways of polyploid generation have been known for some time, 12 only recently have we be- gun to identify the molecular consequences of poly- ploidization. In this review, we first focus on the genetic and environmental factors that influence the rates of polyploidization. Second, we discuss the impact of polyploidization at the molecular level. Third, we summarize recent studies on the impact of poly- ploidy on morphology, physiology, and stress bi- ology. Finally, we discuss current evidence on how polyploidy contributes to adaptation and specia- tion. Our goal in this review is to present a brief overview of our current state of understanding re- garding a few different aspects of polyploidy. For ad- ditional information, we refer the reader to several excellent resources 2,3,13–17 that have covered these topics in greater detail. Causes of polyploidization in flowering plants Cytological pathways leading to polyploidization Diploids mostly propagate by producing haploid ga- metes, which combine to produce diploid progeny (Fig. 1A). In rare cases, polyploids can arise through the somatic doubling of chromosomes in the zygote (Fig. 1B) or through the production of unreduced gametes (Fig. 1C–E). The primary mechanism for polyploid generation is thought to be the latter. 12,18 Theoretical models considering unreduced gamete doi: 10.1111/nyas.12466 1 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C 2014 New York Academy of Sciences.

Upload: hanguyet

Post on 20-Aug-2018

223 views

Category:

Documents


0 download

TRANSCRIPT

Ann. N.Y. Acad. Sci. ISSN 0077-8923

ANNALS OF THE NEW YORK ACADEMY OF SCIENCESIssue: The Year in Evolutionary Biology

The causes and molecular consequences of polyploidyin flowering plants

Gaurav D. Moghe1,2 and Shin-Han Shiu1,2,3

1Programs in Genetics, 2Quantitative Biology, and 3Department of Plant Biology, Michigan State University, East Lansing,Michigan

Address for correspondence: Shin-Han Shiu, Department of Plant Biology, Michigan State University, 2265 Molecular PlantSciences Building, East Lansing, MI 48824. [email protected]

Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploidspecies, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century,a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In thisreview, we summarize our current understanding of the causes and molecular consequences of polyploidization inangiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areaswhere further research may provide a better understanding of polyploidy.

Keywords: whole-genome duplication; plants; adaptation; expression divergence; fractionation; molecular conse-

quences of polyploidy

Introduction

Polyploidization results in multiplication of thegenome and an increase in gene content that fre-quently leads to morphological and physiologicaldifferences between polyploids and their diploidprogenitors.1 Polyploidy is widespread among flow-ering plants2,3 and has been postulated as an answerto Darwin’s “abominable mystery” regarding thecauses behind the rapid acceleration in the diversifi-cation of angiosperms.4,5 It is also a major route fororigination of new genes via gene duplication andsubsequent diversification.6,7 Although we have afairly good understanding about the extent of poly-ploidy in eukaryotes8–10 and the modes of diversifi-cation of duplicate genes derived from polyploidy,11

there is still a considerable debate about whetherpolyploidy indeed confers an evolutionary advan-tage to the organism and if it does, whether it con-tributes to speciation. In addition, although the pri-mary pathways of polyploid generation have beenknown for some time,12 only recently have we be-gun to identify the molecular consequences of poly-ploidization.

In this review, we first focus on the genetic andenvironmental factors that influence the rates of

polyploidization. Second, we discuss the impact ofpolyploidization at the molecular level. Third, wesummarize recent studies on the impact of poly-ploidy on morphology, physiology, and stress bi-ology. Finally, we discuss current evidence on howpolyploidy contributes to adaptation and specia-tion. Our goal in this review is to present a briefoverview of our current state of understanding re-garding a few different aspects of polyploidy. For ad-ditional information, we refer the reader to severalexcellent resources2,3,13–17 that have covered thesetopics in greater detail.

Causes of polyploidization in floweringplants

Cytological pathways leading topolyploidizationDiploids mostly propagate by producing haploid ga-metes, which combine to produce diploid progeny(Fig. 1A). In rare cases, polyploids can arise throughthe somatic doubling of chromosomes in the zygote(Fig. 1B) or through the production of unreducedgametes (Fig. 1C–E). The primary mechanism forpolyploid generation is thought to be the latter.12,18

Theoretical models considering unreduced gamete

doi: 10.1111/nyas.12466

1Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

2X

X

Zygotesomatic doubling

B C

E

Parents

Gametes

F1

A

D

2X

X

2X

2X

X

2X

X

2X

4X

2X

2X

2X

2X

4X

Unreducedgameteformation

Parents

Gametes

F1

F1gametes

F2

2X

X

2X

X

2X

AP X 2X

X 2X

X 2X 3X

2X 3X 4X

Gam

ete

2

Gamete 1

Gam

ete

2

Gamete 1

X 2X 3X

X 2X 3X 4X

2X 3X 4X 5X

3X 4X 5X 6X

2X

2X

2X

X

3X

AP X 2X 3X

Figure 1. Pathways of tetraploid formation from diploidplants. The symbol X represents the base chromosome num-ber of the species, with 1X corresponding to haploid gametes.(A) The normal pathway wherein a diploid is produced as F1progeny of two diploid parents. (B) Somatic doubling leadingto tetraploid (4X) generation from diploid. (C) Fusion of unre-duced gametes can lead to tetraploid generation in one step. (D)A diploid produced in F1 may generate a certain proportionof aneuploid gametes (AP, most of which are not viable) andunreduced gametes that can lead to tetraploid generation in F2.The frequency of unreduced gamete formation can be high ifthe parents belong to different species and F1 is a hybrid. (E)The triploid bridge scenario where an intermediate triploid pro-duces unreduced gametes leading to generation of tetraploidsand individuals of higher ploidy. These pathways of tetraploidformation have been adapted from information presented inRef. 12. For examples of polypoids formed via each pathway,as well as pathways of formation of polyploids of higher ploidylevels, please refer to the original publication.

formation and fertilities of plants with differentploidy levels have been used to predict equilibriumploidy frequencies.19–21 Notably, to fit the exist-ing data on ploidy frequency observed in multipleautopolyploid species, the unreduced gamete fre-quency was estimated to be 0.89%.21 This high rateof unreduced gamete production is consistent withits involvement in angiosperm polyploidy.

Unreduced gametes can be formed in three dif-ferent ways: (1) premeiotic genome doubling dueto endoreplication mechanisms, including endocy-cling (alternating periods of S phase, where DNA isreplicated, and gap phase, without cell division), en-domitosis (mitosis without the final cell division),22

or nuclear fusion; (2) impairments in meiosis, whichcan affect either the first or the second meiotic divi-sions; and (3) postmeiotic genome doubling.12 Theunreduced gametes from diploids (2X, with X beingthe base chromosome number of the species) canlead to a tetraploid (4X) in one step by hybridiza-tion between unreduced male and female gametes(type I pathway (Fig. 1C–D)) or through the cre-ation of an intermediate triploid (type II pathway(Fig. 1E)).19 Given that unreduced gametes can beproduced at an appreciable frequency,21 it is con-ceivable that unreduced gametes generated in twoindividuals, or from the same individual (if selfingis feasible), may hybridize and generate polyploidsthrough the type I pathway.

In the type II pathway, an unreduced gamete hy-bridizes with a normal gamete to produce a triploidplant (3X). The triploid produces mostly aneuploidgametes, which are generally not viable, and a smallpercentage of viable X, 2X, or 3X gametes. Thesegametes can then hybridize with other X, 2X, or 3Xgametes to generate plants of higher ploidy levels(Fig. 1E). Hence, triploid plants are regarded as abridge toward polyploidy (triploid bridge), ratherthan a dead end (triploid block).12 Currently, it re-mains unclear which pathway is more prevalent.13

Although the production of 3X gametes required inthe type II pathway would be rare in nature, unre-duced gametes in artificially generated hybrids ofmultiple Brassica species are produced at a muchhigher frequency than in their parents. These ga-metes have a size distribution corresponding to >2Xgenome complement, and they are more viable thanreduced gametes in the Brassica hybrids. These re-sults support the hypothesis that the triploid bridgescenario may be more prevalent for polyploids gen-erated from interspecific hybridridization.12

Genetic components contributing topolyploidizationSeveral Arabidopsis thaliana genes that can influ-ence the frequency of unreduced gamete forma-tion have been identified.23,24 For example, �60%of the seeds produced from a mutated version of the

2 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

SWI1/DYAD protein are triploid.25 SWI1/DYAD isrequired for a proper meiosis I in both male andfemale germ cells. In the SWI1/DYAD mutant, cellsskip the reduction division in meiosis I and directlyadvance to the equatorial division in meiosis II, pro-ducing predominantly unreduced gametes.26,27 Mu-tations in several other genes lead to the productionof unreduced gametes by affecting different meioticand mitotic steps. For example, mutations in thegene for the GLUCAN SYNTHASE LIKE 8 protein,which lays down the glucan chains at cell plates dur-ing cell division, lead to a flower containing bothdiploid and polyploid somatic cells. The polyploidcells then go on to produce unreduced gametes.28

As discussed earlier, one important step in thepathway to polyploidy is the formation of triploidintermediates. The major challenge upon formingthis intermediate is the triploid block, originally de-scribed as the difficulty in generating viable triploidsthrough diploid–tetraploid crosses,29 which canlead to reproductive isolation of the newly formedpolyploid owing to minority cytotype exclusion.30

A recent study demonstrated that one genetic com-ponent of the triploid block in A. thaliana is thepaternally expressed gene ADMETOS.31 This studyinvolved a mutant screen in a JASON mutant back-ground, which produces unreduced gametes at ahigh frequency, but 30% of the triploid seeds pro-duced are aborted. The ADMETOS-1 JASON dou-ble mutant, on the other hand, has only 2% abortedtriploid seeds. The ADMETOS-1 mutant is a gain-of-function mutant with elevated expression of theADMETOS gene.31 These results suggest that there isgenetic control over triploid formation. While suchgenetic control may exist to create a postzygotic re-productive barrier for gene flow between species,naturally occurring variation in such control mech-anisms may provide an opportunity for polyploidsto be generated.

On the basis of the finding that unreduced gameteformation is a trait with high heritability (e.g., 0.40–0.60 in alfalfa and clover32,33), at least in domesti-cated crops experiencing artificial selection, poly-ploid formation through unreduced gamete andtriploid bridge formation is expected to have a sig-nificant genetic component. Although these geneticstudies are highly informative, it remains unclearwhether these newly identified genes are involved inincreasing or decreasing the rate of polyploid for-mation in nature. If these genes are the targets of

selection for polyploidization frequency, they maydisplay substantial variation between plant speciesand/or populations that have variable relative abun-dances of individuals with different ploidy levels.

Relationship between environment andpolyploidyNearly 80 years ago, it was demonstrated that a cor-relation exists between polyploidy and latitudinalcline,34 suggesting potential habitat differentiationbetween plants with different ploidy levels due to thedifferences in latitudinal environment. In addition,it was shown in 1920 that hot water–treated Pisumroot tips have increased frequency of tetraploidy insomatic cells.35 In 1932, Randolf demonstrated thathigh temperature (47–48 °C) results in an increasedfrequency of tetraploid embryos in maize.36 Subse-quently, a number of studies have established thattemperature stress, herbivory, pathogen attack, nu-tritional stress, and water stress, lead to an elevatedrate of unreduced gamete production.12

In addition to observations linking environmen-tal stress, polyploidy, and unreduced gamete pro-duction, a large number of studies have focused onhow environment influences chromosome behav-ior and unreduced gamete production.18 Althoughunreduced gametes can be produced due to pre-meiotic, meiotic, or postmeiotic aberrations, re-cent studies have shown that environmentally in-duced production of unreduced pollen is mainlydue to meiotic irregularities, particularly duringtelophase II. In Rosa species, the proportion of unre-duced pollen produced due to elevated temperature(36 °C) differs greatly at different microsporestages.37 The elevated temperature led to formationof normal rose pollen tetrads as well as abnormaldyads, triads, and polyads as a result of misorienta-tion of meiotic spindles.

Although similarly affected during telophase II,the formation of A. thaliana unreduced pollen dueto cold shock (4–5 °C) is not attributable to de-fects in spindle fibers attached to the chromosomesbut mainly to abnormalities in equatorial cell plateformation as a result of misplaced microtubules.28

Because the aberration in cell plate formation oc-curs during telophase II, the cell plate separatinghomologous chromosomes is in place but the oneseparating sister chromatids is defective. Therefore,instead of forming pollen tetrads (1X), 2X dyads areformed, each containing two sets of exactly identical

3Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

chromosomes. It is not clear if the differences in themechanistic details (spindles vs. cell plate forma-tion) are due to the differences in the type of stressapplied or to differences between species.

In this section, we reviewed studies focused onfinding the genetic and environmental causes ofpolyploidization, most of which act by affectingmitosis or meiosis, thus producing unreduced ga-metes. A polyploid, once created, has to estab-lish itself, and the process of neopolyploid estab-lishment continues in the backdrop of molecularand physiological changes occurring as a result ofgenome duplication (and merging two differentgenomes in allopolyploids) that a neopolyploid hasto undergo.1 In the remainder of the review, we fo-cus on the impact of polyploidy on genome content,on gene expression, on morphology, and, finally, onadaptation.

Impact of polyploidy on genome content

Changes in genome organizationPolyploids have a tendency to return to a diploidizedstate over time, experiencing changes in chromo-some organization, gene order, expression, epige-netic modification, and biological network topol-ogy, a phenomenon known as diploidization.38

Diploidization may begin with large-scale changesin the genome of neopolyploid plants, such as ab-normal chromosome segregation, rearrangement,and breakage,39,40 and may occur in a haphazardmanner after polyploidization41 (Fig. 2A–B). For ex-ample, in synthetic allotetraploids between double-haploid Brassica oleracea (C genome) and Brassicarapa (A genome), chromosomal segregation aberra-tions lead to extensive aneuploidy as early as the firstgeneration, when the aneuploidy rate is 24%.42 Thisrate rises to 95% in the 11th generation. Despite thehigh rate of aneuploidy, the number of homeologsfor a particular chromosome is frequently main-tained at four copies (i.e., the loss of chromosome 1from the A genome is usually associated with gainof the same chromosome from the C genome, andvice versa). This compensating aneuploidy suggestsa dosage balance requirement, at least in the earlygenerations. Compensating aneuploidy also occursin the naturally occurring allotetraploid Tragopogonmiscellus, in which 85% of aneuploid plants werefound to have the expected chromosome number.43

Chromosomal losses in early generations have also

P1 P2

Chr A

Chr B

A

BP1

P2

t

t

Homeologousgenes

Chromosome loss

Trans-location

C

Gene losses

Chromosomal fragment loss

t

Homeologousgenes

Transposable element

Insertion into gene

Proliferation

Transcriptionalactivation or

repression

P1

P2

Figure 2. Genomic consequences of polyploidy. (A) Some pos-sible scenarios with respect to genomic rearrangements, suchas chromosome loss, chromosomal translocation, and chromo-some fragment loss, have been depicted in a simplified mannerusing only two chromosomes. P1, parent 1; P2, parent 2. (B)The process of gene loss in a parent-of-origin manner, termedfractionation. In the depicted scenario, the chromosomal copyfrom P2 loses most of the genes. (C) Proliferation of transpos-able elements over time. Such proliferation may lead to changesin gene order, gene function, and gene expression.

been reported for synthetic allohexaploids (Triticumaestivum,44 Brassica carinata × B. rapa,44 A. thaliana× Arabidopsis suecica45) as well as autopolyploidpotato,46 alfalfa, and corn.47 Recently, the cause ofsuch chromosomal losses, which occur as the resultof meiotic instabilities, was tracked down to a singlelocus called BOY NAMED SUE (BYS) in synthetic al-lopolyploids of A. thaliana × Arabidopsis arenosa.48

The authors speculate that the BYS locus may play arole in A. suecica, which is a naturally occurring al-lopolyploid of A. thaliana × A. arenosa, in ensuring

4 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

that homeologous chromosomes do not pair witheach other, a process that may lead to chromosomaldosage irregularities in the progeny.48

In addition to changes in chromosome numbers,newly generated polyploids display an elevated rateof genome rearrangements leading to loss of chro-mosomal fragments (Fig. 2A). By tracking a lim-ited number of markers, synthetic autotetraploidsof Paspalum notatum49 and Elymus elongatus50 wereshown to lose �10% of genome sequence in the firstgeneration. In Phlox drumondii, up to 25% reduc-tion in parental DNA content was observed as earlyas the third generation.50 On the contrary, studies insynthetic A. thaliana autopolyploids reveal little tono loss.51 These observations suggest that genomerearrangement can be prominent in allo- and someautopolyploids.

Duplicate gene loss and retentionPolyploidization initially results in multiplicationof gene content; however, the predominant fateof gene duplicates is loss.52 Studies of newly se-quenced genomes shed light on the extent ofgene loss in species that underwent polyploidiza-tion events several million years ago (Ma). In theA. thaliana genome, only 17% of duplicates wereretained after a paleopolyplodization (�) event thattook place �50 Ma.53 In the paleopolyploid Glycinemax, two rounds of whole-genome duplicationstook place �59 and �13 Ma.54 In the homolo-gous genes from the more recent duplication event,56.6% of duplicates are no longer detectable, com-pared to 74.1% genes lost after the older Glycinepolyploidization. Thus, the rates of gene loss are4.4% and 1.3% per million years (Myr) for theyounger and the older duplication event, respec-tively, indicating that gene loss rate was high ini-tially but slowed down over time.54 In B. rapaand Raphanus raphanistrum, which experiencedgenome triplication �25 Ma,55–57 assuming the an-cestral gene number before triplication was similarto that in A. thaliana (�30,000), the number of ex-tant B. rapa genes (�41,000) and R. raphanistrumgenes (�38,000) indicates that as many as 55% ofthe genes derived from genome triplication werelost.58,59

The process of loss of polyploidy-derived genesis referred to as fractionation, a collection of muta-tional mechanisms leading to the removal of dupli-cates derived from polyploidization60,61 (Fig. 2B).

Studies of gene collinearity between duplicate re-gions in A. thaliana,62 Z. mays,63 and B. rapa64 sug-gest a bias in the genes lost from certain parentalgenomes. In B. rapa, one of the three subgenomesexperienced significantly fewer gene losses thanthe others.58,65 This phenomenon is also reflectedat the expression level, where genes located onone subgenome tend to have higher expressionthan others, indicating genome dominance.66 Theduplicated gene copy producing the most RNAmolecules appears to be the one retained.63 It hasrecently been suggested that transposon silenc-ing by small RNAs may contribute to the phe-nomenon of genome dominance, with the parentalgenome having the lowest proportion of trans-posons being the more dominant.66 Fractionationof genes also leads to preferential gene retention,which has been reviewed recently.61 Retained du-plicates derived from polyploidization have a num-ber of distinguishing characteristics compared togenes that remain single copy, including biasedgene function,67,68 higher gene complexity (num-ber of exons and protein domains),69,70 higher lev-els of gene expression,71 significant parental genomedominance,63,72 and higher network connectivity.62

Duplicate genes playing a role in stress response,development, signaling, and transcriptional reg-ulation tend to be retained, a feature consistentacross multiple polyploidization events and timescales.59,70

Why are duplicates with these types of char-acteristics retained? Retained duplicates mayexperience a brief period of complete functionalredundancy but eventually obtain new functions,6

and/or partition ancestral functions leading tosubfunctionalization.73 In addition to these mech-anisms, the retention of duplicate genes may be at-tributable to balanced gene drive/gene balance,74,75

functional buffering,69 dosage selection,76 andescape from adaptive conflict77 (reviewed by Innanand Kondrashov11 and Edger and Pires78). Amongthe mechanisms explaining duplicate retention,some imply adaptive evolution (e.g., neofunc-tionalization, dosage selection) while the othersrequire purifying selection to maintain the ances-tral functions (e.g., subfunctionalization, dosagebalance). Examples of adaptive duplication areaccumulating, but it remains unclear what fractionof gene duplicates are fixed as the result of adaptiveevolution.79

5Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

Mutation and transposable element activitiesBecause more than one gene copy is present, in-creased ploidy can mask the effect of deleteriousmutations.80 Meanwhile, the newly formed poly-ploid species has a very small effective popula-tion size, assuming postzygotic isolation from itsparental diploids. In this situation, genetic driftis expected to play a more dominant role inpolyploid evolution. The selective pressure againstany mutation in polyploid genomes would bemore relaxed, leading to increased frequencies ofotherwise deleterious alleles. Although it is notclear whether the spontaneous mutation rate ishigher in polyploids compared to diploids, there isgenerally a higher mutation density in mutagenizedpolyploids compared to diploids.81 Because this pat-tern is similar between natural and synthetic poly-ploids, and because the mutations tend to exist inheterozygous states, the elevated mutation density islikely a consequence of masking recessive deleteri-ous mutations.81 In a comparison between wheatT. aestivum, which experienced recent whole-genome duplication, and three other nonduplicatedgrass species, there are more nonsynonymous sub-stitutions, gene structural rearrangements, and al-ternative splice forms of genes in wheat,82 suggestingrelaxed selection.

The elevated mutation rate in polyploids mayalso be attributable to elevated transposable ele-ment activities.83,84 The proliferation of transposonsin polyploids is expected owing to reduced pop-ulation size, masked deleterious transposon inser-tion, and/or conflict in transposition repressors dueto genome merger84 (Fig. 2C). Despite this expec-tation, current studies present conflicting resultsregarding whether proliferation of transposons iscorrelated with polyploidy.83,84 For example, thenumbers of transposons in the Au short interspersednuclear element (SINE) family in natural polyploidwheat species are significantly higher than thosein diploids,85 although it is difficult to ascertainwhether the observed difference is due to poly-ploidy, hybridization, and/or lineage divergence.In addition, one of three synthetic allopolyploidshas a higher number of Au SINEs by the fourthgeneration.85 In this case, it remains unclear whethergenome doubling or hybridization contributes tothe higher number of Au SINEs observed.

Studies on the activities of transposons in au-topolyploids are also contradictory. In A. thaliana

synthetic autotetraploids, activation of Sunfish, aDNA transposon, was observed.39 On the otherhand, a study assaying naturally occurring autote-traploid A. arenosa accessions found evidence forpurifying selection against expansion of the Ac-IIItransposon family.86 In addition to the possibilityof transposon proliferation, transposons may be in-volved in recombination events leading to sequencelosses in polyploid genomes.87–89 For example, il-legitimate recombination mediated by TE elementswas shown to underlie the variation observed be-tween diploid and polyploid wheat species in theHARDNESS locus.90 Such transposon-mediated re-combination can also contribute to differential ex-pansion and contraction of subgenomes, as shownin maize.91

Impact of polyploidy on gene expressionand biological networks

Expression divergence between homeologsIn addition to experiencing widespread changes atthe DNA level, polyploids have considerable differ-ences in gene expression compared to diploids, andthis has been reviewed extensively.92–96 Divergencein the expression states of duplicated genes may leadto the following outcomes: they may gain new ex-pression states (neo-functionalization6), partitiontheir ancestral functions (subfunctionalization73),or lose their expression state completely, lead-ing to eventual pseudogenization.52 In A. thaliana,57% and 75% of the duplicates derived from themore recent � and the older � polyploidizationevents, respectively, were found to have divergedin expression.67 Whole-genome duplicates tend todiverge in expression at a slower rate than tandemduplicates, presumably because entire intergenic re-gions are duplicated during polyploidization, butonly a fraction might end up being duplicated dur-ing tandem duplication owing to the random natureof DNA breakage and recombination.97

In allopolyploids, the combination of gene setsin two species is expected to create a transcrip-tome shock, defined as abrupt and rapid changesin patterns of parental gene expression in thepolyploids.98 Through a number of intriguing stud-ies in the past decade or so, several basic featureshave emerged with regard to homeolog expres-sion in allopolyploids. The transcriptome shockcontributes to significant differences in expres-sion levels between homeologs in allopolyploids

6 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

(albeit to varying extents94) and the correspond-ing genes in diploid parents have been documentedin Arabidopsis,99 Brassica napus,100 and cotton.101

However, a recent study also showed that, in wheatsynthetic polyploids, fewer than 1% of genes shownonadditive expression.102 In addition, concerns onhow nonadditivity is defined in polyploids havebeen raised.103 Nonetheless, analysis of nonadditivepatterns of expression in allopolyploid homeologshas led to the discovery of two related phenom-ena, homeolog expression bias and expression leveldominance104 (Fig. 3A).

Homeolog expression bias takes place whenone homeolog has significantly reduced level ofexpression or is silenced altogether in theallopolyploid.105 For example, in the first RNA se-quencing study examining expression bias in cottonpolyploids, 59–62% and 48% of genes are differ-entially expressed when comparing diploids againstthe natural and synthetic polyploids, respectively.106

It was found that genes from a particular subgenomewere expressed in allopolyploids, and the natureof the subgenome differed in natural allopoly-ploids versus synthetic allopolyploids.106 Interest-ingly, among over 25,000 cotton genes contain-ing single nucleotide polymorphisms distinguishinghomeolog origins, only 0.71–0.75% of genes have nodetectable expression in synthetic polyploids. Giventhat the cotton allopolyploidization event took place1–2 Ma,107 there may have been insufficient time forgene loss and/or the expression of pseudo-genizedcopies are still detectable. Related to homeologexpression bias, expression level dominance (origi-nally called genomic dominance) describes a situa-tion where the sum of expression levels of a home-ologous gene pair tends to be more similar to that inone parent, regardless of the expression level of thegene in the parent in question.104,108 These phenom-ena have been well documented in multiple naturaland synthetic allopolyploids. The cause of expres-sion biases may be partially attributed to cis andtrans regulatory differences between the hybridizedgenomes109 and epigenetic regulation, which is dis-cussed in a later section.

Contribution of hybridization and genomedoubling to transcriptome shockIn addition to homeolog expression bias and ex-pression level dominance, another focus is onthe relative contribution of genome doubling and

AP1 P2

Homeologousgenes

Genes

Exp

ress

ion

leve

l

Genes

Genes

0

1

2

0

1

2

0

1

2

0

1

2

Exp

ress

ion

leve

l

Homeologexpression bias

1 432 1 432

1 432

1 432

Expressionlevel dominance

B

PolyploidizationDivergence

DNAmethylation

Gene

PolyploidizationDemethylation

Gene

RNApolymerase

TranscribedmRNA

C

Gene

Repressor

Polyploidizationsmall RNA transcriptionEpigenetic remodeling

Gene

small RNAs

TranscribedmRNA

RNApolymerase

Figure 3. Effects of polyploidy on gene expression and epige-netic regulation. (A) A hypothetical scenario depicting expres-sion divergence upon polyploidization. In “Homeolog expres-sion bias,” the homeologous genes are expressed in a parent-of-origin manner. In “Expression level dominance,” the sumof the expression level of both the genes is similar to that inone parent. P1, parent 1; P2, parent 2. (B) A gene that is si-lenced by DNA methylation in the parent is demethylated uponpolyploidization or hybridization, leading to its transcriptionby RNA polymerase. (C) A gene with a repressor bound to itspromoter region is not expressed in the parent, but upon poly-ploidization is expressed as the repressor is removed owing toregulation by small RNAs transcribed elsewhere in the genome.

7Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

hybridization to nonadditive expression in allopoly-ploids. Through comparisons of hybrid diploids,synthetic allopolyploids, and neopolyploids (partic-ularly Senecio and Tragopogon species, which formedin the past 100 years110,111), the effect of hybridiza-tion and genome doubling on gene expressionchanges has been quantified, and these studies sug-gest that hybridization likely plays a more dominantrole. For example, only 88 genes are differentiallyexpressed between A. thaliana diploid sand syn-thetic isogenic autotetraploids, compared to >1700genes with significantly different expression lev-els between synthetic allotetraploid A. thaliana ×A. arenosa and the average of two parents.112 In astudy of diploid, autotetraploid, and autohexaploidHelianthus decapetalus, ploidy level does not con-tribute significantly to expression differences.113

Similarly in Senecio, twice as many genes in S. ×baxteri, a triploid hybrid between S. vulgaris (2n =4X) and S. squalidus (2n = 2X), are differentiallyexpressed compared to the parental species than ina synthetic allohexaploid derived from the triploidS. × baxteri.98 Interestingly, genome doubling ame-liorates the effect of hybridization in Senecio,98

a finding that is also reported in neopolyploidSpartina.114 Thus, the nonadditive gene expres-sion changes in these allopolyploids is likely at-tributable to interspecific hybridization and notsimply genome doubling.

Although hybridization seems to play a domi-nant role, studies in cotton, Spartina, and domes-ticated rice subspecies suggest the contribution ofgenome doubling may be important. In the nat-ural polyploid cotton, among assayed genes withexpression bias toward one parental diploid, only25% are biased in the same direction as the diploidhybrid,101 suggesting the expression bias in the re-maining 75% is the result of genome doubling.However, allopolyploid cotton was established �1–2 Ma. Thus, one cannot rule out the possibility thatthe expression bias is due to regulatory variationthat accumulated in the past 1–2 Myr. In Spartina,the allopolyploid tends to have a higher number oftransgressively overexpressed genes compared to thespecies hybrid,114 again suggesting a prominent roleof genome doubling. Nonetheless, given that theparental Spartina species are hexaploids, it remainsunclear if the findings are applicable to compar-isons between lower ploidy levels. Finally, genomedoubling seems to have a more prominent role in

transcriptome shock than hybridization in a com-parison between a hybrid of Oryza sativa spp. in-dica and japonica and synthetic tetraploid rice.109

But given that there has been repeated hybridiza-tion between japonica and indica,115 it remains un-clear how hybridization may have influenced thefindings.

Involvement of epigenetic modifications andsmall RNAs in transcriptome shockTranscriptome shock results in nonadditive gene ex-pression and silencing of homeologs. In allopoly-ploids, trans factors and cis regulatory compo-nents from two genetic backgrounds can interactowing to the hybridization between two genomes,contributing to changes in gene expression betweenpolyploids and their diploid progenitors.116,117 Inaddition, epigenetic factors, including DNA methy-lation, histone modifications, and small RNA, havebeen implicated in modulating gene expressionin allpolyploids.66,116,118–122 Extensive DNA methy-lation changes have been reported between al-lopolyploids and their parents in B. napus,123

wheat,124 Spartina anglica,88,125 and Arabidopsis126

(Fig. 3B). Inconsistent with the above observa-tions, the synthetic allopolyploid Cucumis hys-trix × sativus has approximately the samemethylation density as the parents or the F1hybrids.127

The direct involvement of DNA methylation inexpression changes between homeologs has alsobeen demonstrated. In the natural allotetraploidA. suecica, the transcription factor TCP3 wassilenced when chemical inhibitors of DNA methyl-transferases were applied,105 suggesting that methy-lation is important for proper TCP3 expression.Another line of evidence comes from methyl-transferase 1 (MET1) RNA interference (RNAi)lines in the A. suecica background.128 Notably,only 200 genes were found to be differentially ex-pressed between A. suecica wild-type plants andMET1 RNAi lines, and only 34 of these 200 genesoverlap with the �1400 genes with expressionchanges in synthetic tetraploids between A. thalianaand A. arenosa (the presumed diploid parents ofA. suecica).112 In addition, 33 of the 200 differentiallyexpressed genes in MET1 RNAi lines are pseudo-genes or transposons.128 Thus, MET1-mediatedDNA methylation differences between diploidsand polyploids appear to be more relevant to

8 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

controlling heterochromatic states than to con-tributing to transcriptome shock. Nonetheless, theDNA methylation machinery is complex,129 andmore loss-of-function studies will be necessary fora more complete picture of the influence of DNAmethylation on transcriptome shock.

Similar to DNA methylation, there are indica-tions that histone modifications likely play signif-icant roles in transcriptome shock. Using diploidsderived from transgenic autotetraploid A. thalianacontaining epialleles that either silence or allow theexpression of a resistance gene marker,130 a screenfor mutants releasing the silencing effect of the epi-allele resulted in identification of loss-of-functionalleles in DECREASE IN DNA METHYLATION1(DDM1) and HOMOLOGOUS GENE SILENCING1(HOG1).131 Global changes in both DNA and his-tone methylation in the mutant background likelycontribute to silencing release. Although the epial-lele action appears to be tied to the ploidy level,130

it remains to be determined whether the muta-tions in DDM1 and/or HOG1 contribute to sim-ilar phenomenon in a polyploidy background. Inaddition to histone methylation, histone acetyla-tion is implicated in transcriptome shock based onstudies of a histone deacetylase (ATHD1/ATHDA19)mutant.132 Genes differentially regulated betweenwild-type and ATHD1/ATHDA19 mutants overlapsignificantly with genes differentially expressed be-tween synthetic allopolyploid Arabidopsis and thediploid parents.

The expression profiles of small RNAs, includingboth micro-RNA and small interfering (both repeat-associated and trans-acting) RNAs, are affectedpostpolyploidization (Fig. 3C). Such changes havebeen documented in resynthesized allotetraploidsof A. thaliana × arenosa133 and Ae. tauschii ×Triticum turgidum.134 As with DNA methylationand histone modification, mutants in genes con-trolling small RNA biogenesis have been used tostudy the impact of small RNA on transcriptionand other phenotypic changes associated with poly-ploidy. RNAi lines interfering with the expression ofDICER LIKE-1 and ARGONAUTE 1, both involvedin small RNA biogenesis, have been created.135 Sim-ilar to the DNA methylation machinery, the com-plexity of epigenetic regulatory machinery in plantsis well appreciated.136 Additional loss-of-functionstudies in polyploids will be highly informative.In addition to their effect on transcription, as dis-

cussed earlier, small RNAs may contribute to thephenomenon of genome dominance.66 Aside fromtranscriptional regulatory mechanisms, a recentstudy examining ribosome-associated transcripts inthe recently formed (�100,000 years ago) allote-traploid Glycine dolichocarpa indicated that tran-scripts subject to translational regulation tend tobe retained homeologs from an ancient whole-genome duplication event.137 It will be interest-ing to perform similar experiments in the diploidparents and F1s to assess the impact of genomedoubling and genome merger on translationalregulation.

Perturbations of biological networks due topolyploidyPreferential retention and loss of genes, coupledwith extensive transcriptional and genomic changespostpolyploidy, necessarily leads to alterations inthe molecular networks operating in the organ-ism (Fig. 4). The network-level changes, in turn,are expected to affect the phenotype of the organ-ism. Such phenotypic impact has been reviewedrecently, using flowering time as an example.120

While most retention/loss events may be random,there is evidence for preferential retention/loss ofcertain types of genes. According to the gene bal-ance hypothesis, the random loss of genes can re-sult in a perturbation of stoichiometric relation-ships between gene products, leading to genomicimbalance in a newly created polyploid and loss offitness.138 Hence, neopolyploid lineages that retaincertain types of genes may be able to better establishthemselves.

There is a growing body of literature discussingthe functional evolution of gene duplicates derivedfrom whole-genome duplication.76,138,139 For exam-ple, studies in B. rapa show that genes involved in cir-cadian rhythm such as CIRCADIAN CLOCK ASSO-CIATED 1 and LATE ELONGATED HYPOCOTYLwere preferentially retained postpolyploidization,leading to an altered flowering time pathway.140

Such preferential retention was also found inA. thaliana genes duplicated in the � polyploidiza-tion event 50–65 Ma related to specific metabolicpathways,141 as well as MADS-box genes involved invarious aspects of plant development.142 In poplar,two duplicate genes, FLOWERING LOCUS T1 andT2, derived from a paleopolyploidization eventare expressed at different times of the year and

9Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

Gene loss

Sub-functionalization

Gene 1

Gene 2

Genetic/physicalinteraction or

co-expression

Interactingpartners

Neo-functionalization

P1 P2

PolyploidizationDivergence

Homeologousgenes

Homeologousgenes

Figure 4. Effect of polyploidy on gene networks. P1, parent 1;P2, parent 2. An example of two genes—gene 1 and gene 2—inparents P1 and P2 is shown. Each square represents a genetic orphysical interaction of gene 1 or gene 2. After polyploidization,over the course of several generations, the network topologybegins to evolve. If both of the homeologous copies do not un-dergo gene loss through deletion or pseudo-genization and areretained, divergence between them will lead to eventual sub-functionalization or neofunctionalization between duplicates,changing the network topology and, possibly, network function.

have distinct roles in influencing flowering timeand vegetative growth.143 Subfunctionalization oftwo polyploidization-derived phytochrome (PHY)genes in maize—PHY B1 and B2—where the twoproteins have both overlapping and unique func-tions in seedlings and adult plants, is also known.144

Most of our understanding of the impact ofpolyploidy on biological network evolution comesfrom budding yeast (Saccharomyces cerevisiae) thatunderwent a polyploidization event �100 Ma.145

This polyploidization event was associated witha large-scale rewiring of the transcriptional net-work through changes in cis-regulatory motif usage,which led to the evolution of faculatively anaerobicpostpolyploidization species, whereas several pre-polyploidization species are aerobic.146 It was also

found that, despite 100 Myr of evolution, geneticredundancy may still exist between several pairs ofduplicated genes, although there is evidence of sig-nificant partitioning of ancestral functions and gainof new functions between these pairs.147

Impact of polyploidy on morphology andphysiology

Morphological alterationsSome fundamental commonalities in morphologyand physiology are found among polyploid species;however, the specific outcomes of a particular poly-ploidization event can vary widely between taxa (re-viewed in Ref. 148). Anatomically, polyploids havelarger cell volumes, stomatal guard cells, pollen, andseeds compared to diploids. Polyploids also havebroader and thicker leaves with fewer stems per plant(reviewed in Ref. 149). Such changes may affect pro-cesses such as water relations, gas exchange, coldtolerance, and shade tolerance of polyploid plants.1

Some phenotypic modifications may occur owingto increased DNA content in the nucleus and a needto maintain a particular nuclear-to-cytoplasmic vol-ume ratio, while other changes may be induced bygenome restructuring and regulatory and network-level modifications. For example, in a synthetic au-totetraploid line of A. thaliana, larger aerial organscompared to the diploid are the result of faster ex-pansion rates and a longer expansion duration dur-ing cell division. Such behavior is due to upreg-ulation of cyclin-dependent kinases in tetraploidscompared to diploids.150

Polyploidization is also expected to affect themorphology of the reproductive system by affect-ing the size of the flower, the relative sizes of petals,the spatial relationships between different floral or-gans, and the flowering time of the plant.151 Thesechanges can influence pollinator preferences. In ad-dition to morphological changes in reproductivestructure, polyploidy may lead to the breakdownof self-incompatibility. In the Solanaceae family,polyploid species are significantly more likely to beself-compatible than diploid species.152 A broaderstudy of 235 angiosperm species also found a signif-icant association between polyploidy and selfing.153

However, a study on self-sterility data from 1266angiosperm species contrasting self-compatible,self-incompatible, and mix-mating groups foundthat polyploid species did not tend to be moreself-compatible compared to diploids.154 If the

10 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

results of the latter study are true, there may bea short-term breakdown of self-incompatabilityin the neopolyploid, enabling it to establish itspopulation,154 after which self-compatibility isreestablished. Alternatively, other features associ-ated with the mating system such as inflorescencesize, floral display, and pollinator behavior mayminimize the effect of reproductive isolation dueto polyploidization in neopolyploids. Nonetheless,one issue with the 1266-species study is that phy-logenetic relationships are not considered,154 al-though there is nonrandom association betweenphylogeny and mating system. In addition, the self-ing rate was binned into three broad categories.On the other hand, the 235-species study consid-ered species phylogeny and modeled selfing rate as acontinuous variable despite a smaller sample size.153

Thus, the lack of correlation between polyploidy andselfing rate in the 1266-species study can be due toconfounding factors of phylogenetic relations andselfing-rate binning.

Physiological changes and stress tolerancePolyploidy significantly influences photosynthesis(reviewed in Ref. 155), and this effect is particularlyobvious under stress conditions. In greenhouse-grown Betula papyrifer, water stress treatment leadsto a complete cessation of photosynthesis in diploidsbut not in penta- and hexapolyploids. Such behav-ior can be partly attributed to earlier stomata clo-sure in diploids.156 However, it remains unclear ifthe photosynthetic activity under water deficit inpolyploids is advantageous, because it would con-tribute to carbon fixation even under stress, orwhether it is detrimental due to water loss. Underexcess light, the capacity for photoprotection andnonphotosynthetic electron transport are higher inthe natural allotetraploid G. dolichocarpa than in itsdiploid progenitors.157 This enhanced photoprotec-tion appears beneficial because the allotetraploid isreported to photobleach later than its diploid pro-genitors.

Because of the prevalence of polyploid plantsand the perceived broader ecological tolerance (re-viewed in Ref. 149), one potential physiological con-sequence of polyploidy is its increased tolerance toenvironmental stress. However, the degree of envi-ronmental stress tolerance does not necessarily cor-relate with cytotypes (see Ref. 158, and referencestherein). Taking drought tolerance as an example,

in a comparison between the fireweed Chamerionangustifolium diploids and tetraploids (both natu-ral and synthetic) in a controlled environment, thenatural tetraploids took 20–30% longer to wilt com-pared to both diploid and synthetic tetraploids,158

consistent with the higher xylem hydraulic conduc-tivity observed in natural tetraploids. However, thevulnerability of stems to drought-induced cavita-tion was similar among C. angustifolium cytotypes.In field grown tetraploid and hexaploid Atriplexcanescens,159 the leaf-specific hydraulic conductiv-ity as well as susceptibility to cavitation was lowerin plants with higher ploidy levels. The inconsis-tency between earlier studies and the two recent oneshighlighted above can be attributed to, for example,differences in whether the studies were conductedin controlled or natural environments, how phys-iological measurements were taken, and how andwhen the polyploids were established.

Polyploids are also hypothesized to be more re-sistant to pathogens.160 Mathematical models of in-teractions between pathogens and either diploids orneopolyploids have shown that newly formed poly-ploid populations of hosts are expected to be moreresistant.161 However, similar to studies of the re-lationships between polyploidy and abiotic stresstolerance, the few empirical studies conducted sofar have generated mixed results.162,163 For plant–insect interactions, the autotetraploid gooseberry-leaf alumroot Heuchera grossulariifolia is more likelyto be attacked by the specialist moth herbivore Greyapolitella than the diploid.164 In another field study,the resistance of H. grossulariifolia to three mothspecies (G. politella, G. piperella, and Eupithecia mis-turata) was tested.165 Interestingly, G. piperella tendsto attack and lay eggs on diploids, suggesting her-bivore species may provide selective pressure differ-ently due to differences in ploidy levels. Nonetheless,it remains unclear whether there are additional ge-netic differences independent from polyploidy thatcontribute to the difference.

Polyploidy and adaptation

Survival in adverse environmentsThe question of whether polyploidization con-tributes to the long-term evolutionary success ofplant species has been raised repeatedly sinceStebbins.166 There are already a number of excel-lent reviews on this topic;17,149,167,168 thus, in this

11Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

section, we focus on providing a summary of earlierfindings and a discussion of some recent results.

Polyploids are more frequent at higher eleva-tions and higher latitudes and may be more tolerantto dry conditions,38,158,169 suggesting a fitness ad-vantage for polyploids in those environments. Thetiming of multiple polyploidization events in an-giosperms coincides with the timing of the creationof the Cretaceous–Tertiary boundary.170 This coin-cidence has led to the hypothesis that species withgenome doubling could adapt better to the chang-ing environment than their diploid relatives duringthe mass extinction event. However, considering theinfluence of environmental factors on unreducedgamete formation, it is also possible that the intenseclimatic changes during the mass extinction eventmay have increased the frequency of unreduced ga-mete formation, creating polyploids at a faster ratethan normal. In addition, polyploids were foundto be more successful in colonizing the Arctic af-ter deglaciation than diploids.169 A study sampling640 endangered and 81 invasive species worldwidehas led to the conclusion that endangered speciestend to be diploids while invasive species tend to bepolyploids, suggesting that polyploidization may in-crease tolerance to diverse ecological conditions.171

It has also been shown that polyploid A. thalianaaccessions are more tolerant to and have better re-productive success under high salinity compared todiploid cytotypes.172 It will be particularly interest-ing to determine if such high-salinity adaptation canalso be observed under field conditions.

Not all findings support the notion that poly-ploids tend to survive better in adverse environ-ments. A 1940 study of 100 polyploid and diploidplant species found no correlation between poly-ploidy and winter hardiness.173 More recently, in astudy of two diploid and one polyploid species fromeach of 144 North American plant genera, no asso-ciation was found between ploidy level and speciesrange area, minimum/maximum temperature, pre-cipitation, or latitudes.174 Furthermore, as discussedin the previous section, physiological changes as-sociated with polyploidy do not necessarily confersuperior tolerance and/or resistance to abiotic andbiotic factors. These observations suggest that therelationship between polyploidy and adaptation isquite complex and may depend on not only thespecies undergoing polyploidization but also on theenvironment.

Local adaptationIn addition to the meta-analyses discussed earlier,multiple studies provide specific examples of adap-tation that are potentially attributable to polyploidy.In H. grossulariifolia, pollinators visit tetraploid in-dividuals more often than diploid ones.175 Similarly,in the fireweed C. angustifolium, where populationsranges of polyploid and diploid varieties overlap,tetraploids have a disproportionately higher num-ber of bee visits and a greater pollen-siring advan-tage compared to diploids.176,177 The invasivenessof allotetraploid cordgrass S. anglica may indicate afitness increase due to polyploidy; however, this ismore likely a consequence of heterosis than genomedoubling.178

In wild yarrow Achillea borealis, which hashexaploid and tetraploid populations occupyingnearby but different environments, there is clearevidence of local adaptation, and polyploidizationis likely the initial trigger for diversification andadaptation to a new habitat.179 Consistent with thisnotion, the evolvability of the neo-autotetraploidC. angustifolium is higher than both diploid andestablished autotetraploids, suggesting that genomedoubling, without hybridization, may initiallyalter evolutionary rate and contribute to adaptiveevolution.180 In addition, reciprocal transplantexperiments demonstrated that C. angustifoliumdiploids and tetraploids survived best at their nativeelevations.181 Overall, these observations suggestthat polyploidization may have positive fitnessconsequences and can lead to adaptation to local orregional environments.

Species richnessPolyploidy leads to instantaneous reproductive iso-lation of polyploid individuals through the phe-nomenon of minority cytotype exclusion,1,30 butsuch individuals also possess a greater capacity forfunctional innovation. If polyploids in general havebetter fitness compared to diploids, the specia-tion rate of polyploids may be higher than that ofdiploids. Multiple observations suggest a positiveassociation between species richness and percentpolyploid species in different plant clades.7,149,182

In addition, a large number of species in majorplant families, such as Poaceae,183 Asteraceae,184

Brassicaceae,57 and the subfamily Papilionoideae,185

have descended from a polyploid ancestor, sug-gesting a possible increase in diversification rates

12 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

postpolyploidization. Overall, it has been estimatedthat a significant proportion, �15% of angiospermand �31% of fern speciation events, may have beenaccompanied by ploidy increase.186 On the contrary,some other studies provide conflicting results. Onestudy arrived at the conclusion that polyploids tendto have lower diversification rates than diploids andhave a greater chance of extinction.187 It has alsobeen estimated that only 2–4% of polyploidiza-tion events in angiosperms have actually resultedin speciation.149 In addition, analyses of genomesequences of flowering plants suggests that the dif-ference in the estimated timing between successivedetectable paleopolyploidization events is �10–30Myr in flowering plant lineages.5 Thus, consider-ing the abundance of polyploids among floweringplants, most of the polyploidization events were notrecorded in the genomes of extant species. The in-ference is that most of these polyploids have goneextinct.

These observations suggest two possibilities—either a majority of the polyploid lineages indeedgo extinct, making them evolutionary dead ends,166

or they hybridize with their parental species, cre-ating lineages of mixed ploidy. It seems that bothof these scenarios may occur in nature. Hybridiza-tion between polyploids and their diploid ancestorshas been reported in natural populations of mul-tiple species such as C. angustifolium,188 species ofthe genera Epidendrum189 and Jacobaea,190 and sev-eral others,191 in regions known as hybrid zones.191

Mathematical simulations on whether a triploid hy-brid between an autotetraploid and a diploid canhelp a tetraploid population to establish suggestthat even partially fit triploids can assist in long-term tetraploid fixation.19 Thus, polyploidizationmay not necessarily be an evolutionary dead endbut may create interesting possibilities for furtherinnovation in the lineage.

Conclusions

In this article, we highlight the findings that the for-mation of a polyploid is associated with extensivechanges at the genomic, epigenetic, transcriptional,and network levels. These genomic, transcriptomic,and other omic changes must have contributed tomorphological, physiological, and ecological phe-notypic differences between polyploids and theirdiploid progenitors. However, the exact molecu-lar changes responsible for the phenotypic differ-

ences between cytotypes remain unclear in mostcases. Also, we have a relatively better understand-ing of the molecular and phenotypic consequencesof allopolyploidy than autopolyploidy, and studiescomparing and contrasting mechanisms of molec-ular evolution in these two forms of polyploidy arelacking. For example, it is not clear whether therate of neo- and subfunctionalization and pseudo-genization differ between auto- and allopolyploids,given the homeologs in allopolyploids are alreadyslightly divergent from each other. Also, given thatthe extent of functional redundancy is higher in au-topolyploids, do mutations have a stronger deleteri-ous effects in allopolyploids than autopolyploids?Additional research would be needed to addressthese questions.

In a review by Soltis et al.,13 a number of in-triguing questions are raised regarding what we stilldo not know about polyploidy. To expand on thelong list, one challenge lies in establishing the ge-netic basis in cases where polyploids are shown tobe successful. Among the unknowns, one particu-larly challenging question is whether polyploids aremore successful than their diploid progenitors.13 Arelated question concerns determining the ecolog-ical situations under which polyploidy is adaptive.Theoretical considerations as well as empirical evi-dence have provided contradictory answers to thesetwo questions so far.17,149,166–168 Nevertheless, thesecond question is more tractable, as it does notrequire generalization and can be examined exper-imentally on a species-by-species basis. Polyploidyis an extreme form of duplication and can be seenas a mutation mechanism. Considering the nearlyneutral theory of molecular evolution,192 the nullhypothesis is that the effect of polyploidy is neutralor nearly neutral. In this framework, we can testunder what situations (e.g., different abiotic/bioticenvironments) the null hypothesis can be rejected.

Taking C. angustifolium as an example, diploidand tetraploid varieties show significant differencesin drought tolerance.158 Given the understanding ofdrought tolerance in model plants,193,194 a targetedsurvey of candidate gene transcription in field con-ditions can potentially be informative. The optimaltiming for the assay is not trivial to determine, andmolecular changes other than transcription can bemore important. In addition, drought tolerance maynot be the main environmental factor, highlightingthe need to assess potentially relevant abiotic/biotic

13Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

factors in controlled environments in addition tothe field. Nonetheless, a candidate gene approachis a reasonable starting point. In case the candidategene approach does not bear fruit, because samplingthe omes—genomes, transcriptomes, proteomes, ormetabolomes—of nonmodel species is no longera rate-limiting step, a global study of molecularchanges may provide viable hypotheses for fur-ther testing. These considerations are not unique toC. angustifolium but are relevant to other polyploidstudy systems as well. We surmise that good exper-imental designs incorporating both molecular andecological considerations of polyploids have the po-tential to make the most impact in the near future.

Acknowledgments

We would like to thank Jonathan Wendel and JoshuaUdall for discussion, the two anonymous reviewers,as well as the editor for providing critical feedbackon the manuscript. SHS is supported by NationalScience Foundation Grants DEB-0919452 and IOS-1126998.

Conflicts of interest

The authors declare no conflicts of interest.

References

1. Ramsey, J. & D.W. Schemske. 2002. Neopolyploidy in flow-ering plants. Annu. Rev. Ecol. Syst. 33: 589–639.

2. Tate, J.A., P.S. Soltis & D.E. Soltis. 2005. “Chapter 7: poly-ploidy in plants.” In The Evolution of the Genome. T. RyanGregory, Ed.: 371–426. Academic Press.

3. Husband, B.C., S.J. Baldwin & J. Suda. 2013. “The incidenceof polyploidy in natural plant populations: major patternsand evolutionary processes.” In Plant Genome Diversity.Vol. 2. I.J. Leitch, J. Greilhuber, J. Dolezel, et al. Eds.: 255–276. Vienna: Springer.

4. Friedman, W.E. 2009. The meaning of Darwin’s “abom-inable mystery.” Am. J. Bot. 96: 5–21.

5. Jiao, Y., N.J. Wickett, S. Ayyampalayam, et al. 2011. An-cestral polyploidy in seed plants and angiosperms. Nature473: 97–100.

6. Ohno, S. 1970. Evolution by Gene Duplication. New York:Springer-Verlag.

7. Soltis, D.E., V.A. Albert, J. Leebens-Mack, et al. 2009. Poly-ploidy and angiosperm diversification. Am. J. Bot. 96: 336–348.

8. Gregory, R. & B. Mable. 2005. “Chapter 8—polyploidy inanimals”. In The Evolution of the Genome. Elsevier Aca-demic Press.

9. Albertin, W. & P. Marullo. 2012. Polyploidy in fungi: evo-lution after whole-genome duplication. Proc. R. Soc. B 279:2497–2509.

10. Soppa, J. 2013. Evolutionary advantages of polyploidy inhalophilic archaea. Biochem. Soc. Trans. 41: 339–343.

11. Innan, H. & F. Kondrashov. 2010. The evolution of gene du-plications: classifying and distinguishing between models.Nat. Rev. Genet. 11: 97–108.

12. Ramsey, J. & D.W. Schemske. 1998. Pathways, mechanisms,and rates of polyploid formation in flowering plants. Annu.Rev. Ecol. Syst. 29: 467–501.

13. Soltis, D.E., R.J.A. Buggs, J.J. Doyle & P.S. Soltis. 2010. Whatwe still don’t know about polyploidy. Taxon 59: 1387–1403.

14. Soltis, D.E. & P.S. Soltis. 2012. Polyploidy and Genome Evo-lution. New York: Springer.

15. Leitch, I.J., J. Greilhuber, J. Dolezel & J. Wendel. 2013. PlantGenome Diversity. Vol. 2: Physical Structure, Behaviour andEvolution of Plant Genomes. Vienna: Springer-Verlag.

16. Stock, M. & D.K. Lamatsch. 2013. Trends in Polyploidy Re-search in Animals and Plants: Reprint of: Cytogenetic andGenome Research 2013. Vol. 140, Issues 2–4. Basel: S. Karger.

17. Madlung, A. 2013. Polyploidy and its effect on evolutionarysuccess: old questions revisited with new tools. Heredity110: 99–104.

18. Bretagnolle, F. & J.D. Thompson. 1995. Tansley ReviewNo. 78. Gametes with the stomatic chromosome number:mechanisms of their formation and role in the evolution ofautopolypoid plants. New Phytol. 129: 1–22.

19. Husband, B.C. 2004. The role of triploid hybrids in theevolutionary dynamics of mixed-ploidy populations. Biol.J. Linn. Soc. 82: 537–546.

20. Yamauchi, A., A. Hosokawa, H. Nagata & M. Shimoda.2004. Triploid bridge and role of parthenogenesis in theevolution of autopolyploidy. Am. Nat. 164: 101–112.

21. Suda, J. & T. Herben. 2013. Ploidy frequencies in plantswith ploidy heterogeneity: fitting a general gametic modelto empirical population data. Proc. R. Soc. B 280: 20122387.

22. Fox, D.T. & R.J. Duronio. 2013. Endoreplication and poly-ploidy: insights into development and disease. Development140: 3–12.

23. Brownfield, L. & C. Kohler. 2011. Unreduced gamete for-mation in plants: mechanisms and prospects. J. Exp. Bot.62: 1659–1668.

24. De Storme, N. & D. Geelen. 2013. Sexual polyploidizationin plants–cytological mechanisms and molecular regula-tion. New Phytol. 198: 670–684.

25. Ravi, M., M.P.A. Marimuthu & I. Siddiqi. 2008. Gamete for-mation without meiosis in Arabidopsis. Nature 451: 1121–1124.

26. Siddiqi, I., G. Ganesh, U. Grossniklaus & V. Subbiah. 2000.The dyad gene is required for progression through femalemeiosis in Arabidopsis. Development 127: 197–207.

27. Mercier, R., D. Vezon, E. Bullier, et al. 2001. SWITCH1(SWI1): a novel protein required for the establishment ofsister chromatid cohesion and for bivalent formation atmeiosis. Genes Dev. 15: 1859–1871.

28. De Storme, N., G.P. Copenhaver & D. Geelen. 2012. Pro-duction of diploid male gametes in Arabidopsis by cold-induced destabilization of post-meiotic radial microtubulearrays. Plant Physiol. 160: 1808–1826.

29. Marks, G.E. 1966. The origin and significance of intraspe-cific polyploidy: experimental evidence from Solanum cha-coense. Evolution 20: 552–557.

14 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

30. Levin, D.A. 1975. Minority cytotype exclusion in local plantpopulations. Taxon 24: 35–43.

31. Kradolfer, D., P. Wolff, H. Jiang, et al. 2013. An imprintedgene underlies postzygotic reproductive isolation in Ara-bidopsis thaliana. Dev. Cell 26: 525–535.

32. Parrott, W.A. & R.R. Smith. 1986. Recurrent selection for2n pollen formation in red clover. Crop Sci. 26: 1132–1135.

33. Tavoletti, S., A. Mariani & F. Veronesi. 1991. Phenotypicrecurrent selection for 2n pollen and 2n egg production indiploid alfalfa. Euphytica 57: 97–102.

34. Tischler, G. 1935. Die Bedeutung der Polyploidie fur dieVerbreitung der Angiospermen. Bot. Jahrbucher 76: 1–36.

35. Sakamura, T. 1920. Experimentelle studien uber die Zellund Kerntcilung, mit besonderer Rucksicht auf Form,Grosse und Zahl dei Chromosomen. J. Coll. Sci. Imp. Univ.Tokyo 39: 221.

36. Randolph, L.F. 1932. Some effects of high temperature onpolyploidy and other variations in maize. Proc. Natl. Acad.Sci. U. S. A. 18: 222–229.

37. Pecrix, Y., G. Rallo, H. Folzer, et al. 2011. Polyploidizationmechanisms: temperature environment can induce diploidgamete formation in Rosa sp. J. Exp. Bot. 62: 3587–3597.

38. Grant, V. 1981. Plant Speciation. New York: Columbia Uni-versity Press.

39. Madlung, A., A.P. Tyagi, B. Watson, et al. 2005. Genomicchanges in synthetic Arabidopsis polyploids. Plant J. 41:221–230.

40. Gaeta, R.T., J.C. Pires, F. Iniguez-Luy, et al. 2007. Genomicchanges in resynthesized Brassica napus and their effect ongene expression and phenotype. Plant Cell 19: 3403–3417.

41. Buggs, R.J.A., A.N. Doust, J.A. Tate, et al. 2009. Gene lossand silencing in Tragopogon miscellus (Asteraceae): com-parison of natural and synthetic allotetraploids. Heredity103: 73–81.

42. Xiong, Z., R.T. Gaeta & J.C. Pires. 2011. Homoeolo-gous shuffling and chromosome compensation maintaingenome balance in resynthesized allopolyploid Brassica na-pus. Proc. Natl. Acad. Sci. U. S. A. 108: 7908–7913.

43. Chester, M., J.P. Gallagher, V.V. Symonds, et al. 2012. Ex-tensive chromosomal variation in a recently formed naturalallopolyploid species, Tragopogon miscellus (Asteraceae).Proc. Natl. Acad. Sci. U. S. A. 109: 1176–1181.

44. Mestiri, I., V. Chague, A.-M. Tanguy, et al. 2010. Newlysynthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structuralgenomic additivity. New Phytol. 186: 86–101.

45. Matsushita, S.C., A.P. Tyagi, G.M. Thornton, et al. 2012.Allopolyploidization lays the foundation for evolution ofdistinct populations: evidence from analysis of syntheticArabidopsis allohexaploids. Genetics 191: 535–547.

46. Lamm, R. 1945. Cytogenetic studies in Solanum, sect. Tu-berarium. Hereditas 31: 1–129.

47. Shaver, D.L. 1962. A study of aneuploidy in autotetraploidmaize. Can. J. Genet. Cytol. 4: 226–233.

48. Henry, I.M., B.P. Dilkes, A. Tyagi, et al. 2014. The BOYNAMED SUE quantitative trait locus confers increasedmeiotic stability to an adapted natural allopolyploid of Ara-bidopsis. Plant Cell 26: 181–194.

49. Martelotto, L.G., J.P.A. Ortiz, J. Stein, et al. 2007. Genomerearrangements derived from autopolyploidization in Pas-palum sp. Plant Sci. 172: 970–977.

50. Eilam, T., Y. Anikster, E. Millet, et al. 2009. Genome size innatural and synthetic autopolyploids and in a natural seg-mental allopolyploid of several Triticeae species. Genome52: 275–285.

51. Ozkan, H., M. Tuna & D.W. Galbraith. 2006. No DNA lossin autotetraploids of Arabidopsis thaliana. Plant Breed. 125:288–291.

52. Li, W.H., T. Gojobori & M. Nei. 1981. Pseudogenes as aparadigm of neutral evolution. Nature 292: 237–239.

53. Blanc, G., K. Hokamp & K.H. Wolfe. 2003. A recent poly-ploidy superimposed on older large-scale duplications inthe Arabidopsis genome. Genome Res. 13: 137–144.

54. Schmutz, J., S.B. Cannon, J. Schlueter, et al. 2010. Genomesequence of the palaeopolyploid soybean. Nature 463: 178–183.

55. Yang, Y.W., K.N. Lai, P.Y. Tai & W.H. Li. 1999. Rates ofnucleotide substitution in angiosperm mitochondrial DNAsequences and dates of divergence between Brassica andother angiosperm lineages. J. Mol. Evol. 48: 597–604.

56. Town, C.D., F. Cheung, R. Maiti, et al. 2006. Comparativegenomics of Brassica oleracea and Arabidopsis thalianareveal gene loss, fragmentation, and dispersal after poly-ploidy. Plant Cell 18: 1348–1359.

57. Beilstein, M.A., N.S. Nagalingum, M.D. Clements, et al.2010. Dated molecular phylogenies indicate a Miocene ori-gin for Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A.107: 18724–18728.

58. Wang, X., H. Wang, J. Wang, et al. 2011. The genome of themesopolyploid crop species Brassica rapa. Nat. Genet. 43:1035–1039.

59. Moghe, G.D., D.E. Hufnagel, H. Tang, et al. In press. Conse-quences of whole genome triplication as revealed by com-parative genomic analyses of the wild radish Raphanusraphanistrum and three other Brassicaceae species. PlantCell.

60. Langham, R.J., J. Walsh, M. Dunn, et al. 2004. Genomic du-plication, fractionation and the origin of regulatory novelty.Genetics 166: 935–945.

61. Freeling, M. 2009. Bias in plant gene content followingdifferent sorts of duplication: tandem, whole-genome, seg-mental, or by transposition. Annu. Rev. Plant Biol. 60: 433–453.

62. Thomas, B.C., B. Pedersen & M. Freeling. 2006. Followingtetraploidy in an Arabidopsis ancestor, genes were removedpreferentially from one homeolog leaving clusters enrichedin dose-sensitive genes. Genome Res. 16: 934–946.

63. Schnable, J.C., N.M. Springer & M. Freeling. 2011. Differ-entiation of the maize subgenomes by genome dominanceand both ancient and ongoing gene loss. Proc. Natl. Acad.Sci. U. S. A. 108: 4069–4074.

64. Cheng, F., J. Wu, L. Fang, et al. 2012. Biased gene fractiona-tion and dominant gene expression among the subgenomesof Brassica rapa. PLoS One 7: e36442.

65. Tang, H., M.R. Woodhouse, F. Cheng, et al. 2012. Alteredpatterns of fractionation and exon deletions in Brassica rapa

15Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

support a two-step model of paleohexaploidy. Genetics 190:1563–1574.

66. Woodhouse, M.R., F. Cheng, J.C. Pires, et al. 2014. Origin,inheritance, and gene regulatory consequences of genomedominance in polyploids. Proc. Natl. Acad. Sci. U. S. A. 111:5283–5288.

67. Blanc, G. & K.H. Wolfe. 2004. Functional divergence ofduplicated genes formed by polyploidy during Arabidopsisevolution. Plant Cell 16: 1679–1691.

68. Hanada, K., C. Zou, M.D. Lehti-Shiu, et al. 2008. Impor-tance of lineage-specific expansion of plant tandem dupli-cates in the adaptive response to environmental stimuli.Plant Physiol. 148: 993–1003.

69. Chapman, B.A., J.E. Bowers, F.A. Feltus & A.H. Paterson.2006. Buffering of crucial functions by paleologous du-plicated genes may contribute cyclicality to angiospermgenome duplication. Proc. Natl. Acad. Sci. U. S. A. 103:2730–2735.

70. Jiang, W.K., Y.L. Liu, E.H. Xia & L.Z. Gao. 2013. Prevalentrole of gene features in determining evolutionary fates ofwhole-genome duplication duplicated genes in floweringplants. Plant Physiol. 161: 1844–1861.

71. Pal, C., B. Papp & L.D. Hurst. 2001. Highly expressed genesin yeast evolve slowly. Genetics 158: 927–931.

72. Chang, P.L., B.P. Dilkes, M. McMahon, et al. 2010.Homoeolog-specific retention and use in allotetraploidArabidopsis suecica depends on parent of origin and net-work partners. Genome Biol. 11: R125.

73. Force, A., M. Lynch, F.B. Pickett, et al. 1999. Preservationof duplicate genes by complementary, degenerative muta-tions. Genetics 151: 1531–1545.

74. Freeling, M. & B.C. Thomas. 2006. Gene-balanced duplica-tions, like tetraploidy, provide predictable drive to increasemorphological complexity. Genome Res. 16: 805–814.

75. Birchler, J.A. & R.A. Veitia. 2007. The gene balance hypoth-esis: from classical genetics to modern genomics. Plant Cell19: 395–402.

76. Conant, G.C. & K.H. Wolfe. 2008. Turning a hobby intoa job: how duplicated genes find new functions. Nat. Rev.Genet. 9: 938–950.

77. Des Marais, D.L. & M.D. Rausher. 2008. Escape from adap-tive conflict after duplication in an anthocyanin pathwaygene. Nature 454: 762–765.

78. Edger, P.P. & J.C. Pires. 2009. Gene and genome duplica-tions: the impact of dosage-sensitivity on the fate of nucleargenes. Chromosome Res. 17: 699–717.

79. Kondrashov, F.A. 2012. Gene duplication as a mechanismof genomic adaptation to a changing environment. Proc. R.Soc. B 279: 5048–5057.

80. Haldane, J.B.S. 1932. The Causes of Evolution. PrincetonUniversity Press.

81. Tsai, H., V. Missirian, K.J. Ngo, et al. 2013. Productionof a high-efficiency TILLING population through poly-ploidization. Plant Physiol. 161: 1604–1614.

82. Akhunov, E.D., S. Sehgal, H. Liang, et al. 2013. Comparativeanalysis of syntenic genes in grass genomes reveals acceler-ated rates of gene structure and coding sequence evolutionin polyploid wheat. Plant Physiol. 161: 252–265.

83. Parisod, C., K. Alix, J. Just, et al. 2010. Impact of trans-posable elements on the organization and function of al-lopolyploid genomes. New Phytol. 186: 37–45.

84. Parisod, C. & N. Senerchia. 2012. “Responses of transpos-able elements to polyploidy.” In Plant Transposable Ele-ments. M.A. Grandbastien & J.M. Casacuberta, Eds.: 147–168. Berlin, Heidelberg: Springer.

85. Ben-David, S., B. Yaakov & K. Kashkush. 2013. Genome-wide analysis of short interspersed nuclear elements SINESrevealed high sequence conservation, gene association andretrotranspositional activity in wheat. Plant J. 76: 201–210.

86. Hazzouri, K.M., A. Mohajer, S.I. Dejak, et al. 2008. Con-trasting patterns of transposable-element insertion poly-morphism and nucleotide diversity in autotetraploid andallotetraploid Arabidopsis species. Genetics 179: 581–592.

87. Beaulieu, J., M. Jean & F. Belzile. 2009. The allotetraploidArabidopsis thaliana-Arabidopsis lyrata subsp. petraea as analternative model system for the study of polyploidy inplants. Mol. Genet. Genomics 281: 421–435.

88. Parisod, C., A. Salmon, T. Zerjal, et al. 2009. Rapid struc-tural and epigenetic reorganization near transposable el-ements in hybrid and allopolyploid genomes in Spartina.New Phytol. 184: 1003–1015.

89. Petit, M., C. Guidat, J. Daniel, et al. 2010. Mobilization ofretrotransposons in synthetic allotetraploid tobacco. NewPhytol. 186: 135–147.

90. Chantret, N., J. Salse, F. Sabot, et al. 2005. Molecular ba-sis of evolutionary events that shaped the hardness lo-cus in diploid and polyploid wheat species (Triticum andAegilops). Plant Cell 17: 1033–1045.

91. Bruggmann, R., A.K. Bharti, H. Gundlach, et al. 2006. Un-even chromosome contraction and expansion in the maizegenome. Genome Res. 16: 1241–1251.

92. Adams, K.L. & J.F. Wendel. 2005. Novel patterns of geneexpression in polyploid plants. Trends Genet. 21: 539–543.

93. Adams, K.L. 2007. Evolution of duplicate gene expressionin polyploid and hybrid plants. J. Hered. 98: 136–141.

94. Jackson, S. & Z.J. Chen. 2010. Genomic and expressionplasticity of polyploidy. Curr. Opin. Plant Biol. 13: 153–159.

95. Birchler, J.A. 2012. Insights from paleogenomic and pop-ulation studies into the consequences of dosage sensitivegene expression in plants. Curr. Opin. Plant Biol. 15: 544–548.

96. Hegarty, M., J. Coate, S. Sherman-Broyles, et al. 2013.Lessons from natural and artificial polyploids in higherplants. Cytogenet. Genome Res. 140: 204–225.

97. Zou, C., M.D. Lehti-Shiu, M. Thomashow & S.-H. Shiu.2009. Evolution of stress-regulated gene expression induplicate genes of Arabidopsis thaliana. PLoS Genet. 5:e1000581.

98. Hegarty, M.J., G.L. Barker, I.D. Wilson, et al. 2006. Tran-scriptome shock after interspecific hybridization in Seneciois ameliorated by genome duplication. Curr. Biol. 16: 1652–1659.

99. Wang, J., L. Tian, H.S. Lee, et al. 2006. Genomewide non-additive gene regulation in Arabidopsis allotetraploids. Ge-netics 172: 507–517.

16 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

100. Xu, Y., L. Zhong, X. Wu, et al. 2009. Rapid alterations of geneexpression and cytosine methylation in newly synthesizedBrassica napus allopolyploids. Planta 229: 471–483.

101. Flagel, L., J. Udall, D. Nettleton & J. Wendel. 2008. Duplicategene expression in allopolyploid Gossypium reveals twotemporally distinct phases of expression evolution. BMCBiol. 6: 16.

102. Chelaifa, H., V. Chague, S. Chalabi, et al. 2013. Prevalenceof gene expression additivity in genetically stable wheatallohexaploids. New Phytol. 197: 730–736.

103. Gianinetti, A. 2013. A criticism of the value of midparentin polyploidization. J. Exp. Bot. 64: 4119–4129.

104. Grover, C.E., J.P. Gallagher, E.P. Szadkowski, et al. 2012. Ho-moeolog expression bias and expression level dominancein allopolyploids. New Phytol. 196: 966–971.

105. Lee, H.S. & Z.J. Chen. 2001. Protein-coding genes are epi-genetically regulated in Arabidopsis polyploids. Proc. Natl.Acad. Sci. U. S. A. 98: 6753–6758.

106. Yoo, M.-J., E. Szadkowski & J.F. Wendel. 2013. Homoe-olog expression bias and expression level dominance inallopolyploid cotton. Heredity 110: 171–180.

107. Wendel, J.F. & R.C. Cronn. 2003. “Polyploidy and the evo-lutionary history of cotton.” In Advances in Agronomy. pp.139–186. Academic Press.

108. Rapp, R.A., J.A. Udall & J.F. Wendel. 2009. Genomic ex-pression dominance in allopolyploids. BMC Biol. 7: 18.

109. Xu, C., Y. Bai, X. Lin, et al. 2014. Genome-wide disruptionof gene expression in allopolyploids but not hybrids of ricesubspecies. Mol. Biol. Evol.

110. Ownbey, M. 1950. Natural hybridization and amphiploidyin the genus Tragopogon. Am. J. Bot. 37: 487–499.

111. Lowe, A. & R.J. Abbott. 2003. A new British species Senecioeboracensis (Asteraceae) another hybrid derivative of S.vulgaris L. and S. squalidus L. Watsonia 24: 375–388.

112. Wang, J., L. Tian, H.S. Lee, et al. 2006. Genomewide non-additive gene regulation in Arabidopsis allotetraploids. Ge-netics 172: 507–517.

113. Church, S.A. & E.J. Spaulding. 2009. Gene expression ina wild autopolyploid sunflower series. J. Hered. 100: 491–495.

114. Chelaifa, H., A. Monnier & M. Ainouche. 2010. Tran-scriptomic changes following recent natural hybridizationand allopolyploidy in the salt marsh species Spartina ×townsendii and Spartina anglica (Poaceae). New Phytol. 186:161–174.

115. Yang, C., Y. Kawahara, H. Mizuno, et al. 2012. Independentdomestication of Asian rice followed by gene flow fromjaponica to indica. Mol. Biol. Evol. 29: 1471–1479.

116. Chen, Z.J. 2007. Genetic and epigenetic mechanisms forgene expression and phenotypic variation in plant poly-ploids. Annu. Rev. Plant Biol. 58: 377–406.

117. Comai, L. 2000. Genetic and epigenetic interactions in al-lopolyploid plants. Plant Mol. Biol. 43: 387–399.

118. Doyle, J.J., L.E. Flagel, A.H. Paterson, et al. 2008. Evolu-tionary genetics of genome merger and doubling in plants.Annu. Rev. Genet. 42: 443–461.

119. Chen, Z.J. 2010. Molecular mechanisms of polyploidy andhybrid vigor. Trends Plant Sci. 15: 57.

120. Mayfield, D., Z.J. Chen & J.C. Pires. 2011. Epigenetic reg-ulation of flowering time in polyploids. Curr. Opin. PlantBiol. 14: 174–178.

121. Ng, D.W., J. Lu & Z.J. Chen. 2012. Big roles for small RNAsin polyploidy, hybrid vigor, and hybrid incompatibility.Curr. Opin. Plant Biol. 15: 154–161.

122. Madlung, A. & J.F. Wendel. 2013. Genetic and epigeneticaspects of polyploid evolution in plants. Cytogenet. GenomeRes. 140: 270–285.

123. Lukens, L.N., J.C. Pires, E. Leon, et al. 2006. Patterns ofsequence loss and cytosine methylation within a populationof newly resynthesized Brassica napus allopolyploids. PlantPhysiol. 140: 336–348.

124. Shaked, H., K. Kashkush, H. Ozkan, et al. 2001. Sequenceelimination and cytosine methylation are rapid and repro-ducible responses of the genome to wide hybridization andallopolyploidy in wheat. Plant Cell 13: 1749–1760.

125. Salmon, A., M.L. Ainouche & J.F. Wendel. 2005. Geneticand epigenetic consequences of recent hybridization andpolyploidy in Spartina (Poaceae). Mol. Ecol. 14: 1163–1175.

126. Madlung, A., R.W. Masuelli, B. Watson, et al. 2002. Remod-eling of DNA methylation and phenotypic and transcrip-tional changes in synthetic Arabidopsis allotetraploids.Plant Physiol. 129: 733–746.

127. Chen, L. & J. Chen. 2008. Changes of cytosine methyla-tion induced by wide hybridization and allopolyploidy inCucumis. Genome 51: 789–799.

128. Chen, M., M. Ha, E. Lackey, et al. 2008. RNAi of met1reduces DNA methylation and induces genome-specificchanges in gene expression and centromeric small RNAaccumulation in Arabidopsis allopolyploids. Genetics 178:1845–1858.

129. Law, J.A. & S.E. Jacobsen. 2010. Establishing, maintainingand modifying DNA methylation patterns in plants andanimals. Nat. Rev. Genet. 11: 204–220.

130. Mittelsten Scheid, O., K. Afsar & J. Paszkowski. 2003. For-mation of stable epialleles and their paramutation-like in-teraction in tetraploid Arabidopsis thaliana. Nat. Genet. 34:450–454.

131. Baubec, T., H.Q. Dinh, A. Pecinka, et al. 2010. Cooperationof multiple chromatin modifications can generate unantic-ipated stability of epigenetic States in Arabidopsis. PlantCell 22: 34–47.

132. Ha, M., D.W. Ng, W.H. Li & Z.J. Chen. 2011. Coordinatedhistone modifications are associated with gene expressionvariation within and between species. Genome Res. 21: 590–598.

133. Ha, M., J. Lu, L. Tian, et al. 2009. Small RNAs serve as agenetic buffer against genomic shock in Arabidopsis inter-specific hybrids and allopolyploids. Proc. Natl. Acad. Sci. U.S. A. 106: 17835–17840.

134. Kenan-Eichler, M., D. Leshkowitz, L. Tal, et al. 2011. Wheathybridization and polyploidization results in deregulationof small RNAs. Genetics 188: 263–272.

135. Lackey, E., D.W. Ng & Z.J. Chen. 2010. RNAi-mediateddown-regulation of DCL1 and AGO1 induces developmen-tal changes in resynthesized Arabidopsis allotetraploids.New Phytol. 186: 207–215.

17Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Plant polyploidy Moghe & Shiu

136. Pikaard, C.S. & O. Mittelsten-Scheid. 2014. “EpigeneticRegulation in Plants.” In Epigenetics. D. Allis, T. Jenuwein& D. Reinberg, Eds. CSHL Press.

137. Coate, J.E., H. Bar & J.J. Doyle. 2014. Extensive translationalregulation of gene expression in an allopolyploid (Glycinedolichocarpa). Plant Cell 26: 136–150.

138. Birchler, J.A. & R.A. Veitia. 2012. Gene balance hypothe-sis: connecting issues of dosage sensitivity across biologicaldisciplines. Proc. Natl. Acad. Sci. U. S. A. 109: 14746–14753.

139. De Smet, R. & Y. Van de Peer. 2012. Redundancy andrewiring of genetic networks following genome-wide du-plication events. Curr. Opin. Plant Biol. 15: 168–176.

140. Lou, P., J. Wu, F. Cheng, et al. 2012. Preferential retentionof circadian clock genes during diploidization followingwhole genome triplication in Brassica rapa. Plant Cell 24:2415–2426.

141. Bekaert, M., P.P. Edger, J.C. Pires & G.C. Conant. 2011.Two-phase resolution of polyploidy in the Arabidopsismetabolic network gives rise to relative and absolute dosageconstraints. Plant Cell 23: 1719–1728.

142. Veron, A.S., K. Kaufmann & E. Bornberg-Bauer. 2007. Ev-idence of interaction network evolution by whole-genomeduplications: a case study in MADS-box proteins. Mol. Biol.Evol. 24: 670–678.

143. Hsu, C.Y., J.P. Adams, H. Kim, et al. 2011. FLOWERINGLOCUS T duplication coordinates reproductive and vege-tative growth in perennial poplar. Proc. Natl. Acad. Sci. U.S. A. 108: 10756–10761.

144. Sheehan, M.J., L.M. Kennedy, D.E. Costich & T.P. Brutnell.2007. Subfunctionalization of PhyB1 and PhyB2 in the con-trol of seedling and mature plant traits in maize. Plant J.49: 338–353.

145. Wolfe, K.H. & D.C. Shields. 1997. Molecular evidence foran ancient duplication of the entire yeast genome. Nature387: 708–713.

146. Ihmels, J., S. Bergmann, M. Gerami-Nejad, et al. 2005.Rewiring of the yeast transcriptional network through theevolution of motif usage. Science 309: 938–940.

147. Conant, G.C. & K.H. Wolfe. 2006. Functional partitioningof yeast co-expression networks after genome duplication.PLoS Biol. 4: e109.

148. Levin, D. 2002. “Phenotypic consequences of chromosomedoubling.” In The Role of Chromosomal Change in PlantEvolution. pp. 134–149. Oxford University Press.

149. Otto, S.P. & J. Whitton. 2000. Polyploid incidence and evo-lution. Annu. Rev. Genet. 34: 401–437.

150. Li, X., E. Yu, C. Fan, et al. 2012. Developmental, cytologicaland transcriptional analysis of autotetraploid Arabidopsis.Planta 236: 579–596.

151. Te Beest, M., J.J. Le Roux, D.M. Richardson, et al. 2012. Themore the better? The role of polyploidy in facilitating plantinvasions. Ann. Bot. 109: 19–45.

152. Robertson, K., E.E. Goldberg & B. Igic. 2011. Comparativeevidence for the correlated evolution of polyploidy andself-compatibility in Solanaceae. Evolution 65: 139–155.

153. Barringer, B.C. 2007. Polyploidy and self-fertilization inflowering plants. Am. J. Bot. 94: 1527–1533.

154. Mable, B.K. 2004. Polyploidy and self-compatibility: Isthere an association? New Phytol. 162: 803–811.

155. Warner, D.A. & G.E. Edwards. 1993. Effects of polyploidyon photosynthesis. Photosynth. Res. 35: 135–147.

156. Li, W.L., G.P. Berlyn & P.M.S. Ashton. 1996. Polyploids andtheir structural and physiological characteristics relative towater deficit in Betula papyrifera (Betulaceae). Am. J. Bot.U. S. A.

157. Coate, J.E., A.F. Powell, T.G. Owens & J.J. Doyle. 2013.Transgressive physiological and transcriptomic responsesto light stress in allopolyploid Glycine dolichocarpa (Legu-minosae). Heredity 110: 160–170.

158. Maherali, H., A.E. Walden & B.C. Husband. 2009. Genomeduplication and the evolution of physiological responses towater stress. New Phytol. 184: 721–731.

159. Hao, G.-Y., M.E. Lucero, S.C. Sanderson, et al. 2013. Poly-ploidy enhances the occupation of heterogeneous envi-ronments through hydraulic related trade-offs in Atriplexcanescens (Chenopodiaceae). New Phytol. 197: 970–978.

160. Levin, D.A. 1983. Polyploidy and novelty in floweringplants. Am. Nat. 122: 1–25.

161. Oswald, B.P. & S.L. Nuismer. 2007. Neopolyploidy andpathogen resistance. Proc. R. Soc. B 274: 2393–2397.

162. Schoen, D.J., J.J. Burdon & A.H. Brown. 1992. Resistanceof Glycine tomentella to soybean leaf rust Phakopsorapachyrhizi in relation to ploidy level and geographic distri-bution. Theor. Appl. Genet. 83: 827–832.

163. Busey, P., R.M. Giblin-Davis & B.J. Center. 1993. Resistancein Stenotaphrum to the sting nematode. Crop Sci. U. S. A.

164. Thompson, J.N., B.M. Cunningham, K.A. Segraves, et al.1997. Plant polyploidy and insect/plant interactions. Am.Nat. 150: 730–743.

165. Nuismer, S.L. & J.N. Thompson. 2001. Plant polyploidyand non-uniform effects on insect herbivores. Proc. R. Soc.B 268: 1937–1940.

166. Stebbins, C.L. 1950. Variation and Evolution in Plants. Lon-don: Oxford University Press.

167. Otto, S.P. 2007. The evolutionary consequences of poly-ploidy. Cell 131: 452–462.

168. Fawcett, J.A. & Y.V. de. Peer. 2010. Angiosperm polyploidsand their road to evolutionary success. Trends Evol. Biol. 2:e3.

169. Brochmann, C., A.K. Brysting, I.G. Alsos, et al. 2004. Poly-ploidy in arctic plants. Biol. J. Linn. Soc. 82: 521–536.

170. Fawcett, J.A., S. Maere & Y. Van de Peer. 2009. Plants withdouble genomes might have had a better chance to survivethe Cretaceous-Tertiary extinction event. Proc. Natl. Acad.Sci. U. S. A. 106: 5737–5742.

171. Pandit, M.K., M.J.O. Pocock & W.E. Kunin. 2011. Ploidy in-fluences rarity and invasiveness in plants. J. Ecol. 99: 1108–1115.

172. Chao, D.-Y., B. Dilkes, H. Luo, et al. 2013. Polyploids ex-hibit higher potassium uptake and salinity tolerance inArabidopsis. Science 341: 658–659.

173. Bowden, W.M. 1940. Diploidy, polyploidy, and winter har-diness relationships in the flowering plants. Am. J. Bot. 27:357–371.

174. Martin, S.L. & B.C. Husband. 2009. Influence of phy-logeny and ploidy on species ranges of North Americanangiosperms. J. Ecol. 97: 913–922.

18 Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.

Moghe & Shiu Plant polyploidy

175. Segraves, K.A. & J.N. Thompson. 1999. Plant polyploidyand pollination: floral traits and insect visits to diploid andtetraploid Heuchera grossulariifolia. Evolution 53: 1114–1127.

176. Kennedy, B.F., H.A. Sabara, D. Haydon & B.C. Husband.2006. Pollinator-mediated assortative mating in mixedploidy populations of Chamerion angustifolium (Ona-graceae). Oecologia 150: 398–408.

177. Baldwin, S.J. & B.C. Husband. 2011. Genome duplicationand the evolution of conspecific pollen precedence. Proc.R. Soc. B 278: 2011–2017.

178. Ainouche, M.L., P.M. Fortune, A. Salmon, et al. 2009. Hy-bridization, polyploidy and invasion: lessons from Spartina(Poaceae). Biol. Invasions 11: 1159–1173.

179. Ramsey, J. 2011. Polyploidy and ecological adaptation inwild yarrow. Proc. Natl. Acad. Sci. U. S. A. 108: 7096–7101.

180. Martin, S.L. & B.C. Husband. 2012. Whole genome dupli-cation affects evolvability of flowering time in an autote-traploid plant. PLoS One 7: e44784.

181. Martin, S.L. & B.C. Husband. 2013. Adaptation of diploidand tetraploid chamerion angustifolium to elevation butnot local environment. Evolution 67: 1780–1791.

182. Vamosi J.C. & T.A. Dickinson. 2006. Polyploidy and diver-sification: a phylogenetic investigation in Rosaceae. Int. J.Plant Sci. 167: 349–358.

183. Paterson, A.H., J.E. Bowers & B.A. Chapman. 2004. Ancientpolyploidization predating divergence of the cereals, and itsconsequences for comparative genomics. Proc. Natl. Acad.Sci. U. S. A. 101: 9903–9908.

184. Barker, M.S., N.C. Kane, M. Matvienko, et al. 2008. Mul-tiple paleopolyploidizations during the evolution of theCompositae reveal parallel patterns of duplicate gene reten-tion after millions of years. Mol. Biol. Evol. 25: 2445–2455.

185. Cannon, S.B., D. Ilut, A.D. Farmer, et al. 2010. Polyploidydid not predate the evolution of nodulation in all legumes.PloS One 5: e11630.

186. Wood, T.E., N. Takebayashi, M.S. Barker, et al. 2009. Thefrequency of polyploid speciation in vascular plants. Proc.Natl. Acad. Sci. U. S. A. 106: 13875–13879.

187. Mayrose, I., S.H. Zhan, C.J. Rothfels, et al. 2011. Recentlyformed polyploid plants diversify at lower rates. Science333: 1257.

188. Sabara, H.A., P. Kron & B.C. Husband. 2013. Cytotype co-existence leads to triploid hybrid production in a diploid-tetraploid contact zone of Chamerion angustifolium (On-agraceae). Am. J. Bot. 100: 962–970.

189. Marques, I., D. Draper, L. Riofrıo & C. Naranjo. 2014. Mul-tiple hybridization events, polyploidy and low postmatingisolation entangle the evolution of neotropical species ofEpidendrum (Orchidaceae). BMC Evol. Biol. 14: 20.

190. Sonnleitner, M., B. Weis, R. Flatscher, et al. 2013. Parentalploidy strongly affects offspring fitness in heteroploidcrosses among three cytotypes of autopolyploid Jacobaeacarniolica (Asteraceae). PLoS One 8: e78959.

191. Petit, C., F. Bretagnolle & F. Felber. 1999. Evolutionaryconsequences of diploid-polyploid hybrid zones in wildspecies. Trends Ecol. Evol. 14: 306–311.

192. Ohta, T. 1992. The nearly neutral theory of molecular evo-lution. Annu. Rev. Ecol. Syst. 23: 263–286.

193. Umezawa, T., M. Fujita, Y. Fujita, et al. 2006. Engineer-ing drought tolerance in plants: discovering and tailoringgenes to unlock the future. Curr. Opin. Biotechnol. 17: 113–122.

194. Hu, H. & L. Xiong. 2013. Genetic engineering and breedingof drought-resistant crops. Annu. Rev. Plant Biol. 65: 83–108.

19Ann. N.Y. Acad. Sci. xxxx (2014) 1–19 C© 2014 New York Academy of Sciences.