genetic mechanisms of allopolyploid speciation through hybrid genome doubling: novel insights from...

CHAPTER FOUR

Genetic Mechanisms ofAllopolyploid Speciation ThroughHybrid Genome Doubling: NovelInsights from Wheat (Triticum andAegilops) StudiesYoshihiro Matsuoka*,1, Shigeo Takumi†, Shuhei Nasuda{*Department of Bioscience, Fukui Prefectural University, Matsuoka, Eiheiji, Yoshida, Fukui, Japan†Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku,Kobe, Japan{Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho,Sakyo-ku, Kyoto, Japan1Corresponding author: e-mail address: [email protected]

Contents

1. Introduction 2002. Plant Polyploidy and Allopolyploidy 202

2.1 Origin of polyploid species diversity in plants 2022.2 Allopolyploids and autopolyploids 2042.3 Genesis of a polyploid plant 2062.4 Process of allopolyploid speciation through hybrid genome doubling 2072.5 Wheat (Triticum and Aegilops) species as model systems for studies on

allopolyploid speciation 2103. Pre- and Postzygotic Barriers in Plant Hybridization 213

3.1 Kr genes: Example of genetic mechanisms for prezygotic barriers 2133.2 Postzygotic barriers 215

4. Unreduced Gametes 2254.1 Unreduced gamete production in the F1 hybrid between T. turgidum

and Ae. tauschii 2264.2 Cytological mechanisms 2274.3 Genetic mechanisms 2304.4 Maintenance of genes for F1 hybrids’ unreduced gamete production

in the parental species 2345. Allopolyploid Genome Alteration 235

5.1 Chromosomal changes 2375.2 Genic/epigenetic changes 240

6. Concluding Remarks 242References 244

International Review of Cell and Molecular Biology, Volume 309 # 2014 Elsevier Inc.ISSN 1937-6448 All rights reserved.http://dx.doi.org/10.1016/B978-0-12-800255-1.00004-1

199

http://dx.doi.org/10.1016/B978-0-12-800255-1.00004-1

Abstract

Polyploidy, which arises through complex genetic and ecological processes, is animportant mode of plant speciation. This review provides an overview of recentadvances in understanding why plant polyploid species are so ubiquitous and diverse.We consider how the modern framework for understanding genetic mechanisms ofspeciation could be used to study allopolyploid speciation that occurs through hybridgenome doubling, that is, whole genome doubling of interspecific F1 hybrids by theunion of male and female unreduced gametes. We outline genetic and ecologicalmechanisms that may have positive or negative impacts on the process of allopolyploidspeciation through hybrid genome doubling. We also discuss the current status of stud-ies on the underlying genetic mechanisms focusing on the wheat (Triticum andAegilops) hybrid-specific reproductive phenomena that are well known but deserverenewed attention from an evolutionary viewpoint.

1. INTRODUCTION

Polyploidy, which consists in having two or more sets of nuclear

genomes (i.e., entire somatic chromosomes) in a single nucleus, is observed

in a diverse array of eukaryotes, including fungi, insects, fishes, amphibians,

reptiles, and plants (Lewis, 1980). Biologists have long recognized the sig-

nificant role of polyploidy in evolution. For several decades in the twentieth

century, polyploidy was studied mainly through biosystematics approaches

and later through empirical approaches with a particular focus on the genetic

and ecological details of the underlying mechanisms. The recent develop-

ment of molecular tools enabled in-depth analyses of various intriguing

genetic and genomic phenomena found in synthetic and natural polyploids.

In the past 20 years, polyploidy became widely recognized as an important

mode of plant speciation and a number of intensive and extensive studies that

were done using model systems provided novel insights into the genetic

underpinning of polyploidy. As a consequence, a drastic conceptual reno-

vation came about: polyploidy, which once was considered as mere addition

of genomes, is now viewed as the product of a highly dynamic process in

which restructuring of the transcriptome, metabolome, and proteome

occurs through various genetic, epigenetic, and genomic changes (Leitch

and Leitch, 2008).

Recent advances in characterizing the genetic, epigenetic, and genomic

mechanisms for polyploidization have provided empirical backing for the

recognition of polyploidy as a major driving force in plant diversification.

200 Yoshihiro Matsuoka et al.

The global genome restructuring that occurs during polyploidization may

confer, in addition to reproductive isolation, novel phenotypes that open

avenues for exploiting fitness peaks in an adaptive landscape. However, to

better understand the significance of polyploidy in the broad picture of plant

evolution, several other genetic and ecological aspects of polyploid specia-

tion must further be learned because polyploid speciation is a complex pro-

cess that includes a variety of mechanisms ranging from species crosses and

viable hybrid formation to spontaneous genome doubling, fertility restora-

tion, and the establishment of new polyploids as persisting entities in an

ecosystem.

The primary aim of this chapter is to consider how the modern frame-

work for understanding the genetic mechanisms of speciation could be used

to study the evolution through allopolyploidy, that is, a type of polyploidy

that results from interspecific hybridization and subsequent genome dou-

bling. For this, we focus on a distinctive mode of allopolyploid speciation

and attempt to evaluate what kind of roles such well-known speciation/

reproductive mechanisms as prezygotic barriers, postzygotic barriers,

unreduced gamete production, and genome alteration may have in the pro-

cess. In Section 2, we first review the recent advances in understanding why

plant polyploid species are so ubiquitous and introduce an emerging view for

the origin of their remarkable diversity (Section 2.1). Then, the terminology

for describing the types of polyploids and the categories for classifying plant

polyploids are outlined (Section 2.2). We also outline the genetic and eco-

logical mechanisms that may have positive or negative impacts on the pro-

cess of allopolyploid speciation (Section 2.3) and point out a mode of

allopolyploid speciation that is characterized by the occurrence of whole

genome doubling typically through the union of male and female unreduced

gametes produced by the F1 hybrid of the parental individuals (Section 2.4).

In this chapter, we call this mode “allopolyploid speciation through the

hybrid genome doubling (HGD) pathway.” Subsequently, common wheat

(Triticum aestivum L.) and its relatives are introduced as a usable model system

for allopolyploid speciation studies (Section 2.5). In Sections 3–5, the cur-

rent status of the studies on the genetic mechanisms that underline allopoly-

ploid speciation through the HGD pathway is discussed.

During the last 50 years, a large body of genetic and cytogenetic work has

been done on various intriguing reproductive phenomena of wheat inter-

specific hybrids. In our view, those phenomena deserve a renewed attention

from the standpoint of evolution because they can provide valuable insights

into the genetic mechanisms for allopolyploid speciation. For this reason,

201Plant Polyploidy via Hybrid Genome Doubling

special emphasis is put on the results from the wheat studies in Sections 3–5

to show their significance in understanding the genetic underpinning of allo-

polyploid evolution, referring to the relevant work that was done using

other model plant systems. The discussion that we present herein highlights

the fertile field of polyploid research where plant speciation studies meet

reproduction biology and underscores the need for further development

of empirical and theoretical basis for “hybrid genetics” that can deal with

the highly diverse Mendelian and non-Mendelian mechanisms for the com-

plex phenotype expression in interspecific hybrids.

2. PLANT POLYPLOIDY AND ALLOPOLYPLOIDY

2.1. Origin of polyploid species diversity in plantsCurrently, the evidence for a significant impact of polyploidy on the evo-

lution of vascular plants is overwhelming. Based on chromosome numbers,

Stebbins (1950) estimated the frequency of polyploidy to be roughly

30–35% in angiosperms, whereas Grant (1981) inferred that 47% of angio-

sperm species, 58% of monocot species, and 43% of dicot species were poly-

ploid. In ferns, the estimated frequency of polyploids is 95% (Grant, 1981).

In a recent survey of chromosome counts, 34.5% of vascular plants species

are polyploid relative to their generic base numbers (Wood et al., 2009).

Analyses of fossil data suggested that about 70% of angiosperms went

through polyploidy during their evolution (Masterson, 1994). More

recently, genome-wide nucleotide sequence analyses provided substantial

evidence for ancient genome duplication (i.e., ancient polyploidy) in exam-

ined species, including Arabidopsis (Vision et al., 2000), Oryza (Paterson

et al., 2004), Populus (Tuskan et al., 2006), Vitis (Jaillon et al., 2007), Carica

(Ming et al., 2008), Zea (Schnable et al., 2009), Brachypodium (Vogel et al.,

2010), Malus (Velasco et al., 2010), Glycine (Schmutz et al., 2010), and

Hordeum (Thiel et al., 2009). Amodel-based analysis of large sets of expressed

sequence tags suggested a genome duplication event in the common ances-

tor of virtually all extant angiosperms (Cui et al., 2006).

There are two possible explanations for the origin of the remarkable

diversity of polyploid plant species. One explanation is that polyploid species

are abundant because the diversification rates (i.e., speciation rates minus

extinction rates) are increased in the polyploid species relative to their dip-

loid ancestors. In this view, polyploidy can be regarded as a mechanism that

facilitates adaptive evolution through the expression of transgressive pheno-

types, gene redundancy, and changes in reproduction modes (Bicknell and


Koltunow, 2004; Hegarty andHiscock, 2008). The dynamic molecular pro-

cess of polyploidization may provide raw material for expressing novel phe-

notypes on which natural selection can act (Soltis and Soltis, 2009). In

contrast, the other explanation hypothesizes that polyploid species are abun-

dant simply because they are formed relatively frequently under natural con-

ditions. In this view, polyploidy per se has a marginal role in adaptive

evolution, representing a type of mutation through which novel phenotypes

may arise and only occasionally increase in frequency within populations

(Stebbins, 1971; Wagner, 1970). In fact, several inherent disadvantages

are associated with polyploidization, including the disrupting effects of

nuclear and cell enlargement, difficulties in mitosis and meiosis, and epige-

netic instability (Comai, 2005). Furthermore, newly formed polyploids may

face several ecological challenges under natural conditions such as minority

cytotype exclusion through competition with the diploid ancestors (Sobel

et al., 2010). Accordingly, natural newborn polyploids may most likely

go extinct before they are established as persisting entities.

Soltis et al. (2009) examined the association of ancient polyploidy with

species richness. They first inferred the points of ancient whole genome

duplication in angiosperm phylogeny based on the published genome

sequence data and statistically tested the significance of the differences in spe-

cies richness between the ancient polyploid clades and their sister diploid

clades. Their results suggested that ancient polyploidy might have increased

species richness in several angiosperm clades, including Brassicaceae,

Cleomaceae, Fabaceae, Poaceae, and Solanoideae, consistent with the view

that, in the long term, polyploid species have higher diversification rates than

their diploid ancestors. However, studies on recently formed polyploid spe-

cies provided opposing results. Mayrose et al. (2011) estimated diversifica-

tion rates of polyploid species and their diploid ancestors for 63 generic-level

groups of angiosperm and seed-free vascular plant species by the use of the

binary state speciation and extinction model (Maddison et al., 2007). The

diversification rates measured by Maddison et al. (2007) were significantly

reduced in the polyploid species because the speciation rates of polyploid

species were lower than that of their diploid ancestors, whereas the extinc-

tion rates of polyploid species were higher than that of their diploid ances-

tors. Therefore, it does not seem that polyploidy drives adaptive evolution in

the short term. These results supported the idea that the current diversity of

plant polyploid species is most likely a consequence of high rates of forma-

tion. In fact, the frequencies of speciation that are accompanied by ploidy

increase were estimated to be 15% in angiosperms and 31% in ferns


(Wood et al., 2009). The results of Soltis et al. (2009) and Mayrose et al.

(2011) may seem contradictory, but they provide a unified picture of

polyploid plant species evolution and diversification: polyploidy is most

often an evolutionary dead end, but, in the long term, the high frequency

of polyploid formation can lead to the accumulation of rare successful poly-

ploids that overcome the hurdles against speciation (Mayrose et al., 2011).

The emerging view on the origin of polyploid species diversity raises the

question of the conditions under which newly formed polyploids could be

established as species. Newly formed polyploids may have distinctive phe-

notypes, such as hybrid vigor, increased drought tolerance, and pest resis-

tance, whereas no consistent advantage associated with polyploidy is

known (Comai, 2005; Levin, 1983). Empirical and theoretical studies indi-

cated that the possibility for newly formed polyploids to be established as

persisting species might be increased in unstable, rapidly changing environ-

ments (Ehrendorfer, 1980; Oswald and Nuismer, 2011). Several contempo-

rary lineages of the diverse polyploid plant species, therefore, might

represent the descendants of polyploids that were formed in the

Cretaceous–Tertiary boundary period (65 million years ago) and survived

the most recent mass extinction in which up to 60% of plant species dis-

appeared through catastrophic environmental change caused by a massive

asteroid impact and/or increased volcanic activity (Fawcett et al., 2009;

Wilf and Johnson, 2004).

2.2. Allopolyploids and autopolyploidsBy definition, polyploid species have two or more sets of nuclear genome,

but the pattern of speciation throughwhich the state of polyploidy is reached

may vary. Kihara and Ono (1926) found two distinctive types of natural

polyploids and coined the terms “allopolyploids” (i.e., polyploids having

multiple sets of different genomes) and “autopolyploids” (i.e., polyploids

having multiple sets of the same genome). In the field of evolutionary biol-

ogy, these terms are now used to classify polyploids based on an “anteced-

ents” criterion: autopolyploids are formed through doubling of a somatic

chromosome set derived from a single species, whereas allopolyploids result

from the merger of different somatic chromosome sets derived from

diverged species. In the field of genetics, these terms have different defini-

tions that are based on a cytogenetic criterion: autopolyploids are individuals

that show polysomic inheritance, whereas allopolyploids are individuals that

show disomic inheritance (Doyle and Egan, 2010).


Either criterion, however, is not always applicable. For example, it

would be necessary to identify the ancestral diploid species to show that a

polyploid species is a true allopolyploid using the “antecedents” criterion.

The ancestral diploid species can be identified through comparative

approaches, but the exact identity of the allopolyploid genome often remains

unknown, especially when the polyploid species was formed in the distant

past. Also, the instances of segmental allopolyploids that show polysomic and

disomic inheritance depending on which locus in the genome is considered

may pose a serious problemwhen applying the cytogenetic criterion. In fact,

how to classify the diverse array of natural and synthetic polyploids is a long-

debated, unsettled matter (Soltis et al., 2010). Despite the difficulties that are

encountered when classifying natural polyploid species using those criteria,

the terms allopolyploids and autopolyploids are useful in many polyploid

studies. From here on, we adopt the “antecedents” criterion to classify poly-

ploids and use the term allopolyploids and autopolyploids to indicate their

mode of origin.

The relative abundance of allopolyploid and autopolyploid species is not

known. Previously, autopolyploid species were thought to be much less

common than allopolyploid species, partly because newly formed autopoly-

ploids experience multivalent problems in meiosis at an increased rate rela-

tive to newly formed allopolyploids (Grant, 1981; Stebbins, 1950). This

view, however, is no longer maintained on several grounds. For example,

the mean pollen viabilities and mean seed fertilities do not significantly differ

between allopolyploids and autopolyploids, whereas multivalents occur

more frequently in autopolyploids (28.8%) than in allopolyploids (8.0%)

(Ramsey and Schemske, 2002). Furthermore, autopolyploids may be

formed more often than allopolyploids under natural conditions, simply

because within-species crosses (to form autopolyploids) are much more fre-

quent than between-species crosses (to form allopolyploids) (Ramsey and

Schemske, 1998). Nevertheless, the successful establishment of new auto-

polyploids as persisting species may be rare in the face of competition from

the diploid ancestors because little phenotypic divergence between typical

nascent autopolyploids and their diploid ancestors can cause extensive eco-

logical niche overlap. Autopolyploid species, therefore, might not be so

common as allopolyploid species, but further work is required to support

this view (Coyne and Orr, 2004).

The term “hybridization” also has dual meanings. Traditionally, the term

is used to indicate crossing between species. In the fields of genetics and ecol-

ogy, however, the concept of hybridization is now widened to include


crossing between ecotypes or genetically differentiated populations within a

single species (Ellstrand and Schierenbeck, 2000). Successful hybridization is

a prerequisite for allopolyploid speciation to occur. Also, hybridization may

have a significant impact on the evolution of autopolyploid species, because

natural autopolyploid species may arise from crossings between ecotypes

within a single species (Stebbins, 1985). Accordingly, we hereafter use

the term hybridization in the broad sense.

2.3. Genesis of a polyploid plantThere are three cytological mechanisms that cause ploidy increase: union of

unreduced gametes, somatic chromosome doubling, and polyspermy (Grant,

1981).Regardless of themodeof origin (i.e., allopolyploid or autopolyploid),

most natural polyploid individuals are thought to arise through a sexual

mechanism, the union of unreduced gametes produced by the parental non-

hybrid or hybrid individuals (Harlan and deWet, 1975). Unreduced gametes

(also called 2n gametes), which have the complete set of parental somatic

chromosomes, are produced throughmeiotic nonreduction (also calledmei-

otic restitution) during male and female gametogenesis (Bretagnolle and

Thompson, 1995). The union of unreduced gametes through fertilization

can give rise to allopolyploids when hybridization occurs between species

and autopolyploids when hybridization occurs within a single species. The

mean natural frequency of unreduced gametes is estimated to be 0.56% in

nonhybrid plants and 27.52% in hybrid plants (Ramsey and Schemske,

1998). Primula kewensisWatson, an allopolyploid species that originated from

a seed-setting shoot of a sterile F1 hybrid between P. floribunda Wall. and

P. verticellata Forssk., represents a well-known case of new allopolyploid for-

mation through somatic chromosome doubling (Newton and Pellew, 1929).

Asexual somatic chromosome doubling is known to occur in zygotes

(i.e., young embryos) and meristematic cells, but little is known about the

frequency of its occurrence under natural conditions (Ramsey and

Schemske, 1998). Similarly, polyspermy (i.e., the fertilization of an egg by

two male nuclei) is thought to represent a less common mechanism.

The production of unreduced gametes provides three possible pathways

for polyploid formation. The first pathway involves the union of male and

female unreduced gametes that are directly produced by the parental non-

hybrid individual (when selfing) or individuals (when outcrossing). This

one-step pathway would enable immediate rise of new polyploids, whereas,

given the low natural frequency of unreduced gametes (0.56% for non-

hybrids), polyploids that arise through this pathway might be rare under


undisturbed conditions (deWet, 1980; Ramsey and Schemske, 1998). The

second pathway involves the union of male and female unreduced gametes

that are produced by the F1 hybrid of the parental individuals. In contrast to

the first pathway, this pathway consists of two consecutive steps: (1) the for-

mation of F1 hybrids of the parental individuals and (2) genome doubling

through selfing or outcrossing of the F1 hybrid individual(s) that produce(s)

unreduced gametes. The third pathway involves the “triploid bridge,” that

is, triploid intermediate individuals that are formed through union of a

reduced and a nonreduced gamete produced by the parental diploid (and

nonhybrid) individual (when selfing) or individuals (when outcrossing).

Such triploid individuals are often semi-fertile and may sporadically produce

unreduced triploid gametes that can cross with normal haploid gametes to

form tetraploid individuals. This is also a two-step pathway, but, in contrast

to the second pathway, it requires unreduced gametes be formed in both the

first step (in which the triploid intermediate is formed) and the second step

(in which the tetraploid individual is formed). The term “triploid bridge” is

only applicable when the parental individuals are diploid, but essentially, the

same phenomenon may cause an increase in the offspring’s ploidy when one

or both parental individuals are of higher ploidy. Some previous results sug-

gest that this pathway may be an important route to natural formation of

autopolyploids and allopolyploids (Bretagnolle and Thompson, 1995;

Ramsey and Schemske, 1998).

The relative importance of these three possible pathways in natural poly-

ploid formation is not known (Soltis and Soltis, 2009). Notably, the second

pathway is not frequently described in the recent literature, whereas the one-

step and triploid bridge pathways are commonly highlighted. Experimental

evidence, however, suggests the occurrence of the second pathway in a nat-

ural setting (Harlan and deWet, 1975; Ramsey and Schemske, 1998). This

pathway is similar to the triploid bridge pathway in that it consists of two steps

toward ploidy increase, but distinctive becausewhole genomedoubling takes

place in a single event: the union of unreduced gametes that are produced by

the F1 hybrids. Fromhere on, we call allopolyploid speciation that undergoes

the second pathway “allopolyploid speciation through the hybrid genome

doubling (HGD) pathway” and attempt to obtain a detailed picture of this

somewhat underappreciated mode of polyploid speciation.

2.4. Process of allopolyploid speciation through hybridgenome doubling

In general, allopolyploid speciation through the HGD pathway has three

important stages: formation of viable and fertile F1 hybrid (stage I),


formation of allopolyploid through HGD (stage II), and establishment of the

allopolyploid as a species (stage III) (Fig. 4.1). Stage I, where F1 hybrid indi-

viduals are formed through interspecies crossing, marks the onset of allo-

polyploid speciation. By definition, successful interspecific hybridization

is a prerequisite for the process of allopolyploid speciation. The actual

genome doubling occurs at stage II: allopolyploid individuals are formed

through union of unreduced gametes produced by the F1 hybrids. At stage

III, the new allopolyploid individuals formed via HGD start to propagate as

reproductively isolated entities and ultimately become established as species.

Various types of positively or negatively affecting mechanisms are

involved in the process of allopolyploid speciation through the HGD path-

way. At stage I, a suite of interspecific hybridization barriers, including both

prezygotic and postzygotic mechanisms, prevent F1 hybrids from forming

because the typical parental species are reproductively isolated under normal

conditions (Coyne and Orr, 2004). The interspecific hybridization barriers

have important roles in maintaining reproductive boundaries in the majority

(�70%) of plant species, but, at the same time, at least 25% of plant species

are estimated to be involved in hybridization and introgression with other

species (Mallet, 2005, 2007; Rieseberg et al., 2006). Interspecific hybridiza-

tion, therefore, could be viewed as relatively widespread feature of plant spe-

cies. Nevertheless, spontaneous hybridization tends to occur between

outcrossing perennial species that can stabilize hybridity through agamo-

spermy and vegetative spread. Furthermore, interspecific hybridization

rarely produces F1 hybrids that give rise to new evolutionary lineages,

whereas, in the long term, such rare evolutionarily successful F1 hybrids

may repeatedly arise (Ellstrand et al., 1996). Accordingly, interspecific

hybridization per se is not a common adaptive mechanism in plants, but

Figure 4.1 Three important stages of the allopolyploid speciation through the HGDpathway. Formation of viable and fertile F1 hybrid (stage I, pink), formation of allopoly-ploid through hybrid genome doubling (stage II, yellow), and establishment of the allo-polyploid as a species (stage III, green).


frequent formation of F1 hybrids may widen the opportunities for the suc-

cessful occurrence of allopolyploid speciation through the HGD pathway.

At stage II, functional unreduced gametes play a crucial role in HGD.

Because of postzygotic hybridization barriers, most natural interspecific F1hybrids are nonviable or infertile if they grow into mature plants. Such F1hybrids, however, may partially restore fertility and produce allopolyploid

F2 individuals through formation of functional male and female unreduced

gamete and their subsequent union. Formation of unreduced gametes,

therefore, is important for allopolyploid speciation through the HGD path-

way. Other genetic mechanisms that potentially promote the process of spe-

ciation at stage II include hybrid vigor (or heterosis) and allopolyploid

genome alteration. Hybrid vigor may increase the chance for the F1 hybrids

to grow and reproduce in the face of competition with the parental species

through expression of transgressive phenotypes, whereas allopolyploid

genome alteration contributes to stabilizing the hybrids’ polyhaploid

genome (Birchler et al., 2010; Doyle et al., 2008; Facon et al., 2005). Eco-

logically, minor cytotype exclusion may impede the stage II process partic-

ularly when outcrossing between the F1 hybrids is required to reproduce.

The newly formed allopolyploids produce reduced, rather than

unreduced, gametes through normal meiosis and propagate as reproduc-

tively isolated individuals. At stage III, the genetic and ecological mecha-

nisms other than unreduced gamete formation (i.e., hybrid vigor,

allopolyploid genome alteration, and minor cytotype exclusion) continue

to influence the establishment of the newly formed allopolyploids as species.

The new allopolyploids have a complete set of disomic chromosomes

derived from the parental species, but true disomic inheritance is not always

achieved immediately after their formation: multivalents that cause reduc-

tion in fertility commonly occur in their meiosis (Ramsey and Schemske,

2002). In the early-generation allopolyploids, karyotypic changes through

recombination between homeologous chromosomes may occur and, ulti-

mately, lead to chromosomal diploidization (Gaeta et al., 2007). Conse-

quently, the allopolyploid genomes are cytologically stabilized and the

fertility of newly formed allopolyploids is improved. Stable disomic inher-

itance, increased fertility, and possible expression of transgressive pheno-

types through hybrid vigor may contribute to the establishment of the

allopolyploids as species, whereas minor cytotype exclusion remains a major

obstacle to the speciation.

From this overview, it is evident that the allopolyploid speciation

through the HGD pathway is a very complex process that includes various


genetic and ecological mechanisms. Because most newly formed allopoly-

ploid individuals likely go extinct before they are established as species,

the allopolyploid speciation through the HGD pathway could be viewed

as the rare incidence that takes place when the impact of the promoting

mechanisms outweighs that of the impeding mechanisms. Successful F1hybrid formation and unreduced gamete production are the key mecha-

nisms on which the occurrence of this mode of speciation is highly depen-

dent, whereas relative importance of other mechanisms may greatly vary

contingent on the circumstances of the speciation events. Accordingly, bet-

ter understanding of the underpinning of allopolyploid speciation through

the HGD pathway requires detailed genetic and ecological studies on those

positively and negatively affecting mechanisms and their possible interplay.

2.5. Wheat (Triticum and Aegilops) species as model systemsfor studies on allopolyploid speciation

Natural allopolyploid plant taxa, which have evolved through the HGD

pathway, may provide usable model systems to better understand the genetic

and ecological mechanisms that underlie allopolyploid speciation through

this pathway. Cultivated wheat and its wild relatives, which taxonomically

belong to the genera Triticum and Aegilops, represent well-documented

examples of natural allopolyploid taxa. The genus Triticum has six species,

including allohexaploid commonwheat (T. aestivum L.) and its wild and cul-

tivated relatives, whereas Aegilops consists of 22 wild species (Tables 4.1 and

4.2). Allopolyploidy is a major driving force in the diversification in those

genera: four Triticum and 12 Aegilops species have allotetraploid or

allohexaploid (or both) genomes. Because three of the four Triticum

genomes are derived from ancestralAegilops diploids (B and G genomes from

Aegilops speltoides Tausch and D genome from Aegilops tauschii Coss. (for-

merly known as Ae. squarrosa L.)), Triticum and Aegilops could be viewed

as a single evolutionary complex, whereas several modern and historical

taxonomic classifications propose the separation of the Triticum species from

the Aegilops species on morphological and practical grounds (Kihara, 1944;

Kilian et al., 2007; McFadden and Sears, 1944; van Slageren, 1994).

The Triticum and Aegilops species have two distinctive features that are

suitable for allopolyploid speciation studies. First, the overall picture of

the pattern of diversification through allopolyploidy is available: most likely

paternal and maternal lineages are known for virtually all Triticum and

Aegilops polyploid species (Tsunewaki, 2009, 2010). The well-clarified

interploidy relationships greatly facilitate comparative studies between the


Table 4.1 The nomenclature of the Triticum species

Species and subspeciesGenomeconstitutiona

Example ofcommon namesb

Triticum monococcum L. AA Einkorn

subsp. aegilopoides (Link) Thell. Wild einkorn

subsp. monococcum Cultivated

einkorn

Triticum urartu Tumanian ex Gandilyan AA

Triticum turgidum L. AABB

subsp. dicoccoides (Korn. ex Asch. & Graebn.)

Thell.

Wild emmer

subsp. dicoccon (Schrank) Thell. Cultivated emmer

subsp. durum (Desf.) Husn. Durum or

macaroni wheat

subsp. polonicum (L.) Thell. Polish wheat

subsp. turanicum (Jakubz.) A. Love &D. Love Khorassan wheat

subsp. turgidum Rivet wheat

subsp. carthlicum (Nevski) A. Love & D. Love Persian wheat

subsp. paleocolchicum (Menabde) A. Love &

D. Love

Georgian wheat

Triticum timopheevii (Zhuk.) Zhuk. AAGG

subsp. armeniacum (Jakubz.) van Slageren Wild timopheevii

subsp. timopheevii Cultivated

timopheevii

Triticum aestivum L. AABBDD Common wheat

subsp. aestivum Bread wheat

subsp. compactum (Host) MacKey Club wheat

subsp. sphaerococcum (Percival) MacKey Indian dwarf

wheat

subsp. macha (Dekapr. & Manabde) MacKey

subsp. spelta (L.) Thell. Spelt

Tritucm zhukovskyi Menabde & Ericz. AAAAGG

aAfter Kimber and Tsunewaki (1988).bProvided only when available.After van Slageren (1994). For other taxonomic classifications, see the Wheat Classification Table Site(http://www.k-state.edu/wgrc/Taxonomy/taxintro.html).

http://www.k-state.edu/wgrc/Taxonomy/taxintro.html


Table 4.2 The nomenclature of the Aegilops species

Section SpeciesGenomeconstitutiona

Aegilops Aegilops umbellulata Zhuk. UU

Aegilops triuncialis L. UUCC

Aegilops biuncialis Vis. UUMM

Aegilops columnaris Zhuk. UUMM

Aegilops geniculata Roth UUMM

Aegilops neglecta Req. ex Bertol. UUMM/

UUMMNN

Aegilops kotschyi Boiss. UUSS

Aegilops peregrina (Hack. in J. Fraser)

Maire & Weiller

UUSS

Comopyrum Aegilops comosa Sm. in Sibth. & Sm. MM

Aegilops uniaristata Vis. NN

Cylindropyrum Aegilops markgrafii (Greuter) Hammerb CC

Aegilops cylindrica Host CCDD

Sitopsis Aegilops bicornis (Forssk.) Jaub. & Spach SbSb

Aegilops longissima Schweinf. & Muschl. SlSl

Aegilops searsii Feldman & Kislev ex

Hammer

SsSs

Aegilops sharonensis Eig SshSsh

Aegilops speltoides Tausch SS

Vertebrata Aegilops tauschii Coss. DD

Aegilops crassa Boiss. DDMM/

DDDDMM

Aegilops ventricosa Tausch DDNN

Aegilops vavilovii (Zhuk.) Chennav. DDMMSS

Aegilops juvenalis (Thell.) Eig DDMMUU

aAfter Kimber and Tsunewaki (1988). Underlined: modified genome.bChanged from “Aegilops caudata L.” based on the note in the Wheat Classification Table Site.After van Slageren (1994). For other taxonomic classifications, see the Wheat Classification Table Site(http://www.k-state.edu/wgrc/Taxonomy/taxintro.html).




polyploid species and its ancestors. Second, artificial interspecific crosses are

easily made in those genera (Sharma, 1995). Many artificial F1 hybrids

between the species of those genera are viable and capable of producing allo-

polyploid F2 individuals through spontaneous HGD or induced by colchi-

cine treatment. The high interspecific crossability enables detailed genetic

analyses of the mechanisms that underlie the allopolyploid speciation

through the HGD pathway, including hybridization barriers, unreduced

gamete formation, gene expression changes, and polyploid genome alter-

ation. In addition, some Triticum polyploid species can be crossed with

rye (Secale cereale L.), barley (Hordeum vulgare L.), maize (Zea mays L. subsp.

mays), and several other grass species, providing additional materials for stud-

ies on the genetic consequences of distant interspecific crosses

(Sharma, 1995).

Over the past five decades, various novel reproductive phenomena,

namely, unexpectedly high crossability with rye, hybrid dysgenesis, hybrid

sterility, uniparental chromosome elimination during embryogenesis, fre-

quent unreduced gamete production, and rapid genome alteration at the

chromosome and DNA sequence levels, have been found in wheat and

its interspecific hybrids. Genetic and cytogenetic studies on those phenom-

ena set the foundations for wheat chromosome engineering, gene mapping,

and breeding. In our view, however, those phenomena deserve a renewed

attention from the standpoint of evolution because they can provide valu-

able insights into the genetic underpinning for allopolyploid speciation

through the HGD pathway. In the following sections, we focus on the

Triticum and Aegilops species as model systems for allopolyploid speciation

studies. Recent results from investigations on the reproductive phenomena

observed in wheat interspecific hybrids are reviewed and their implications

for the genetic underpinning of allopolyploid speciation are discussed in ref-

erence to the work done on other model systems.

3. PRE- AND POSTZYGOTIC BARRIERS IN PLANTHYBRIDIZATION

3.1. Kr genes: Example of genetic mechanismsfor prezygotic barriers

Interspecific hybridization barriers play a critical role in the first stage of allo-

polyploid speciation through HGD because the formation of viable F1hybrids that have some degrees of fertility is a prerequisite for the occurrence

of allopolyploid speciation (Fig. 4.1). Two major classes of hybridization


barriers that impede gene flow between species are known: prezygotic

(before-fertilization) and postzygotic (after-fertilization) barriers. Prezygotic

barriers may provide more effective impediments to hybrid formation than

postzygotic barriers, given that they act sequentially in a natural setting

(Ramsey et al., 2003). In the modern theory of speciation, several types

of prezygotic barriers are recognized, including behavioral isolation, habitat

isolation, temporal isolation (phenological differences, for example), polli-

nator isolation, and mechanical isolation (Coyne and Orr, 2004). Gametic

isolation is a form of prezygotic barrier that acts after mating but before fer-

tilization. In plants, gametic isolation prevents interspecific hybridization

from occurring through mechanisms such as pollen–pistil incompatibility

and competition between conspecific and heterospecific pollen for fertiliza-

tion (Heslop-Harrison, 1982).

The Kr genes, which control the crossability of wheat species, represent

well-documented genetic mechanisms for gametic isolation in the grass spe-

cies. In the early twentieth century, it was known that most varieties of com-

mon wheat rarely set seeds when pollinated with rye pollen with the

exception of a landrace ofChinese origin that sets viable F1 seeds at an exceed-

ingly high frequency (80%) (Backhouse, 1916). Originally, Kr1 (located on

chromosome5B) andKr2 (locatedonchromosome5A)were identified as the

dominant alleles that are responsible for the poor crossability between com-

monwheat and rye (Lein, 1943). Later, additional commonwheat–rye cross-

ability genes,Kr3 (on chromosome 5D),Kr4 (on chromosome 1A), and SKr

(on chromosome 5B), were reported (Krolow, 1970; Tixier et al., 1998;

Zheng et al., 1992). Microscopic observations showed that the Kr genes

inhibit the growth of rye pollen tube in the wheat pistil: in the presence of

the dominant alleles of the Kr1 and Kr2 genes, rye pollen tube elongation

is arrested between the wheat style base and top of the embryo sac (Jalani

and Moss, 1980; Lange and Wojciechowska, 1976). Genetic studies further

suggested that the Kr genes might also influence the crossability of common

wheat with other species than rye: wild and cultivated barley andAe. tauschii.

(Fedak and Jui, 1982; Koba and Shimada, 1993; Snape et al., 1979).

The natural variation for the crossability of common wheat with rye has

an intriguing geographic distribution in Eurasia: most common wheat land-

races that have high crossability with rye are from eastern Asia, whereas vir-

tually all tested European common wheat landraces are not receptive to rye

pollen (Zeven, 1987). Historically, rye was introduced only recently in east-

ern Asia, whereas the mixed cultivation of common wheat and rye was once

a common practice in Europe. In fact, rye still grows as a weedy relict of past


cultivation in some parts of Europe. The geographic pattern of reproductive

isolation of common wheat from rye, that is, crossable when allopatric but

not crossable when sympatric, is reminiscent of the action of reinforcement,

the enhancement of prezygotic isolation in sympatry by natural selection

against hybrids or mating between diverging taxa (Coyne and Orr, 2004).

Usually, the F1 hybrid plants between common wheat and rye are sterile,

but viable and vigorous in their growth habitat (Thompson, 1926). In the

fields where common wheat and rye grow together or in close vicinity, such

F1 hybrid plants, if formed, may become undesirable weeds that make no

contribution to the yield but compete with the crop for light, water, and

nutrition. Accordingly, the gametic isolation based on the Kr gene system

might have been maintained in Europe by conscious or unconscious agri-

cultural selection against the weedy F1 hybrid plants (or the ability of com-

mon wheat to produce weedy F1 hybrid plants). In eastern Asia, however,

the lack of the conditions for producing weedy hybrid plants might have led

to the mutational loss of the Kr gene system in common wheat (Riley and

Chapman, 1967). Several theoretical and empirical studies suggest that rein-

forcement is one of the plausible mechanisms for plant speciation, but the

details of its genetic underpinning remain to be addressed (Rieseberg and

Willis, 2007). Molecular genetic analyses of theKr gene system may provide

insights into whether the action of reinforcement was involved in the main-

tenance of the gametic isolation of common wheat from rye (Alfares et al.,

2009; Mishina et al., 2009).

3.2. Postzygotic barriersMany plant species are reproductively isolated from other species primarily

by such prezygotic barriers as differences in habitats, pollinators, and

flowering time (Kay, 2006; Lowry et al., 2008; Martin and Willis, 2007;

Nosil et al., 2005; Ramsey et al., 2003). This suggests that the establishment

of prezygotic barriers is an important process in speciation through lineage

splitting. Prezygotic barriers, however, can be leaky particularly when hab-

itats undergo natural or human-mediated disturbances: at least 25% of plant

species are estimated to be involved in hybridization and introgression with

other species (Mallet, 2005, 2007; Rieseberg et al., 2006). Because even

small amounts of gene flow are sufficient to cause cohesion of genetically

differentiated populations and species, the ephemeral nature of prezygotic

barriers represents an impediment to speciation through lineage splitting,

whereas it may facilitate the occurrence of allopolyploid speciation through


the HGD pathway that requires the formation of viable and, at least, semi-

fertile interspecific hybrids (Hartl and Clark, 1989). In contrast, postzygotic

barriers, which often are based on genic incompatibilities that arise as a con-

sequence of alternate allelic mutations and fixation in separated populations,

may provide stable and essentially irreversible means for reproductive isola-

tion. For a given pair of incipient species, the strength of such postzygotic

barriers may increase as their genomes diverge and, ultimately, allopolyploid

speciation through HGD becomes no longer possible even under the eco-

logical/environmental conditions for natural interspecific hybrids to form

due to prezygotic barrier leakage (Moyle et al., 2004; Scopece et al.,

2007, 2008). Accordingly, postzygotic barriers can have a central role in

preventing allopolyploid speciation through the HGD pathway from occur-

ring particularly when the reproductive isolation by prezygotic barriers is

incomplete.

Postzygotic barriers can be classified into two forms: extrinsic and intrin-

sic. In general, the extrinsic postzygotic barriers include ecological inviabil-

ity (e.g., difficulties for hybrids to find a suitable ecological niche) and

behavioral sterility (e.g., sexually unattractive courtship behavior of hybrids

that lower effective fertility of hybrids), whereas the intrinsic postzygotic

barriers include hybrid inviability and sterility (e.g., developmental abnor-

malities that significantly reduce hybrids’ fitness) (Coyne and Orr, 2004).

Recent plant speciation studies have mostly focused on intrinsic postzygotic

barriers and much has been learned about the underlying genetic mecha-

nisms and their evolutionary origins. Intrinsic postzygotic barriers may arise

from chromosome rearrangements and/or genic changes. Chromosome

rearrangements often contribute to hybrid sterility in plants, but their evo-

lutionary significance remains to be addressed (Rieseberg, 2001). In contrast,

the classic gene-based model known as Dobzhansky–Muller or DM (also

often referred to as Bateson–Dobzhansky–Muller or BDM) is now widely

accepted as one of the plausible explanations for the evolution of intrinsic

postzygotic barriers (Bateson, 1909; Dobzhansky, 1937; Muller, 1942).

The DM model predicts that, when geographically isolated populations

accumulate independent allelic mutations, which may be adaptively neutral

or advantageous, at one or more loci, dysfunctional interactions between the

resultant alleles may cause developmental abnormalities that reduce the

hybrids’ fitness. In both plants and animals, several recent genetic mapping

studies of hybrid incompatibility loci provided empirical support for

nuclear–nuclear and nuclear–cytoplasmic DM incompatibilities (Bikard

et al., 2009; Bomblies et al., 2007; Brideau et al., 2006; Lee et al., 2008;

Long et al., 2008; Presgraves et al., 2003; Wright et al., 2013).


In the Triticum and Aegilops species, a wide range of postzygotic repro-

ductive phenomena that negatively influence the hybrids’ viability and fer-

tility are known (Endo, 1980; Tsunewaki, 2009). The phenotypic and

genetic attributes of those phenomena have been studied in great detail

mainly because of their importance in breeding and agronomic applications,

but it is only recently that the molecular basis that underlies their expression

began to emerge. In addition, the relevance of those phenomena to wheat

allopolyploid speciation has largely been a neglected topic in the literature.

Nevertheless, new light has lately been shed on the molecular underpinning

of three reproductive phenomena of wheat, namely, hybrid dysgenesis,

hybrid sterility caused by gametocidal genes, and uniparental chromosome

elimination in hybrid embryos. Here, we summarize what is known about

the genetic mechanisms for these phenomena and discuss their possible

influence on allopolyploid speciation through the HDG pathway.

3.2.1 Hybrid dysgenesisDevelopmental abnormalities that are specifically expressed in F1 or in later-

generation hybrids, such as necrosis, chlorosis, dwarfness, and reduced

growth vigor, are collectively called hybrid dysgenesis. Recent studies suc-

cessfully identified the major genes involved in the expression of hybrid

necrosis/sterility and showed that hybrid dysgenesis often evolves through

mechanisms that are consistent with the DM model (Bomblies et al.,

2007; Chen et al., 2008; Jeuken et al., 2009; Kruger et al., 2002; Long

et al., 2008; Mizuta et al., 2010; Wright et al., 2013; Yamamoto et al.,

2010). Functionally, many of those causative genes are involved in pathogen

response, suggesting that disease resistance genes might have an important

role in the evolution of hybrid dysgenesis (Bomblies and Weigel, 2007).

Furthermore, empirical evidence that supports the long-standing hypothesis

that the reciprocal silencing of duplicated genes be a frequent cause of hybrid

dysgenesis through DM epistatic interactions has been obtained (Lynch and

Force, 2000; Werth and Windham, 1991).

One classic example of wheat hybrid dysgenesis that involves the typical

two-locus epistatic interactions, as predicted by the DM model, is lethal or

semilethal hybrid necrosis, gradual premature death of leaf and sheath tissues

on hybrid plants. The hybrid necrosis phenotypes are often observed in F1hybrids between the hexaploid common wheat varieties and between com-

mon wheat and tetraploid wheat (Triticum turgidum L.). Early studies showed

that two complementary dominant genes, Ne1 and Ne2, control a type of

hybrid necrosis (Caldwell and Compton, 1943; Hermsen, 1963;

Tsunewaki, 1960). TheNe1 gene is mapped to the long arm of chromosome


5B, and theNe2 gene to the short arm of chromosome 2B (Chu et al., 2006;

Nishikawa et al., 1974; Zeven, 1972). Geographically, commonwheat land-

races that are homozygous for the recessive alleles at both Ne1 and Ne2 loci

(i.e., noncarriers) are widespread, whereas theNe1-allele-carrying andNe2-

allele-carrying landraces are most frequently found in the Asian and

European/American regions, respectively (Tsunewaki, 1970; Tsunewaki

and Nakai, 1967). In contrast, about 70% of the modern breeding varieties

have the dominant allele of the Ne2 gene, most likely owing to the tight

genetic linkage with disease resistance gene loci that have extensively been

used in the breeding programs over the past 100 years. As a result, the non-

carrier modern breeding varieties are now relatively rare: most have either

Ne1 or Ne2 (Pukhalskiy et al., 2000). Hybrid chlorosis (i.e., insufficient

chlorophyll production in the leaves of hybrid plants) and hybrid dwarfness

(i.e., significant plant height reduction in hybrid plants relative to their par-

ents) provide other examples of the T. aestivum–T. aestivum and T. aestivum–

T. turgidum F1 hybrid dysgenesis that is controlled by the multilocus epistatic

DM interactions. The typical two-interacting-locus control is the norm for

the hybrid chlorosis phenotypes that are genetically characterized to date,

but three loci that differ in the strength of dominance and degree of quan-

titative phenotypic effect are involved in a type of T. aestivum–T. aestivum

hybrid dwarfness (Canvin and McVetty, 1976; Hermsen, 1967;

Kawahara, 1993; Nishikawa, 1967; Tsunewaki, 1992, 2004; Tsunewaki

and Hamada, 1968). Accordingly, the genomes of hexaploid and tetraploid

Triticum wheats harbor various independent multilocus genetic systems that

may cause DM incompatibilities in their hybrids. Nevertheless, the rele-

vance of these hybrid dysgenesis phenotypes to the wheat allopolyploid spe-

ciation through the HGD pathway is not obvious because the F1 hybrids in

which they are expressed do not undergo genome doubling.

Various dysgenesis phenotypes have also been found in the triploid

ABD-genome F1 hybrids between the direct ancestors of common wheat,

T. turgidum (as the female parent, AABB genome) and Ae. tauschii (as the

male parent, DD genome) (Nishikawa, 1953, 1960, 1962a,b). The expres-

sion of those phenotypes is greatly dependent on the genotypes of the paren-

tal species (Matsuoka et al., 2007). The dysgenesis phenotypes of the

T. turgidum–Ae. tauschii F1 hybrids are classified into four types: type II

necrosis (low-temperature sensitive), type III necrosis (temperature insensi-

tive), chlorosis, and severe growth abortion (Mizuno et al., 2010a). Genetic

analyses indicated that two complementary genes, Net1 on the AB genome

and Net2 on the D genome, control the type II necrosis, suggesting the


involvement of epistatic DM incompatibility in the expression of the phe-

notype in the triploid ABD-genome hybrid (Nishikawa, 1962b). Molecular

mapping studies successfully located one of the major genes (i.e., Net2) that

are causative of type II necrosis on the short arm of chromosome 2D,

whereas a gene that is involved in the expression of type III necrosis was

found to exist on the short arm of chromosome 7D (Matsuda et al.,

2012; Mizuno et al., 2010a, 2011). When the T. turgidum–Ae. tauschii F1hybrid plants express the necrosis phenotypes, autoimmune-like responses

occur as a result of epistatic interactions between gene from the AB and

D genomes (Mizuno et al., 2010a, 2011). All this evidence suggests that

hybrid dysgenesis that arose through the evolutionary process consistent

with the DM model might possibly have influenced the natural process of

allohexaploid speciation of common wheat in some fashion.

Type II necrosis is characterized by its marked growth repression under

low-temperature conditions (4 �C). The wheat plants showing the symp-

toms of the type II necrosis share several phenotypic attributes with the

maize Corngrass1 mutants. Because the overexpression of microRNA

(miR156) is responsible for the extremely bushy dwarf phenotype of the

Corngrass1 mutants, some microRNA activities might be involved in the

temperature-dependent phenotypic plasticity of type II necrosis expression

through the Net1–Net2 incompatibility (Chuck et al., 2007; Takumi and

Mizuno, 2011). In contrast to the type II and type III necrotic phenotypes,

relatively little is known about the molecular basis of the chlorosis and

severe-growth-abortion phenotypes. Recently, Hatano et al. (2012)

reported the dysfunction of mitotic cell division at shoot apices of the

T. turgidum–Ae. tauschii F1 hybrids, showing the severe-growth-abortion

phenotype. Furthermore, they found significant decrease in cell cycle-

related and division-related gene expression in the crown tissues including

shoot apical meristems, consistent with the observations in Arabidopsis that

suppression of cell cycle-related gene expression may induce both growth

inhibition and necrotic cell death (Lin et al., 2007; Wang and Liu, 2006).

Interestingly, the arrest of shoot apical meristem cell division appears

to occur prior to the expression of autoimmune responses in both

severe-growth-abortion and type II necrosis phenotypes. Accordingly, cell

cycle-related genes, rather than disease-resistant genes, might possibly have

primary role in the expression of these phenotypes in the T. turgidum–Ae.

tauschii hybrids (Hatano et al., 2012; Mizuno et al., 2011).

In addition to several plant and animal hybrid dysgenesis genes that were

found in the last 10 years, recent evidence from model plant systems


highlighted the importance of genome reprogramming, such as changes in

the patterns of gene expression, DNA methylation, and imprinting, as the

candidate mechanisms for hybrid dysgenesis. For example, a maternally

expressed transcription factor is known to control hybrid lethality during

seed development in interploidy hybrid crosses ofArabidopsis, indicating that

the developmental programming of the mother may regulate the viability of

interploidy hybrid offspring (Dilkes et al., 2008). Similarly, disruption of

expression patterns of imprinted genes by hybridization can cause arrest

in embryo and endosperm development in Arabidopsis and Oryza

(Ishikawa et al., 2011; Kohler et al., 2005; Walia et al., 2009). Furthermore,

unexpected transposon activation, which is triggered by epigenetic expres-

sion changes of small interfering RNAs that confer transposon silencing in

the parental species, may be responsible for some Arabidopsis seed develop-

ment failure (Martienssen, 2010; Martienssen et al., 2008; Ng et al., 2012).

Whether genome reprogramming is involved in the expression of wheat

hybrid dysgenesis phenotypes is yet to be addressed.

3.2.2 Gametocidal genes of wheatInterspecific hybrids are usually fully or partially sterile. This may have a neg-

ative impact on the occurrence of allopolyploid speciation through the

HGD pathway by reducing the fitness of F1 hybrids. In plants, such intrinsic

mechanisms as chromosomal rearrangements and nuclear–nuclear/

nuclear–cytoplasmic DM incompatibilities contribute to the sterility of

hybrids (Fishman and Willis, 2006; Moyle and Graham, 2005; Rieseberg,

2001). In the wheat species, a group of nuclear genes called “gametocidal

(or Gc) genes” causes hybrid sterility in a distinctive fashion, whereas

nuclear–cytoplasmic DM incompatibilities and chromosomal

rearrangements also are known to cause hybrid sterility (Murai and

Tsunewaki, 1993; Ohta, 1995). Gc genes are a type of selfish genetic ele-

ments that ensure their preferential transmission through causing sterility

by introducing chromosomal breaks in male and female gametes that lack

the Gc elements (Endo, 1978, 1988a, 1990; Finch et al., 1984; Nasuda

et al., 1998). In the early studies, the chromosomes harboring Gc genes

(i.e., “Gc chromosomes”) were discovered as preferentially transmitted alien

chromosomes in the alloplasmic and chromosomal addition lines of com-

mon wheat (Endo and Katayama, 1978; Friebe et al., 1999; Miller et al.,

1982; Tsunewaki, 1980, 1993). To date, 20 chromosomes derived from

seven Aegilops species were found to harbor Gc genes: Aegilops caudata L.

(Endo and Katayama, 1978), Aegilops triuncialis L. (Endo and Tsunewaki,


1975), Aegilops cylindrica Host (Endo, 1979, 1996), Ae. speltoides Tausch

(Tsujimoto and Tsunewaki 1983; Tsujimoto and Tsunewaki, 1988),

Aegilops longissima Schweinf. & Muschl. (Endo, 1982; Friebe et al., 1993;

Maan, 1975), Aegilops sharonensis Eig (Endo, 1982; Maan, 1975; Miller

et al., 1982), and Aegilops geniculata Roth (Friebe et al., 1999). In contrast,

no Triticum species that has such chromosome is known.

Previous genetic studies showed that, when a single Gc chromosome is

added to the commonwheat genome, chromosomal breaks occur in themale

and female gametes that lack theGc chromosome,whereas the chromosomes

in the gametes that have theGcchromosome remain intact (Finch et al., 1984;

Nasuda et al., 1998). The induced chromosomal breaks can arrest cell cycle

during gametogenesis and cause gametophytic sterility. The selective occur-

rence of chromosomal breaks suggests that Gc genes have dual functions:

sporophytic induction and gametophytic suppression of chromosomal breaks

in gametogenesis (Fig. 4.2). This model for Gc gene activity that assumes

both “breaking” and “protecting” functions strikingly resembles the classic

typle II restriction–modification (RM) system of bacteria: linkage configura-

tions of restriction endonucleases (R) that cleave double-strand DNA at

recognition sequences and methyltransferases (M) that prevent cleavage

from occurring by modifying the recognition sequences (Tsujimoto, 2005;

Wilson, 1991). In fact, putative natural mutant alleles and an ethyl

methanesulfonate (EMS)-induced allele of Gc genes that lack the “breaking”

function are known, indicating that, in reality, each Gc gene is a complex of

two functionally antagonistic elements (Endo, 1990; Friebe et al., 2003; King

and Laurie, 1993; Tsujimoto and Tsunewaki, 1985). Nevertheless, virtually

nothing is known about the molecular mechanism that underlies the Gc

genes’ chromosome-breaking activity. Particularly, how the “protecting”

function modifies the sites that are targeted by the “breaking” function

and whether some epigenetic marking systems are involved in this phenom-

enon are the key questions that remain to be addressed.

How Gc genes evolved remains an open question, but the RM system-

like nature of the dual function model suggests that the origin of Gc activity

is distinct from that of the mechanism that generates DM incompatibility.

The known Gc chromosomes belong to homeologous group 2, 3, or 4

(Endo, 2007). Interestingly, comparative studies that used the common

wheat lines having two different Gc chromosomes showed that the Gc genes

of the same homeologous group behave in a similar fashion (except for the

one derived from Ae. geniculata), whereas, when combined, the

homeologous-group-4 genes and the homeologous-group-2 genes can


interact and enhance the occurrence of chromosomal breaks (Nasuda, 2006;

Tsujimoto, 1995). Accordingly, the Gc genes of the same homeologous

groups may possibly share a common evolutionary origin.

The details of Gc gene activity have been studied using the artificial com-

mon wheat lines that have one or two introduced Gc chromosome(s). Some

Gc genes that induce nonlethal mutations provide a useful genetic tool for

Figure 4.2 Model for the gametocidal action in themicrospore genesis of the Gc homo-zygous (left) and hemizygous (right) plants. The model is analogous to the restriction–modification (RM) system in bacteria (Wilson, 1991). Selective chromosome breakage bythe Gc chromosomes (gray chromosome labeled with “Gc”) can be explained on theassumption that the “breaking” product of the Gc gene (i.e., the “restriction” analog,denoted by circled “B” in red) induces breaks only when the “protecting” product ofthe gene (i.e., the “modification” analog, denoted by squared “P” in blue) becomesunable to prevent breakage. In the gametophytes that lack the Gc gene, the“protecting” product may be either diluted out or degraded faster than the “breaking”product. In the bacterial RM system, DNA methyltransferases prevent cleavage fromoccurring by modifying the recognition sequences. For this reason, we assume in thismodel that the “protecting” product is involved in chromatin modification (indicated bylight green mark with “m”), whereas the molecular details of the “protecting” functionare not known. The chromosome color indicates the chromatin status: gray (methyl-ated), green (methylated), and orange (hypomethylated).


chromosome manipulation (Endo, 2007). In contrast to the progress in

understanding the activity of Gc genes in the common wheat genome back-

ground, surprisingly little is known about their behavior in wheat interspe-

cific hybrids. If the Gc genes indeed are selfish genetic entities that have an

RM system-like nature, they may behave as segregation distorters (i.e., rou-

tinely overrepresented genes or alleles in the population of meiotic products)

in natural hybrid crosses. Importantly, some Gc genes that are added to the

common wheat genome induce chromosomal breaks in the hybrid genomes

only when they are transferred through male gametes. The hybrid zygotes

that arise from such crosses may be aborted or develop into viable seeds

depending on how severe the induced chromosomal mutations are

(Endo, 1988b, 1990). This sex-dependent zygotic induction of chromo-

somal breaks has some implication for the possible influence of Gc gene

activity on allopolyploid speciation through the HGD pathway. If natural

hybridization took place between a female-parent species that lacks a Gc

gene and a male-parent species that has it, the Gc gene could present a

postzygotic barrier that reduces the possibility of allopolyploid speciation

bymaking the F1 hybrids lethal or semilethal by causing chromosomal muta-

tions at an increased rate. The Gc gene-based postzygotic barrier, however,

would not be effective, if the Gc gene were maternally transmitted to the

hybrids in the same cross combination. Accordingly, the parent-of-origin

effect of the Gc genes might have influenced the directions of hybrid crosses

that led to successful allopolyploid speciation through the HGD pathway.

Better understanding of the role of Gc gene in the evolution of Triticum

and Aegilops species requires studies on the Gc gene behavior in the original

genetic background.

3.2.3 Complete uniparental chromosome elimination as a possiblepostzygotic barrier for allopolyploid speciation

Reproductive phenomena that are specifically observed in the interspecific

hybrids are extraordinarily diverse at both the molecular and phenotypic

levels. Interspecific hybridization often results in developmental and repro-

ductive abnormalities because of functional incompatibility between genes

that originate from divergent genomes. However, there are hybrid-specific

phenomena, other than developmental and reproductive abnormalities, to

which very little attention has been given from an evolutionary viewpoint,

despite their potential role as barriers for allopolyploid speciation through

the HGD pathway. One such phenomenon is complete uniparental chro-

mosome elimination, that is, the entire loss of chromosomes that are


inherited from one of the parental species in the interspecific hybrids. When

complete uniparental chromosome elimination occurs, the paternally (or less

frequently maternally) inherited chromosomes are selectively lost from the

genome of an interspecific F1 hybrid individual during the early zygotic

stages after fertilization. As a result, the F1 hybrid grows as a haploid indi-

vidual that is mostly sterile. The hybrid may spontaneously revert to a fertile

diploid through meiotic nonreduction followed by selfing or chromosome

doubling in somatic tissues (Ravi and Chan, 2010). Such a diploid is biolog-

ically equivalent to one of the parental species. Complete uniparental chro-

mosome elimination, therefore, could be viewed as a possible mechanism

for postzygotic barriers that may prevent allopolyploid speciation through

the HGD pathway from occurring, whereas the genetic and cytological

mechanisms for complete uniparental chromosome elimination have been

studied mainly because haploid plants have great practical value in breeding

(Chan, 2010; Matzk et al., 1997).

Complete uniparental chromosome elimination typically not only

occurs in the F1 hybrids between distantly related species (e.g., between

wheat and maize (Laurie and Bennett, 1986); wheat and sorghum (Laurie

and Bennett, 1988)) but also occurs in the F1 hybrids between closely related

species (between barley (H. vulgare L.) and Hordeum bulbosum L. (Kasha and

Kao, 1970); barley and Hordeum marinum Hudson (Finch, 1983)). In addi-

tion, selective somatic elimination of some chromosomes that are inherited

from one of the parental species (i.e., partial uniparental chromosome elim-

ination) is reported in the F1 hybrids between Hordeum lechleri Steud. and

H. vulgare, oat (Avena sativa L.) and maize, and common wheat and barley

(Barclay, 1975; Linde-Laursen and von Bothmer, 1999; Riera-Lizarazu

et al., 1996). Currently, we know of no direct evidence for complete uni-

parental chromosome elimination to act as an effective postzygotic barrier

under natural conditions: this hypothesis, however, could be tested by

the use of H. vulgare subsp. spontaneum (the wild ancestor of barely) and

its close relativeH. bulbosum as a model system because their natural habitats

widely overlap in the Near and Middle East regions (von Bothmer

et al., 1995).

While the molecular basis for complete uniparental chromosome elim-

ination remains unclear, there are several hypotheses about how the selective

chromosome/genome elimination takes place during hybrid embryogenesis

in plants (Gernand et al., 2005). Recent studies in Arabidopsis (Ravi and

Chan, 2010) and barley (Sanei et al., 2011) demonstrated that, as previous

studies suggested, functional alterations in the centromeres are associated


with the occurrence of complete uniparental chromosome elimination

(Finch, 1983; Jin et al., 2004; Kim et al., 2002; Mochida et al., 2004). Cen-

tromeres are the fundamental chromosomal structure where proteins nucle-

ate to form kinetochores that bind to spindle microtubules and mediate

chromosome segregation during cell division. The functional centromeres

in plants and animals are known to have centromere-specific Histone H3

variants called CENH3s. Ravi and Chan (2010) introduced artificially mod-

ified a functionalCENH3 gene into the cenh3 null mutant that is lethal when

homozygous.When the mutants expressing the functional CENH3 proteins

were crossed to wild typeArabidopsis as the male parent, most of the resultant

hybrids were haploids lacking the paternally inherited chromosomes. Sanei

et al. (2011) studied elimination of the paternally inherited chromosomes

during the early development of the H. vulgare–H. bulbosum F1 hybrid

embryos and found that centromere inactivity ofH. bulbosum chromosomes

triggers the mitosis-dependent process of complete uniparental chromo-

some elimination. They further showed that it is centromeric loss of

CENH3 proteins, rather than uniparental silencing of CENH3 genes that

causes centromere inactivity. These studies highlighted the significant role

of the CENH3 protein in the successful interspecific hybrid formation

through stabilization of mitotic cell division during embryogenesis. It is

not known whether other factors, such as differences in timing of essential

mitotic processes due to asynchronous cell cycles (Gupta, 1969; Sanei et al.,

2011) and asynchrony in nucleoprotein synthesis leading to a loss of the most

retarded chromosomes (Bennett et al., 1976; Laurie and Bennett, 1989), are

involved in the occurrence of complete uniparental chromosome

elimination.

4. UNREDUCED GAMETES

Unreduced gametes (or 2n gametes), which have the full somatic

chromosome set of the parent, provide the general raw material for poly-

ploid evolution because most natural polyploids are thought to form

through union of unreduced gametes produced by the parents rather than

somatic chromosome doubling and polyspermy (Harlan and deWet,

1975). For this reason, understanding the genetic mechanisms that underlie

unreduced gamete production is essential to carry out polyploid speciation

studies. Cytological description of unreduced gamete production was done

in a number of plant species, but it was not until recently that molecular

studies began to elucidate its underlying genetic mechanisms (Brownfield


and Kohler, 2011). In the model plant Arabidopsis thaliana, a triple meiotic-

gene mutant named MiMe, which produces male and female unreduced

gametes at very high rates (100% for the male gametes and 85% for the

female gametes), was created (d’Erfurth et al., 2009). This and other recent

advances in understanding the molecular basis for unreduced gamete pro-

duction provide fundamental knowledge and tools that could be used to

introduce apomixis (i.e., asexual clonal reproduction through seeds) in sex-

ual crop species for perpetuation of agronomically valuable genotypes.

In allopolyploid speciation through the HGD pathway, union of

unreduced gametes that are produced by interspecific F1 hybrids is respon-

sible for the occurrence of HGD. In contrast to our knowledge on non-

hybrid model plant systems, little is known about the genetic details of

unreduced gamete production in interspecific F1 hybrids. Interspecific

hybrids tend to produce unreduced gametes at high rates: the mean of

observed unreduced gamete frequencies is about 50-fold higher in hybrid

individuals (27.52%) than in nonhybrid individuals (0.56%) (Ramsey and

Schemske, 1998). The hybridity of the producer’s genome, therefore,

appears to be an important factor in the production of unreduced gametes.

This fact raises a question: to what extent the recent findings that were

obtained by the use of nonhybrid systems are relevant to the understanding

of the genetic mechanisms for hybrid unreduced gamete production. This

question deserves careful examination because unreduced gametes have a

central role in HGD and, ultimately, its subsequent allopolyploid speciation.

4.1. Unreduced gamete production in the F1 hybrid betweenT. turgidum and Ae. tauschii

Direct ancestors of commonwheat (T. aestivum),T. turgidim (AABBgenome)

and Ae. tauschii (DD genome), provide suitable materials for studying the

genetic mechanisms for F1 hybrid unreduced gamete production.

Allohexaploid commonwheat (AABBDDgenome) originated in theMiddle

East/Transcaucasus region ca. 8000 years ago and is derived from a natural

hybrid cross between a cultivated form of T. turgidum (female parent) and

the wild species Ae. tauschii (male parent) (Hillman, 1978; Kihara, 1944;

McFadden and Sears, 1944). By making artificial crosses between

T. turgidum and Ae. tauschii, an essential part of natural T. aestivum formation

can be reproduced using neither chemicals nor embryo rescue techniques.

Through such crosses, triploid F1 hybrids (ABD genome) that spontaneously

undergo genome doubling by setting hexaploid seeds (AABBDD genome)

via union of unreduced gametes can be obtained (Kihara, 1946; Kihara

and Lilienfeld, 1949; Matsuoka, 2011; Matsuoka and Nasuda, 2004). In


wheat, therefore, an occurrence of HGD through union of unreduced gam-

etes is detectable as a selfed seed set of the triploid F1 hybrids. Artificial crosses

can also provide such hybrids that display various postzygotic barriers, that is,

such abnormalities as severe dwarfness and necrotic dysgenesis (Matsuoka

et al., 2007; Mizuno et al., 2010a, 2011; Nishikawa, 1960). The use of the

T. turgidum–Ae. tauschii system is useful to address several important questions

about unreduced gamete production in F1 hybrids, including (1) what cyto-

logicalmechanism is responsible for F1 hybridunreducedgamete production,

(2) how many and what kind of genes are involved in it, and (3) how is the

ability to cause F1 hybrid unreduced gamete production maintained in the

parental species. In the following parts of this section, we review recent

advances in addressing these questions, by putting the emphasis on the

insights provided by the studies on the T. turgidum–Ae. tauschii F1 hybrids.

4.2. Cytological mechanismsSeveral cytological processes that cause meiotic nonreduction (or meiotic

restitution) are known (Bretagnolle and Thompson, 1995). In addition,

unreduced gametes may arise, although much less frequently, through nor-

mal meiotic cell division that occurs subsequent to endopolyploidization of

somatic germ-line cells or postmeiotic doubling of the chromosomes of nor-

mal haploid spores (Lewis, 1980; Ramanna and Jacobsen, 2003). The mei-

otic processes that cause nonreduction are categorized into two basic

pathways: one that omits meiosis I (termed first division restitution or

FDR) and one that omits meiosis II (termed second division restitution

or SDR). In the FDR pathway, paired homologous chromosomes do not

separate and fail to move to opposite poles; they stay on the equatorial plate

to form a restitution nucleus. Cytokinesis occurs only after restitution

nucleus formation and unreduced dyads result from a mitosis-like division.

In the SDR pathway, paired homologous chromosomes separate in associ-

ation with normal cytokinesis, but, after this stage, no further cell division

occurs. The sister chromatids fail to move to opposite poles and unreduced

dyads form at the end of this process. Various characteristic phenomena,

including irregular cytokinesis and aberrant spindle formation, are observed

in the meiocytes that undergo the FDR and SDR pathways. How those

phenomena relate to the occurrence of meiotic nonreduction is not clear

(Bretagnolle and Thompson, 1995).

The FDR and SDR pathways represent the major meiotic mechanisms

for unreduced gamete production, but determining which division, meiosis

I or meiosis II, is actually skipped is not always a straightforward task. In


nonhybrid individuals, the skipped division can be determined by sister

chromatid analysis of the unreduced gametes: two nonsister chromatids

and two sister chromatids residing in the unreduced gametes indicate omis-

sion of the first and second division, respectively (Bretagnolle and

Thompson, 1995). This can be particularly difficult to determine for inter-

specific F1 hybrids that often lack homologous chromosome pairing. In such

cases, sister chromatid analysis is no longer capable of distinguishing SDR

from FDR. In the case of the triploid F1 hybrid between T. turgidum

(AABB genome) and Ae. tauschii (DD genome) that has a polyhaploid

ABD genome, all the chromosomes do not have homologues for meiotic

pairing. Functional unreduced gametes are produced through a mitosis-like

process that involves a single cell division, but it is not clear which mecha-

nism, FDR or SDR, drives this process (Fig. 4.3) (Cai et al., 2010; Fukuda

and Sakamoto, 1992a,b; Matsuoka and Nasuda, 2004; Xu and Dong, 1992;

Xu and Joppa, 1995; Zhang et al., 2007, 2010).

Matsuoka et al. (2013) analyzed the single-cell-division meiotic process

in pollen mother cells of T. turgidum–Ae. tauschii F1 hybrids using molecular

Figure 4.3 Cytological observations of nonreductional meiosis in pollen mother cells oftriploid F1 hybrids between T. turgidum and Ae. tauschii (2n¼21). (A) Prophase. (B) Lateprophase. Twenty-one univalents are visible. (C) Metaphase. Univalent chromosomesare aligned at the spindle equator. At this stage, chromosome pairing is rarely observed,indicative that homeologous pairing is suppressed by the action of the Ph gene(Okamoto, 1957; Riley and Chapman, 1958). At the late metaphase, the 21 univalentssplit into chromatids, but fail to move to the spindle poles and remain clustered inthe center of the cell. (D) Restitution nucleus (polar view). (E) Restitution nucleus (sideview). The chromatids start to move to the spindle poles. (F) Anaphase. (G) Telophase.(H) Dyad daughter cells, each of which has 21 chromosomes.


cytogenetic techniques that enable description of meiotic stages with respect

to the cell cycle-dependent phosphorylation of histoneH3. Phosphorylation

of histone H3 at Ser10 is dependent on the cell cycle, and an antibody against

phosphorylated histone H3 provides a reliable indicator of cell division in

normal plant meiosis: the antibody gives entire-chromosome immuno-

signals in meiosis I and pericentromeric immunosignals in meiosis II

(Houben et al., 1999; Manzanero et al., 2000). PhosphoH3S10 signals were

observed on entire chromosomes of prophase and metaphase pollen mother

cells of the T. turgidum–Ae. tauschii F1 hybrids (Fig. 4.4A–E). The entire-

chromosome signals were visible at late prophase, strongest at early

metaphase, and weaker at late metaphase (Fig. 4.4B–E). No phosphoH3S10

signals were observed at the early restitutive nucleus stage, indicating that the

chromosomes were decondensed (Fig. 4.4F). At the late restitutive nucleus

stage and anaphase, the phosphoH3S10 signals were observed at the per-

icentromeric region of the chromosomes (Fig. 4.4G–I). At telophase, during

which cytokinesis takes place, the chromosomes were decondensed and the

signals no longer visible (Fig. 4.4J). At the restitutive nucleus stage, total

reconstruction of the spindle structure was observed. Early in this stage,

the bipolar spindle structure formed at metaphase (Fig. 4.4C) was fully dis-

sociated (Fig. 4.4F), whereas, later in this stage, the bipolar spindle structure

was reconstructed (Fig. 4.4G and H).

Figure 4.4 Immunostaining of nonreductional meiosis in pollenmother cells of the trip-loid F1 hybrids between T. turgidum and Ae. tauschii with alpha-tubulin and phosphor-ylated histone H3 at Ser 10 (phosphoH3S10) antibodies. Merged images of thechromatin (blue), alpha-tubulin (green), and phosphoH3S10 (red) signals are shown.(A) Early prophase. (B) Late prophase. (C) Early metaphase. (D) Late metaphase. (E) Latemetaphase (polar view). (F) Restitutive nucleus. (G) Late restitutive nucleus. (H) Res-titutive metaphase. (I) Anaphase. (J) Telophase.


The results of Matsuoka et al. (2013) showed that in the single-cell-

division process of the triploid T. turgidum–Ae. tauschii F1 hybrids, cytoki-

nesis did not occur when the chromosomes underwent the condensation

pattern of normal meiosis I, whereas cytokinesis occurred when the chro-

mosomes underwent the condensation pattern of normal meiosis II. In addi-

tion, the restitutive nucleus stage, in which the chromosomes underwent

significant changes in condensation pattern, represented a critical stage in

the single-cell-division process. Accordingly, the omission of the first divi-

sion of normal meiosis (i.e., FDR) was found to be one of the cytological

mechanisms responsible for meiotic nonreduction in male sporogenesis of

the T. turgidum–Ae. tauschii F1 hybrids. Whether FDR is a common meiotic

mechanism for unreduced gamete production in other interspecific F1hybrids, however, is yet to be addressed.

4.3. Genetic mechanismsIn general, unreduced gamete production in plants is influenced by both

genetic and environmental factors (Ramsey and Schemske, 1998). In a num-

ber of nonhybrid diploid species that include those from the genera Zea,

Solanum, Trifolium, and Medicago, natural unreduced gamete production is

known to be under genetic control (Mok and Peloquin, 1975; Parrott

and Smith, 1986; Rhoades and Dempsey, 1966; Tavoletti et al., 1991).

Interestingly, the inheritance of unreduced gamete production is often very

simple: in maize, a single gene named elongate (el) controls 2n egg formation,

whereas, in potato, a small number of genes are involved in the production

of 2n pollen. Furthermore, distinctive influence of various environmental

factors, such as herbivory, virus-disease infection, and temperature stress

in particular, on the nonhybrids’ unreduced gamete production has been

reported (Belling, 1925; De Storme et al., 2012; Kostoff, 1933; Kostoff

and Kendall, 1929; Pecrix et al., 2011). In contrast, relatively few studies

focused on the genetic and environmental factors that influence unreduced

gamete production in interspecific F1 hybrids. Grant (1952) reported the

influence of nutrient stress in Gilia F1 hybrids and, more recently, Mason

et al. (2011) found that Brassica F1 hybrids show the genotype specific

response to cold temperature conditions in their viable male unreduced

gamete production. Despite progress in our understanding, the details of

the genetic mechanisms for F1 hybrid unreduced gamete production and

the interplay with environmental factors remain to be learned.

In the triploid F1 hybrids between T. turgidum and Ae. tauschii, union of

functional male and female gametes that are produced through


nonreductional meiosis is mostly responsible for hexaploid-F2 seed setting:

such reproductive mechanisms as pollen–pistil incompatibility and seed

abortion have no detectable effect on the seedset (Matsuoka et al., 2013).

For this reason, the F1 hybrids’ selfed seed set rates, which depend on the

functions of viable male and female unreduced gamete frequencies, can

be used as a measure of the productivity of unreduced gametes. In previous

studies, the F1 hybrids’ selfed seed set rates greatly varied depending on the

genotypes of the parental T. turgidum and Ae. tauschii accessions, suggesting

that the unreduced gamete production in those hybrids is genetically con-

trolled (Fukuda and Sakamoto, 1992a,b; Kihara et al., 1965). This observa-

tion was confirmed by a large-scale artificial cross study that showed the

existence of extensive natural cryptic variation in Ae. tauschii for the ability

to cause unreduced gamete production in the triploid F1 hybrids with

T. turgidum. The unreduced gamete productivity of the F1 hybrids with a

tester T. turgidum cultivar (measured as the selfed seed set rates) varied from

7.5% to 68.3% depending on the genotype of the Ae. tauschii (Matsuoka

et al., 2007). This work underscored the potential of Ae. tauschii natural

accessions for studying the genetic mechanisms that underlie F1 hybrid

unreduced gamete production.

On the basis ofAe. tauschii’s extensive cryptic natural variation in its abil-

ity to cause unreduced gamete production in the F1 hybrids with

T. turgidum, Matsuoka et al. (2013) addressed the question of how many

Ae. tauschii genes are involved in the F1 hybrid unreduced gamete produc-

tion by means of quantitative trait locus (QTL) analysis. For this purpose,

they chose two representative Ae. tauschii accessions: one that produces a

high rate of selfed seeds (>50%) hybrid when crossed with a T. turgidum cul-

tivar Langdon (T. turgidum L. ssp. durum cv. ‘Langdon’) and one that pro-

duces a low rate of selfed seeds (<10%) hybrid with the same cultivar.

Then, by crossing Langdon with the F1 hybrid between the representatives,

a population of triploid segregants (279 plants) was generated. When the

triploid segregants were grown in a greenhouse with the hybrids that pro-

duce selfed seeds at a high rate (14 plants) and with the hybrids that produce

selfed seeds at a low rate (17 plants), seed set rates varied from 0.37 to 0.74 in

the high selfed seed set-rate hybrid (mean 0.56) and from 0.02 to 0.27 in the

low selfed seed set-rate hybrid (mean 0.14), whereas the segregants showed a

widely ranging rate varying from 0.06 to 0.73 (mean 0.33). Based on the

observed variances, the broad-sense heritability of HGD was calculated as

0.42. This result showed that, in the T. turgidum–Ae. tauschii hybrids,

unreduced gamete production is under genetic control; however, in consis-

tence with the observation for the Gilia and Brassica hybrids, environmental


factors influence the expression of this trait to a considerable degree (Grant,

1952; Mason et al., 2011).

The QTL analysis identified six genomic regions ofAe. tauschii that were

associated with the unreduced gamete production in the triploid F1 hybrids

with T. turgidum (Table 4.3; Fig. 4.5). Because the production of unreduced

gametes correlates with selfed seed set rates, these loci may harbor genes that

regulate such reproductive activities as gametogenesis, fertilization, and seed

development in the hybrids. Nevertheless, many, if not all, of the six loci

were assumed to regulate nonreductional meiosis and subsequent gamete

production processes based on the predominant role of functional

unreduced gametes in the seed setting of the T. turgidum–Ae. tauschii F1hybrids. On the basis of their genomic location, only two of the six genes

might correspond to known wheat reproductive genes: one that affects

homeologous pairing (Ph2) and one that is involved in female sterility

(Taf1) (Dou et al., 2009; Mello-Sampayo, 1971; Mello-Sampayo and

Lorente, 1968; Upadhya and Swaminathan, 1967). Consequently, the other

loci may represent a novel group of reproduction genes in wheat. QTL anal-

ysis provided evidence for the relatively complex genetic nature of

unreduced gamete production in interspecific F1 hybrids.

Because QTL analysis was done for the triploid population, in which

only the paternal Ae. tauschii component segregates, the influence of mater-

nal component on the F1 hybrid unreduced gamete production is not

known. Another line of evidence suggests thatT. turgidum cultivar Langdon,

Table 4.3 Ae. tauschii QTLs and epistatic interaction that affect genome doublingfrequency in the triploid F1 hybrids with T. turgidumQTL/QTL combinationa Chromosomeb Positionc LOD PVE (%)d

1 1 19.8 2.5 2.7

2 2 24.3 8.0 14.1

3 3 50.7 7.4 10.2

4 3 94.4 3.4 4.9

5 6 118.0 2.2 2.9

6 7 94.4 6.3 11.3

2�6 1.5 4.6

aEpistatic interaction between QTLs are denoted by “�.”bAe. tauschii chromosome that harbor the QTL.cQTL position in centimorgan.dThe proportion of the phenotypic variance explained by the QTL/epistatic interaction.


the maternal parent of the segregants, has genes for unreduced gamete pro-

duction that function in hybrid genome backgrounds (Xu and Joppa, 2000).

Both maternal and paternal genetic factors, therefore, are most likely

involved in the T. turgidum–Ae. tauschii F1 hybrids’ unreduced gamete pro-

duction. Interestingly, the synthetic haploid of Langdon (AB genome) sets

seeds of normal disomic plants (AABB genome) through union of male and

female unreduced gametes produced via nonreductional meiosis, indicating

that, even when the Ae. tauschii genome is absent, the Langdon genome is

capable of producing unreduced gametes (Jauhar et al., 2000). However, the

selfed seed set rate of the synthetic Langdon haploid (2.75 seeds per plant,

measured as selfed seed set rate) is greatly increased by addition of the Ae.

tauschii genome as the T. turgidum–Ae. tauschii F1 hybrids set roughly

10–106 or more seeds per plant. Accordingly, the Ae. tauschii genes for F1hybrid unreduced gamete production seem to have considerable positive

impact on HGD when the Langdon genome is merged. To what extent

the additive effects of the Ae. tauschii genes are responsible for improvement

of the F1 hybrid unreduced gamete productivity and whether epistatic

Figure 4.5 Multiple interval mapping of Ae. tauschii QTLs associated with theunreduced gamete production in the triploid F1 hybrids with T. turgidum. Black trianglesindicate the approximate positions of centromeres.


interactions between the Langdon andAe. tauschii genes are involved remain

to be addressed. Clearly, most of the complex genetic mechanisms involved

in the production of unreduced gametes in the T. turgidum–Ae. tauschii F1hybrids still need to be elucidated.

4.4. Maintenance of genes for F1 hybrids’ unreduced gameteproduction in the parental species

Unreduced gamete production often is a generation-specific phenomenon

that is expressed in F1 individuals, but not in the parental species nor in the F2and subsequent generations. The fitness of F1 individuals is greatly improved

by unreduced gamete production, whereas its adaptive significance for the

parental species is not clear. How genes involved in F1 hybrid unreduced

gamete production are maintained in the parental species is an intriguing

question, but, to date, few studies have addressed it. In the case of the

T. turgidum–Ae. tauschii F1 hybrids, one possible evolutionary model for

the Ae. tauschii genes is that the six loci that the QTL analysis identified have

some “normal” (presumably reproductive) function of adaptive value.

Mutations occur at the loci, but only the nondeleterious mutations, that

do not critically affect the “normal” function, accumulate over time. Most

such mutations likely remain phenotypically cryptic in Ae. tauschii, but each

resultant allele may positively or negatively affect unreduced gamete pro-

duction when placed in the hybrid genome background. Consequently,

the observed Ae. tauschii natural variation in the ability to cause unreduced

gamete production in the F1 hybrids with T. turgidum could be a by-product

of nondeleterious mutations that occurred at those loci (Fukuda and

Sakamoto, 1992a,b; Kihara et al., 1965; Matsuoka et al., 2007).

On the basis of the assumptions that (1) in Ae. tauschii those six loci have

some adaptive value and (2) the observed natural variation in unreduced

gamete production in the F1 hybrids with T. turgidum is a by-product of

nondeleterious mutations that occurred at those loci, the evolutionary

model predicts that the ability to cause F1 hybrid unreduced gamete produc-

tion is a trait that is widely shared by natural Ae. tauschii populations. Ae.

taushcii has three distinctive intraspecific lineages (named TauL1, TauL2,

and TauL3) that are defined by the patterns of nuclear and chloroplast

DNA variation (Matsuoka et al., 2008, 2013; Mizuno et al., 2010b). Geo-

graphically, the TauL1 accessions widely spread across a range that spans

from central Syria to western China, whereas the TauL2 and TauL3 acces-

sions are restricted to the Transcaucasus/Middle East region and Georgia,

respectively (Fig. 4.6). In a comparative analysis, the ability to cause F1


hybrid unreduced gamete production varied little between the TauL1,

TauL2, and TauL3, but varied greatly within the lineages, indicating that,

as expected from the evolutionary model, the ability is a widespread trait that

may have a deep evolutionary origin (Fig. 4.7). Accordingly, the Ae.

tauschii’s ability to cause F1 hybrid unreduced gamete production might have

been maintained by natural selection on those loci that most likely have

some reproductive function: similar strength of the selection might have

resulted in fewer between-lineage differences (Fig. 4.7). In addition, the

wide within-lineage variability of the ability may suggest that a considerable

amount of natural allelic variation has been accumulated in the six loci

through nondeleterious mutations. Nondeleterious mutations that occur

in the parental species, therefore, might have some important role in the

expression of unreduced gamete production in their hybrids.

5. ALLOPOLYPLOID GENOME ALTERATION

Allopolyploid individuals show considerable genetic instability at the

chromosomal and genic/epigenetic levels in their early generations. Such

genetic instability may be the cause of the phenotypic variability observed

in various newly formed allopolyploids (Anssour et al., 2009; Kostoff,

Figure 4.6 Geographic distribution of the Ae. tauschii accessions. Purple, green, and redcircles denote the TauL1, TauL2, and TauL3 accessions, respectively. The TauL1 acces-sions from central China are not shown.


1938;Matsushita et al., 2012; Schranz andOsborn, 2004). Depending on the

environmental circumstances, the novel phenotypes of morphological,

reproductive, and life-history traits that newly formed allopolyploids may

have can be either advantageous or deleterious in terms of adaptation.

Figure 4.7 Box plots of genome doubling frequencies of the Langdon–Ae. tauschiitriploid F1 hybrids produced by Matsuoka et al. (2007). (A) Year 2004. (B) Year 2005.In each year, the mean hybrid genome doubling frequencies do not significantly differbetween the lineages (p¼0.08–0.84, year-wise Steel–Dwass tests for all possible pairs).


For this reason, allopolyploid genome alteration may positively or negatively

influence the process of allopolyploid speciation through theHDG pathway.

Despite recent progress in analyzing the changes in the transcriptome,

genome architecture, and epigenetic landscape that are associated with

polyploidization, convincing evidence for the link between genome alter-

ation and successful occurrence of polyploid speciation is currently lacking.

Especially, the question of how the genomes of newly formed allopolyploids

that undergo massive chromosomal/genic/epigenetic alteration are stabi-

lized in the later generations lies at the heart of that issue because stable trans-

generational inheritance that confers the consistent expression of adaptive

traits provides the genetic basis for the establishment of newly formed poly-

ploids as a species. In this section, we focus on the genome stabilization ques-

tion and review the classic and recent studies on the chromosomal and

genic/epigenetic changes of allopolyploid genomes in the wheat and other

model plant species.

5.1. Chromosomal changesChromosomal changes are commonly observed in association with

polyploidization. Several types of karyotypic instability, including aneu-

ploidy, intra- and intergenomic rearrangements, chromosome breakage

and fusion, and loss of rDNA repeats, are inherent to newly formed poly-

ploids and occur at high rates. For example, aneuploidy is found in 28.3%

and 29.0% of the progeny of surveyed nascent allopolyploids and autopoly-

ploids, respectively (Ramsey and Schemske, 2002). In a recent study, Xiong

et al. (2011) observed extensive aneuploidy in the early generations of newly

synthesized Brassica napus L. allotetraploids: 95% individuals were aneuploid

at the 10th selfed generation. Similarly, the natural populations ofTragopogon

miscellus Ownbey, a very young wild allotetraploid species that is about

40 generations old, is 69% aneuploid (Chester et al., 2012). Furthermore,

frequent and extensive chromosome substitutions and large structural

rearrangements were commonly observed in the synthetic lines of

B. napus and natural populations of T. miscellus. These results suggest that

the stabilization of chromosome inheritance in allopolyploid speciation

through the HGD pathway is a protracted process that continues over a rel-

atively long period of time.

The numerical and structural changes in chromosomes may cause com-

plex nondisomic patterns of chromosomal inheritance in allopolyploid indi-

viduals, whereas regular meiotic pairing and segregation are essential for


stable reproduction. For this reason, cytological diploidization, the process

through which the complex meiotic behavior of newly formed polyploids

becomes disomic or “diploid-like” to produce genetically balanced gametes,

represents a critical mechanism for allopolyploid speciation. One known

factor that influences the diploid-like meiotic behavior of allopolyploids is

the activity of regulator genes that restrict pairing of homeologous chromo-

somes, that is, chromosomes that are not homologous but share relatively

high synteny because of a common ancestry. Such genes have been reported

in several allopolyploid species, including wheat (T. aestivum), tall fescue

(Festuca arundinacea Schreb.), oat (A. sativa) and oilseed rape (B. napus)

(Cifuentes et al., 2010; Jenczewski and Alix, 2004). Furthermore, recent

studies on the structural and functional details of the wheat (Pairing

homeologous or Ph) and Brassica (Pairing regulator in B. napus or PrBn) genes

provided important comparative insights into the origins and roles of those

genes in the cytological diploidization that occurred in the evolution of these

two widely divergent taxa (Al-Kaff et al., 2008; Griffiths et al., 2006;

Jenczewski et al., 2003; Nicolas et al., 2009). Another known factor that

influences the diploid-like meiotic behavior of allopolyploids is the struc-

tural and nucleotide sequence divergence that weakens the pairing affinity

between homeologous chromosomes. In allopolyploids, such divergence

may result from the differences that already exist between the parental chro-

mosomes and/or the response to allopolyploidization that arises de novo as

the consequence of homeologous recombination, chromosome breakage/

fusion, transposon excision/insertion, intrachromatid exchanges, and rDNA

restructuring (Gaeta and Pires, 2010; Le Comber et al., 2010). The relative

significance of these two factors in realizing cytological diploidization, how-

ever, is not known.

Frequent chromosomal changes have been observed in synthesized lines

of allohexaploid T. aestivumwheat (i.e., synthetic common wheat lines) that

are produced by artificially crossingT. turgidum andAe. tauschii, whereas nat-

ural common wheat varieties produce 1–3% aneuploid individuals under

normal conditions (Riley and Kimber, 1961). Early studies reported somatic

chromosome number variation and nondisomic meiotic configurations in

the F2 individuals of the synthetic common wheat lines, and more impor-

tantly, these studies showed that aneuploidy occurring in the later genera-

tions may vary in frequency between the lines depending on the parental

genotypes (Tabushi, 1964). Recent studies that used in situ hybridization

techniques to discriminate the genomes and chromosomes of synthetic

common wheat lines confirmed these early observations: roughly 4–30%


of early generation (selfed generation S1 and S2) individuals and 20–100% of

later generation (S8 and later) individuals were aneuploid, whereas the fre-

quencies greatly varied between the lines (Mestiri et al., 2010; Zhang et al.,

2013). In contrast, structural changes were nearly absent, indicating that the

chromosome changes in nascent synthetic common wheat lines, in essence,

are numerical. One possible explanation for this finding is that the invariable

activity of the Ph1 gene minimized the occurrence of homeologous pairing

(Okamoto, 1957; Riley and Chapman, 1958). Accordingly, the lack of

detectable chromosome changes other than aneuploidy in the Ph1-carrying

synthetic common wheat lines provides support for the idea that

homeologous recombination can be a major cause of genome restructuring

in newly formed allopolyploids (Gaeta and Pires, 2010).

The synthetic common wheat studies provided further insights into how

the genomes of newly formed allopolyploids are stabilized in the later gen-

erations. Consistent with the findings in the synthetic B. napus lines and nat-

ural T. miscellus populations, aneuploidy was persistent in synthetic common

wheat lines: progressive karyotype stabilization did not occur after 9–10 gen-

erations even when multigenerational selection for euploidy was applied,

suggesting that the allopolyploid wheat chromosome inheritance may take

several generations before stabilization (Chester et al., 2012; Xiong et al.,

2011; Zhang et al., 2013). However, in contrast to the cases of B. napus

and T. miscellus, the synthetic common wheat studies underscored the pos-

sibility that, even in the absence of homeologous pairing/recombination

that could drive structural and nucleotide sequence divergence, the allopoly-

ploid chromosome inheritance may eventually be stabilized in the later gen-

erations. This suggests that the stabilization of chromosome inheritance in

natural common wheat might have been achieved through some sort of

novel genetic mutations and/or heritable epigenetic modifications other

than homeologous recombination (Zhang et al., 2013). In fact, the observa-

tion that aneuploid frequencies greatly vary between the synthetic common

wheat lines depending on the parental species’ genotypes supports the exis-

tence of some genetic mechanisms that influence the regulation of chromo-

some number regulation in allopolyploid wheat meiosis (Mestiri et al., 2010;

Tabushi, 1964; Zhang et al., 2013). As a caveat, however, we note that the

direct descendants of the Ae. tauschii populations that gave birth to natural

T. aestivum as the paternal parent is yet to be identified (Matsuoka et al.,

2013). The same is true for the maternal species T. turgidum: what cultivated

varieties actually gave rise to natural T. aestivum is not known (Matsuoka,

2011; Matsuoka and Nasuda, 2004). Since both Ae. tauschii and


T. turgidum are genetically diverse, the genetic attributes of the accessions

that were used to produce the synthetic common wheat lines may not be

identical to those of the ancestral populations or varieties. For this reason,

the possibility remains that the T. aestivum speciation that took place under

natural conditions 8000 years ago did not undergo persistent aneuploidy as

was observed in the synthetic common wheat lines.

5.2. Genic/epigenetic changesThe merger in a common nucleus of two or more genomes that are derived

from divergent parental species could be a “genomic shock,” that is, a sud-

den major perturbation of the nuclear and cellular systems (McClintock,

1984). In the short term, increased dosage of genetic materials in the nucleus

can bring about deleterious effects because unbalanced gene expression cau-

ses unfavorable physiological and morphological changes. It is believed that,

in such cases, unbalanced gene expression is stabilized through genetic

diploidization, that is, the process in which the expression of genes in a poly-

ploid is reduced to a level comparable to that of genes in the parental species

by gene silencing and/or dosage compensation (Grant, 1981; Liu and

Wendel, 2003; Soltis and Soltis, 1993). In fact, a number of recent studies

identified various non-Mendelian molecular activities that may be involved

in genetic diploidization in newly formed allopolyploids, including non-

random sequence elimination (Feldman et al., 1997; Kashkush et al.,

2002; Ozkan et al., 2001, 2003; Shaked et al., 2001; Skalicka et al., 2005;

Tate et al., 2009), epigenetic modifications (Kovarik et al., 2008;

Madlung et al., 2002; Shaked et al., 2001; Shitsukawa et al., 2007; Zhao

et al., 2011), and transposon mobilization (Kashkush et al., 2003;

Kraitshtein et al., 2010; Petit et al., 2010). Rapid sequence elimination

was observed in some newly formed allopolyploids, but not in others

(Bottley et al., 2006; Chague et al., 2010; He et al., 2003; Liu et al.,

2001). Altered patterns of gene expression are commonly reported for var-

ious natural and synthetic allopolyploids of Arabidopsis (Chang et al., 2010;

Wang et al., 2004, 2006), Brassica (Gaeta et al., 2007), Coffea (Bardil et al.,

2011), Gossypirum (Adams et al., 2003; Flagel and Wendel, 2010; Flagel

et al., 2008; Hovav et al., 2008; Yang et al., 2006), Tragopogon (Buggs

et al., 2010; Koh et al., 2010), Triticum (Bottley and Koebner, 2008;

Bottley et al., 2006; Chague et al., 2010; Chelaifa et al., 2013; He et al.,

2003; Mochida et al., 2003; Qi et al., 2012), and Spartina (Chelaifa et al.,

2010). In cotton, gene expression alteration, which introduced homeolog


expression biases that persisted long after in the later generations, was found

to take place instantaneously with interspecific hybridization. Furthermore,

comparative analyses of cotton F1 hybrids and their allopolyploid descen-

dants suggested that it is the genome merger (i.e., hybridization), rather than

genome doubling, that had a profound impact on the alteration of gene

expression patterns (Doyle et al., 2008; Flagel et al., 2008).

In theory, multiple copies of genetic factors that reside in a common

nucleus may have long-term evolutionary significance because the numer-

ical and functional redundancy relax purifying selection and provide raw

genetic material upon which mutation, drift, and selection can act

(Ohno, 1970; Zhang, 2003). Polyploidization, therefore, opens new ave-

nues for the resultant duplicated genes to develop new functions (neo-

functionalization) or modulate ancestral functions (subfunctionalization).

In contrast to the sequence changes that occur rapidly in response to hybrid-

ization and genome doubling, the neofunctionalization and sub-

fuctionalization processes are gradual but might ultimately contribute to

stabilize unbalanced gene expression in allopolyploids by reducing func-

tional redundancy. Accordingly, at least two temporally distinctive mecha-

nisms appear to be involved in the stabilization of newly formed

allopolyploid genomes at the molecular level: the rapid genetic and epige-

netic activities that cause various molecular changes to reduce the negative

impact of genomic shock and the long-term evolutionary process that diver-

sify the functions of duplicated genes.

Wheat studies made major contributions to our understanding of the

genetic and epigenetic activities that cause the molecular changes in the

nascent allopolyploid genomes. The examples of early findings include dos-

age compensation and intergenomic suppression that control the levels of a

group of seed storage proteins (high-molecular-weight glutenin subunits) in

the endosperm (Galili and Feldman, 1984; Galili et al., 1986). Later, rapid

nonrandom elimination of specific noncoding low-copy and high-copy

number DNA sequences was found as a probable preprogrammed process

that significantly reduces the amounts of newly formed allopolyploids’

nuclear DNA (Ozkan et al., 2003; Eilam et al., 2008, 2010). In the newly

formed Triticum and Aegilops allopolyploids, chromosome-specific

sequences that may influence the levels of chromosomal homology are elim-

inated from one genome immediately or a few generations after the forma-

tion. Accordingly, the rapid nonrandom sequence elimination might

contribute to achieving cytological diploidization through increasing nucle-

otide sequence divergence between homeologous chromosomes (Feldman


and Levy, 2012). At the gene expression level, allopolyploidization was

found to affect the splicing patterns of a wheat transcription factor gene

WDREB2 under abiotic stress conditions (Egawa et al., 2006; Terashima

and Takumi, 2009). Drought tolerance levels at the seedling stage were gen-

erally higher in the synthetic common wheat lines than in the parental Ae.

tauschii accessions. The abscisic acid-inducible gene expression changes that

occur in response to allopolyploidization might be involved in the inter-

ploidy drought-tolerance-level differences (Kurahashi et al., 2009; Iehisa

and Takumi, 2012). Furthermore, the expression level and pattern changes

of endogenous small RNAs (i.e., microRNAs and small interfering RNAs),

which are involved in such adaptively important cellular processes as gene

expression, heterochromatin formation, and transposon silencing, were

observed in the newly formed T. turgidum–Ae. tauschii F1 hybrids (Kenan-

Eichler et al., 2011).

Because the genic/epigenetic changes reported in wheat and other plant

species are experimentally reproducible, some sort of genetic control for

those non-Mendelian activities may exist. Addressing the details of the

yet-to-be-discovered genetic control may provide important clues to better

understanding how influential the genic/epigenetic changes are on the

occurrence of allopolyploid speciation through the HGD pathway. Further-

more, population-level studies on the roles of natural selection and genetic

drift in achieving genetic diploidization are required to clarify if the muta-

tional changes that occur in association with allopolyploidization may bring

about predictable evolutionary consequences.

6. CONCLUDING REMARKS

In the last five decades, several intriguing reproductive phenomena

have been found in the wheat interspecific hybrids, namely, unexpectedly

high crossability with rye, dysgenesis, gametocidal action, uniparental chro-

mosome elimination during embryogenesis, frequent unreduced gamete

production, and rapid genome alteration at the chromosome and sequence

levels. Genetic and cytogenetic studies that relied on the relative ease of

making hybrid crosses between wheat, barley, rye, and other Triticeae spe-

cies provided valuable insights into the mechanisms that underlie these phe-

nomena. In this review, we attempted to put some of the findings of those

studies into an evolutionary context and discuss their contribution to our

understanding of the genetics of allopolyploid speciation through the


HGD pathway. Our discussion on the reproductive phenomena of inter-

specific wheat hybrids from an evolutionary standpoint provides insights

into the genetic mechanisms that underlie allopolyploid speciation and high-

lights the potential of the Triticum and Aegilops species as a model system for

allopolyploid speciation studies.

At the same time, the discussion that we present above identifies numer-

ous important questions that concern the expression of phenotypes/phe-

nomena that are specifically observed in hybrids. For example, what

genetic mechanisms other than DM incompatibility underlie wheat hybrid

dysgenesis under natural conditions? To what extent are the genome-

reprogramming mechanisms such as the changes in the patterns of gene

expression, DNA methylation, and imprinting responsible for the expres-

sion of wheat hybrid dysgenesis? How do the maternal and paternal genes

interact when unreduced gametes are produced in F1 hybrids? Through

what mechanisms the chromosome inheritance was stabilized after hybrid-

ization? How are the nonrandom genic/epigenetic molecular changes reg-

ulated in hybrid individuals? What kind of roles do the population genetic

forces (such as natural selection and genetic drift) have in achieving genetic

diploidization? To address these questions, further development of empirical

and theoretical basis for “hybrid genetics” that can deal with the diverse

Mendelian and non-Mendelian mechanisms for the complex phenotype

expression in interspecific hybrids is required.

Until recently, the very large genome sizes and complex polyploid gene

expression patterns have been major obstacles to perform in-depth molec-

ular analyses in the Triticum and Aegilops species relative to other model spe-

cies of Arabidopsis and Oryza. This situation, however, has been changing

since the advent of the next-generation sequencing technologies

(Varshney et al., 2009). The recently published draft genome sequences

of common wheat and its diploid ancestors, along with the already available

high-volume transcriptome information, will enable to study allopolyploid

speciation through the HGD pathway in the Triticum and Aegilops species by

the use of comparative and functional genomics approaches (Mochida et al.,

2008; Brenchley et al., 2012; Ling et al., 2013; Jia et al., 2013). Addressing

the questions that were identified in this chapter, in particular, the ones that

concern the expression of hybrid-specific phenotypes/phenomena, by

applying such genome-based methodologies to the Triticum and Aegilops

system should shed novel light on the genetic mechanisms for allopolyploid

speciation through the HGD pathway.


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