Int. J. Mol. Sci. 2012, 13(7), 8696-8721; doi:10.3390/ijms13078696

Review
Multiple Mechanisms and Challenges for the Application of Allopolyploidy in Plants
Kenji Osabe 1,, Takahiro Kawanabe 2,, Taku Sasaki 3,, Ryo Ishikawa 4,5, Keiichi Okazaki 6, Elizabeth S. Dennis 1, Tomohiko Kazama 7 and Ryo Fujimoto 6,*
1
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, ACT 2601, Australia; E-Mails: kenji.osabe@csiro.au (K.O.); liz.dennis@csiro.au (E.S.D.)
2
Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi 987-8607, Japan; E-Mail: tkawa@beach.ocn.ne.jp
3
Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohrgasse 3, Vienna 1030, Austria; E-Mail: taku.sasaki@gmi.oeaw.ac.at
4
Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8510, Japan; E-Mail: r-ishika@port.kobe-u.ac.jp
5
Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK; E-Mail: ryo.ishikawa@jic.ac.uk
6
Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata 950-2181, Japan; E-Mail: okazaki@agr.niigata-u.ac.jp
7
Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan; E-Mail: tomo-kazama@bios.tohoku.ac.jp
*
Author to whom correspondence should be addressed; E-Mail: leo@agr.niigata-u.ac.jp; Tel./Fax: +81-25-262-6615.
These authors equally contributed to this work.
Received: 30 May 2012; in revised form: 4 July 2012 / Accepted: 4 July 2012 /
Published: 13 July 2012

Abstract

: An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and the requirement for chromosome doubling. However, allopolyploids are widely observed among plant species, so allopolyploids have succeeded in overcoming these limitations and may have a selective advantage. As techniques for making allopolyploids are developed, we can compare transcription, genome organization, and epigenetic modifications between synthesized allopolyploids and their direct parental lines or between several generations of allopolyploids. It has been suggested that divergence of transcription caused either genetically or epigenetically, which can contribute to plant phenotype, is important for the adaptation of allopolyploids.
Keywords:
allopolyploid; self-compatibility; cytoplasmic male sterility; reproductive barrier; epigenetics

1. Introduction

Polyploidization (whole genome duplication) is an important process in plant speciation [1]. Polyploidy is common in angiosperms, and in general there are two types of polyploids, autopolyploid (auto = same) and allopolyploid (allo = different). Autopolyploids are produced by multiplication of the genome from a single species. Allopolyploids are typically derived from hybridization between two (or more) distantly related species and combine divergent genomes with their own chromosome complements. Merging genomes from different species provides not only genome variation, but also novel opportunities to generate diversification through their interactions that allow allopolyploidy to function as a potential source of new species [1,2].

Several different pathways of allopolyploid formation have been described. The one-step model is that allotetraploids are formed by fusion of unreduced male and female gametes from two diploid species. Direct hybridization between two autopolyploid species is also categorized in a one-step model. The two-step model is that an allotetraploid is formed by an inter-specific cross between two diploid species followed by somatic doubling in meristematic tissues [3]. The triploid-bridge model is that triploids are formed by fusion of unreduced and reduced gametes from two diploid species and then unreduced gametes from triploids fuse with reduced gametes from diploids, which can generate stable allotetraploids [3,4].

Generation of natural allopolyploids may be sporadic because of limitations such as co-existing populations of parental lines, hybrid incompatibility (pre- and post-zygotic reproductive barriers), unreduced gametes, and chromosome doubling. However, allopolyploids are widely observed among plants and have been formed multiple times [5], indicating that allopolyploids succeed in breaking down hybrid incompatibility, forming unreduced gametes and undergo chromosome doubling during evolution. The most common route to allopolyploid formation is via unreduced gametes, which have been identified in many plant taxa [3]. Unreduced gametes are formed by meiotic dysfunction at the meiosis I (FDR: first division restitution) or at meiosis II (SDR: second division restitution). After successful generation of new allopolyploids, correct segregation of chromosomes is important for producing offspring as allopolyploids have more than two sets of chromosomes; suppression of crossovers between homoeologous chromosomes is required to ensure fertility. In allopolyploids, diploid-like meiotic behavior is observed, indicating that correct pairing of homologous chromosomes is controlled, in the case of wheat, the ph1 locus performs this function [6].

Allopolyploids may have a selective advantage because of their common occurrence in nature. Heterosis, gene dosage, gene redundancy, and reproductive system advantages of allopolyploids have been suggested as the basis of this advantage [7,8]. Heterosis or hybrid vigour refers to the phenotypic superiority of a hybrid over its parents. Heterozygosity of the different genomes might induce growth vigour and become fixed in allopolyploids [9]. Several inter-specific hybrids show greater vigour than the average of their parental lines [911]. The hybrid between Arabidopsis arenosa and Arabidopsis thaliana shows a hybrid-vigour-like phenotype, and this phenomenon is considered to result from an alteration of circadian rhythm genes in hybrids [9,12]. The variation of dosage-regulated gene expression could be increased in allopolyploids, which may contribute to generating a new plant phenotype [8,13]. Gene redundancy has the potential to mask recessive deleterious alleles by dominant alleles [7]. In addition to genetic robustness against null mutations, it has been suggested that duplicated genes produce a diversity of expression that facilitates adaptive evolution [14]. Another advantage of allopolyploids is their reproductive system. Most allopolyploids show self-compatibility that can favor rapid reproduction, while some of their parents are self-incompatible [7,15]. Although self-compatibility has the potential to lead to inbreeding depression by the accumulation of recessive alleles, allopolyploids are more tolerant than diploids to this because of their genome redundancy.

Allopolyploids include important crops such as wheat, cotton, and canola, and all have improved agricultural traits relative to their diploid progenitors. Wheat was domesticated about 10,000 years ago, and bread wheat, Triticum aestivum, has a genome composition of AABBDD, which arose by inter-specific hybridization between T. turgidum (AABB) and Aegilops tauschii (DD) [16,17]. Durum (pasta) wheat has a genome composition of AABB. In cotton (Gossypium), there are two major branches of Gossypium diploid species, the New World (D-genome group) and the Old World (A, G, etc.). The commercially important cottons are naturally formed allopolyploids (AADD) such as Gossypium hirsutum (Upland cotton) and G. barbadense (Pima or Egyptian cotton), and they have superior fiber yield and quality relative to their ancestral species [18,19]. Canola (Brassica napus) is an allopolyploid (AACC), with the A and C genomes corresponding to the genomes of Brassica rapa and Brassica oleracea, respectively [20]. B. rapa (Chinese cabbage, turnip, etc.) and B. oleracea (cabbage, broccoli, etc.) are cultivated mainly as vegetables, while canola is cultivated as an oil crop. In this way, allopolyploidy has played a crucial role in the domestication of crops and their selection for desirable products [16].

Artificially synthesized allopolyploids are excellent material to understand early events following hybridization because the exact progenitors are known. Methods for synthesizing allopolyploids have been developed and artificially synthesized allopolyploids have been widely generated. Molecular studies using artificially synthesized allopolyploids have revealed genomic rearrangements [2123], DNA methylation alterations [2426], transposon activation [2729], and transcriptome changes [11,3036]. Transcriptome changes caused genetically or epigenetically (transcriptional states of genes can be controlled by changes to the structure of chromatin without any change in the DNA sequence) have the potential to provide a source of developmental novelty, and might be important for the evolutionary success of allopolyploids.

2. Techniques for Synthesizing Allopolyploids

In order to successfully produce synthetic allopolyploids, various factors related to inter-specific hybridization and subsequent procedures should be considered (Figure 1). As the level of cross-ability varies between parental materials, various combinations of genotypes have been tested in inter-specific breeding programs of many crops [3739]. Whether a genotype is used as the maternal or paternal parent is important in inter-specific hybridization because unilateral incompatibility is often observed, especially in crossing combinations between self-incompatible and self-compatible species [40]. In lilies, crosses between remotely related species succeeded in only one direction [41]. Environmental factors such as temperature can also influence cross-ability: seed set was promoted at 15 °C in the inter-specific crosses of tulips [42], and at 23–26 °C in the crosses between Cucumis sativus and C. metuliferus [43]. The production of synthetic allopolyploids requires knowledge about the cross-ability of the species and sensitive techniques to overcome the limitations of incompatibility.

In lilies, the pollen tubes arrest halfway down the stylar canal after inter-specific pollination (post-pollination pre-zygotic barriers), but this can be efficiently overcome by placing pollen on the cut-style [44,45]. This technique led to the generation of new hybrid lilies such as LA (between L. longiflorum and Asiatic hybrids) hybrids, which were distributed commercially. In earlier studies, mentor pollen techniques were successfully applied to overcome pre-zygotic barriers in Populus [46], apple [47], Cucumis [48], and pear [49]. Application of plant growth regulators to ovaries at the time of pollination improved seed set after inter-specific hybridization of Lilium [50]. Applications of these techniques are species specific, and further studies are required for bypassing pre-zygotic barriers.

Embryo rescue including embryo, ovule, and ovary culture is necessary to produce hybrids between distantly related species where a post-zygotic barrier is caused by insufficient endosperm formation (Chapter 3). For successful embryo rescue, it is necessary to first determine the optimal isolation time of immature hybrid embryos (days after pollination). In the case of a cross between B. oleracea and B. rapa, this timing was 20–30 days after pollination. In vitro culture conditions of embryos has been extensively discussed [51,52] and various culture procedures have been applied to produce inter-specific hybrids. For instance, the culture of ovules obtained from the cross between Nicotiana tabacum and N. acuminata [53] was conducted using liquid Nitsch H medium containing 5% sucrose. The hybrid embryos obtained from the cross between B. oleracea var. alboglabra and Brassica campestris were cultured on White’s medium, containing 0.8% agar, 4% sucrose, and 10% coconut milk [54]. Asano and Myodo [55], working with Lilium embryos derived from the cross of distantly related species, showed that Murashige and Skoog medium is suitable for the culture of immature embryos when it was adjusted to pH 5.0 and supplemented with 20–40 g/L sucrose and 10−4–10−2 mg/L NAA (Naphthalene acetic acid). Okazaki et al. [56] revised the optimum sucrose concentration to 6% for embryo culture of lilies.

Hybrids obtained from distantly related inter-specific crosses are mostly sterile and cannot be used in cross breeding [5759]. Restoration of hybrid fertility can be achieved by zygotic or somatic chromosome doubling and by gamete non-reduction (unreduced gamete) [6063]. The anti-microtubule agent, colchicine, is effective for somatic (mitotic) polyploidization [64]. Dinitroaniline herbicides such as trifluralin, oryzalin, or amiprophosmethyl also act as anti-microtubule agents and they are applied at a lower concentration (0.001–0.01%) compared to colchicine treatment (0.05–0.2%) [6368]. Oryzalin was more efficient for inducing chromosome doubling and less toxic than colchicine [65,68]. Various methods of application of colchicine were adopted: treating flower buds under vacuum, soaking plantlets with colchicine solution, dropping colchicine on to the apical meristem, applying it to the leaf axils with cotton wool, etc. [64]. Nitrous oxide (N2O) has been applied to zygotes [69], seedlings [70], pollen mother cells [71,72], and anther somatic cells [73], as a polyploidizing agent in lieu of colchicine treatment. Nitrous oxide may act through depolymerization of microtubules [74]. Nitrous oxide is suitable for treating organs inside tissues because the gas can permeate to reach the tissues of interest, e.g., developing microspores within tulip bulbs [71]. Additionally, the gas is expected to be rapidly dissipated from treated tissues when the pressure is released, thereby preventing further harmful after-effects. For these reason nitrous oxide has been applied as a polyploidizing agent to overcome hybrid sterility in lilies [73,75].

Somatic chromosome doubling of a diploid inter-specific hybrid produces an allotetraploid containing two diploid genomes from two different species. In allotetraploids, the homologous chromosome from each parental species pairs during meiosis and leads to normal meiosis and fertile gamete production [60,62,63,76]. At the same time, such a preferential homologous chromosome pairing has the drawback of inhibiting meiotic recombination between genomes coming from different progenitors. The resulting fertile gametes show a few variations, so that the progeny of allotetraploids exhibit fixed heterozygosity [61,7779]. By contrast, spontaneous formation of unreduced gametes from aberrant meiosis (sexual polyploidization), i.e., FDR or SDR, occurs in diploid species as well as allodiploids [61,79]. Lim et al. [80] reported a new type of 2n gamete formation mechanism, IMR (indeterminate meiotic restitution), which combines characteristics of FDR and SDR: during the first meiotic division, some of the univalents divide equationally (as in FDR) and some bivalents disjoin reductionally (as in SDR) before telophase, leading to a dyad without further division. Such 2n-gametes can be used for the production of sexual progeny either through crossing or selfing [62,8084]. In addition, sexual polyploidization forces homoeologous chromosome pairing during meiosis in allodiploids, promoting genetic recombination between homoeologous chromosomes. Therefore, unlike in somatically doubled allotetraploids, fertile pollen derived from sexual polyploidization can transmit huge genetic variation to the progeny, which is preferable for introgression breeding via backcrossing with diploid parental species [78,79,84].

3. Reproductive Barrier

There are many reproductive barriers to the natural formation of allopolyploids at pre- and post-zygotic stages [85]. Pre-zygotic barriers include geographic or pollinator isolation (i.e., flower structure or color) [85] and flowering time [85,86]. The inhibition of pollen tube germination, arrest of pollen tube growth in ovules, and unilateral incompatibility (asymmetric patterns of pollen rejection in crosses between different species) are involved in post-pollination pre-zygotic barriers [85]. Once the pollen-tube germination and fertilization have been successful, there are still reproductive barriers such as hybrid inviability, a post-zygotic barrier [85]. Under- or over-proliferation of endosperm, which supports embryo development by providing nutrients crucial for viable seed formation, is one post zygotic barrier, which depends on the crossing combination [8790]. A common characteristic of unusual endosperm development observed in inter-specific and inter-ploidy crosses is due to a premature or delayed cellularization. Recent studies suggested that the altered development of endosperm is due to dysregulation of genomic imprinting [91]. Another post-zygotic barrier is hybrid sterility caused by sets of interacting genes and is described as the Dobzhansky-Muller incompatibility model [85]. Sometimes inter-specific hybrids show male-sterility, even though they have succeeded in polyploidization. One type of male-sterility is caused by incompatibility between the nuclear genome and the maternally derived mitochondrial genome, termed cytoplasmic male sterility (CMS) [92]. Inter-specific and inter-generic crosses sometimes lead to CMS, because a change of nuclear component has impacts on mitochondrial gene expression [93]. In this chapter, we introduce genomic imprinting and CMS in detail as their molecular mechanisms have recently become clear. The understanding of imprinting and CMS will enable us to generate allopolyploids and inter-specific hybrids efficiently.

3.1. Genomic Imprinting

In general, maternally and paternally inherited alleles of each gene are expressed equivalently in diploids but, in some genes, the two alleles are expressed at different levels depending on their parent of origin, termed genomic imprinting. Genomic imprinting is observed in both mammals and flowering plants and is regulated by DNA methylation or histone modifications. Genes involved in genomic imprinting have been extensively studied using the model plant, A. thaliana [94]. Analyses of mutants showing a prolonged syncytial phase and delayed endosperm cellularization identified genes encoding the components of a Polycomb complex [94]. In endosperm, only the maternal alleles of MEA (MEDEA) and FIS2 (FERTILIZATION INDEPENDENT SEED 2) are expressed, while the paternal alleles are silenced [95,96]. On the other hand, PHE1 (PHERES 1), a gene identified as a downstream target of the Polycomb complex, was expressed from the paternal allele [97]. Imprinting of these genes is regulated by differences in genomic DNA methylation patterns between the embryo and endosperm [94]. MEA and FIS2 are maternally expressed while PHE1 is paternally expressed, and they regulate endosperm development in opposite directions. This antagonistic regulation may explain the observed phenotypes of inter-specific crosses, and is consistent with the parental conflict hypothesis [98]. Recently, Meg1 (Maternally expressed gene 1) in maize has been shown to be required for the development of the endosperm nutrient transfer cells between seed and maternal tissue. Meg1 also plays important roles in the regulation of maternal nutrient uptake and sucrose partitioning. This result demonstrated the first functional evidence that an imprinted gene is involved in a balanced distribution of maternal nutrients to filial tissues in plants, although Meg1 is a maternally expressed imprinted gene that promotes rather than restricts nutrient allocation (Figure 2) [99].

Several studies have indicated the involvement of genomic imprinting in reproductive barriers. The hybrid endosperm derived from A. thaliana as the female parent and its close relative, A. arenosa as the male parent, shows overgrowth with altered or arrested embryo development [100]. The imprinted gene expression patterns of MEA and PHE1 were disrupted and bi-allelic expression was detected in the hybrid endosperm. The overgrowth phenotype of endosperm is probably caused by the maternal de-repression of PHE1, suggested by the findings that the maternal phe1 mutation improves fertility [100102]. Disruption of PHE1 imprinting may cause a prolonged and stable interaction with AGL62 (AGAMOUS-LIKE 62), which inhibits cellularization [103,104]. Altered expression of the PHE1 homolog, OsMADS87, is observed in the endosperm of hybrids between cultivated and wild rice species [105]. These findings suggest that disruption of the regulation of genomic imprinting may be caused by the difference of epigenetic modifications on PHE1 between species, and it may act as a reproductive barrier in species hybridization and allopolyploidization. This idea also supports the ‘Endosperm balance number (EBN) hypothesis’, in which the ratio 2:1 of maternal to paternal EBN value is important for a successful cross [8890]. Analysis of genomic imprinting in allopolyploids will provide important findings on its role in species hybridization.

3.2. Cytoplasmic Male Sterility

Inter-specific hybrids sometimes show male-sterility, which is known as hybrid sterility. Occasionally male sterility is caused by incompatibility between mitochondrial and nuclear genomes (alloplasmic male sterility), a type of CMS (Cytoplasmic male sterility). CMS phenotypes range from floral abnormalities to failure of pollen maturation. CMS is often observed in natural plant populations, and can also be artificially produced by successive backcrossing resulting from inter-specific exchange of nuclear and cytoplasmic genomes. CMS is a maternally inherited phenotype and known to be governed by the mitochondrial genome. Plant mitochondria are quite different from those of animal mitochondria: the animal mitochondrial genome is less than 20 kb in size and has a circular structure, while plant mitochondrial genomes are large (200 to more than 2400 kb; dependent on species) and complex having a multipartite structure because of large repetitive sequences [106]. Such repetitive sequences in plant mitochondrial DNA can induce recombination, and create chimeric orfs (open reading frames) [92]. Expression of certain new orfs is associated with CMS. From a comparison of mitochondrial genomes or gene expression between CMS and normal cytoplasms, CMS-associated genes have been reported in many species [107]. These genes often show a chimeric structure with the mitochondrial genes in normal mitochondria and have transmembrane domains. Expression of the CMS-associated gene is occasionally suppressed by a particular nuclear factor being transported into mitochondria, and results in fertility restoration. A gene for this nuclear factor is called Rf (Restorer of fertility).

Rf genes are grouped into two types, PPR (pentatricopeptide repeat) type and non-PPR type. The PPR proteins are nuclear-encoded RNA binding proteins, which function in post-transcriptional processes (RNA editing, RNA splicing, RNA cleavage and translation) in organelles [108]. Rf genes in Petunia hybrida (Rf-PPR592), Raphanus sativus (Rfo/Rfk), Oryza sativa L. (Rf1a and Rf1b) and Sorghum bicolor (Rf1) encode PPR proteins [109114]. These PPR type RF proteins have been investigated and reported to have roles in decreasing CMS-associated gene products in each mitochondrion [115117]. These analyses suggest that PPR type RF proteins are key factors that directly eliminate causes of CMS in mitochondria. The non-PPR type Rf genes include Rf2a of maize (Zea mays), which encodes aldehyde dehydrogenase, and Rf2 and Rf17 of rice (O. sativa), which encode glycine-rich and ACPS-like (acyl-carrier protein synthesis-like) domain containing proteins, respectively [118120]. RF2a in maize does not reduce the accumulation of a CMS-associated gene product, URF13, although RF2a is required for normal anther development [121]. The presence of Rf17 in rice also does not affect the RNA profile of a CMS-associated gene, CW-orf307 [122]. The reduced expression of Rf17 restores the fertility of CW-type CMS rice. The expression of Rf17 is dependent on the mitochondrial haplotypes [119], indicating that signals from the mitochondria to the nucleus (retrograde signals) control the expression of Rf17.

Retrograde signals from mitochondria determine whether accumulation of CMS-associated gene products in mitochondria leads to male sterility [123]. It is hypothesized that CMS is caused by insufficient ATP-production for pollen development due to the toxic effects of CMS-associated gene products in mitochondria. A new hypothesis is suggested from the point of view of retrograde signaling as shown in Figure 3. CMS associated gene products are accumulated in CMS mitochondria, which leads to an abnormal mitochondrial state and triggers emission of enhanced retrograde signals to disturb the expression of nuclear-encoded genes essential for pollen development. Such imbalance of nuclear gene expression during anther development leads to male sterility (Figure 3a). When a PPR type Rf gene exists in the nuclear genome, the RF protein is transported into mitochondria and suppresses expression and/or accumulation of CMS-associated gene products. As a result of RF function, the CMS mitochondria recover and reduce retrograde signals, so that the expression pattern of nuclear-encoded genes becomes identical to that of fertile plants with normal mitochondria, resulting in fertility restoration (Figure 3b). In the case of fertility restoration by non-PPR type RF proteins, the accumulation of the CMS-associated gene products is not changed. The RF protein may act to improve the metabolic state of CMS mitochondria, resulting in a bypass for fertility restoration (Figure 3c). Studies on the molecular entity of retrograde signals from CMS mitochondria will elucidate the details of CMS/Rf systems. This knowledge will help us to avoid hybrid sterility caused by incompatibility between mitochondrial and nuclear genomes when generating inter-specific hybrids.

4. Self-Compatibility

Self-incompatibility is a mechanism for preventing self-fertilization in many plant species. Self-incompatibility recognition specificity of stigma and pollen is controlled by a single multi allelic locus, called an S locus. There are two major classes of self-incompatibility, gametophytic and sporophytic. In gametophytic self-incompatibility, the S phenotype of pollen is determined by its own haploid genome, while in sporophytic self-incompatibility the S phenotype of pollen is determined by the parental diploid genome [124].

Brassicaceae species have sporophytic self-incompatibility, and the self-incompatibility response is based on the S allele specific interaction between the stigma determinant, SRK (S receptor kinase), and the pollen determinant, SP11/SCR (S-locus protein 11/S-locus cysteine-rich protein) (hereafter called SP11): SRK and SP11 derived from the same S alleles bind to each other, and this interaction triggers inhibition of pollen tube germination or elongation [124,125]. These two genes, SRK and SP11, are normally not separable by recombination and are transmitted to progeny as one set, termed S haplotypes [124,125]. There are dominant relationships of S haplotypes in the pollen of S heterozygous plants (class-I; dominant, class-II, recessive) [125]. Transcription of class-II SP11 genes is suppressed in the pollen of the class-I/class-II S heterozygous plants [125], and this suppression is associated with stage and tissue specific de novo DNA methylation in the promoter regions of class-II S haplotypes [126]. Recently, Tarutani et al. [127] showed that small RNAs, Smi (SP11 methylation inducer), are expressed from the S locus of class-I S haplotypes, and are homologous to the promoter region of class-II S haplotypes. The Smi RNAs can drive the de novo DNA methylation of the promoter region of the class-II SP11 allele leading to suppression of its expression in the pollen of the class-I/class-II S heterozygous plants [127].

Okamoto et al. [15] suggested that the dominant relationship mentioned above is important for self-compatibility of B. napus. As B. napus is an allotetraploid having an AC genome, it has S loci derived from both the A and C genomes. Most B. napus have both class-I and class-II S haplotypes (one is derived from A genome and the other is from C genome), and class-I S haplotypes have lost the function of SP11 or SRK by spontaneous mutations. Complementation experiments confirmed that loss of function in class-I SP11 by mutations caused self-compatibility in ‘Westar’ of B. napus [128]. In the artificially synthesized inter-specific hybrid between B. rapa with class-I S homozygous alleles and B. oleracea with class-II S homozygous alleles, expression of SP11 in class-II S haplotype was suppressed, indicating that there is a dominant relationship occurred between different chromosomes [129]. So when class-I SRK lost its function by mutation, B. napus became self-compatible because the expression of class-II SP11 was suppressed by a dominant relationship (Figure 4) [15]. When class-I SP11 lost its function by mutation, expression of class-II SP11 was still suppressed by the dominant relationship (Figure 4) [15], as the expression of class-I SP11 is not essential for suppression of class-II SP11 in the S heterozygotes [130]. Mutations occurring in the S determinant genes (SRK or SP11) of both A and C genome alleles at the same time is highly unlikely. However, if there is a dominant relationship between S haplotypes of the A and C genome, a mutation of only a dominant S haplotype is sufficient for loss of self-incompatibility. Thus a dominant relationship may be utilized for generating self-compatible allopolyploids in the process of evolution.

In addition to the genetic mutations described above, the possibility that epigenetic change contributes to generating self-compatibility of allopolyploids has been suggested [131]. Although an inter-specific hybrid between A. thaliana and A. lyrata has never been detected in nature, this inter-specific hybrid was obtained by crossing between self-compatible A. thaliana as a female parent and self-incompatible A. lyrata as a male parent [10,11]. In the stigma of the hybrid, the expression of SRK derived from A. lyrata was reduced, and became compatible with the pollen of parental A. lyrata [131]. The stigma of BC1F1 (backcrossed A. lyrata to inter-specific F1 hybrid between A. thaliana and A. lyrata) showed a self-incompatibility response, suggesting that the disruption of the expression pattern of SRK in inter-specific hybrids, which leads to self-compatibility, may be due to the epigenetic changes [131]. As several studies have reported that there are widespread changes to gene expression between hybrids and their progenitors (chapter 6), de novo changes in expression of self-incompatibility recognition specificity genes might be important for self-compatibility.

Out-crossing enforced by self-incompatibility may play a role in the avoidance of inbreeding depression, and self-incompatibility is advantageous in the process of evolution over the long term [7,132]. When there is mate limitation, self-compatibility rather than self-incompatibility is advantageous in the short-term (reproductive assurance) [132]. Allopolyploids are generally self-compatible, though their putative parental lines are self-incompatible [15]. Synthesized inter-specific hybrids between self-incompatible parental lines are self-incompatible [15,129], suggesting that allopolyploids lose self-incompatibility. Natural formation of allopolyploids may be uncommon, and self-compatibility can be advantageous for species survival when mating partners are limited: self-compatibility can establish new populations from individual plants [132]. Moreover, as allopolyploids have more than two different genomes (heterozygosity), the risk of inbreeding depression is smaller than in diploid plants and reduces the selective pressure to maintain out-crossing [7]. It can be speculated that self-compatibility has been selected in allopolyploids during evolution.

5. Genetic and Epigenetic Changes

Synthetic allopolyploid plants can readily provide material to investigate the changes that occur immediately after polyploidization and through subsequent generations. Unlike natural allopolyploids, the parents can be selected, and this allows comparison between the parents and the synthesized allopolyploids. Evidence of genomic changes has been demonstrated in synthesized allopolyploids such as wheat, B. napus, cotton, and Arabidopsis suecica, and there are variable levels of genomic changes among different allopolyploids. In synthesized wheat, genomic elimination occurred shortly after allopolyploid formation [133]. By contrast, there is no genomic elimination or rearrangement in euploid plants of wheat allohexaploids [134]. Most of the synthesized allohexaploids exhibit homologous pairing at metaphase I, but some aneuploids were observed especially in S0 generations, which are dependent on the progenitor combinations [134]. No homoeologous pairing is observed in synthesized wheat, which might be due to the function of the Ph1 gene [134]. In synthesized B. napus, genetic changes are rare at the S0 generation [25,135], but genetic changes are much more frequent in the S5 generations [22]. Phenotypic variation increased in the following generations and was associated with DNA fragment losses due to homoeologous chromosome rearrangements, suggesting that chromosomal rearrangements may play a role in phenotypic variation [22]. In synthesized B. napus, homoeologous pairing, aneuploidy, and homoeologous chromosome compensation are observed, and pollen viability is negatively correlated with increasing aneuploidy [136138]. Though there is variation in the level of crossover suppression between homoeologous chromosomes in natural B. napus, natural B. napus shows stronger control over homoeologous paring than synthesized B. napus [136,139]. A low level of genomic changes was detected in synthesized A. suecica. Synthetic A. suecica are meiotically stable and the frequencies of aneuploidy and chromosome abnormalities are relatively low [28], but rapid rearrangements in some specific regions such as rDNA loci were detected [140].

In addition to genetic changes, epigenetic modifications such as DNA methylation or histone modification are also affected in allopolyploids, probably caused by “genome shock” as McClintock predicted [21,141143], and recent studies indicate that small RNAs have diverse roles in allopolyploid formation. Some transposons were transcriptionally activated or transposed in hypo-methylated mutants [144147]. Transcriptional activation in specific transposons occurred in allopolyploids, which might be caused by “genome shock” [23,28,141]. Microarray analyses indicated that genome-wide transposon activation did not occur in inter-specific hybrids between A. thaliana and A. arenosa or between A. thaliana and A. lyrata [11,33].

One of the best known epigenetic phenomena observed in allopolyploids is nucleolar dominance, a phenomenon where one parental set of nucleolar rRNA genes is epigenetically silenced in the hybrids or allopolyploids, and the direction of silencing is consistent [148]. This phenomenon is observed in many organisms such as plants, fruit flies, frogs, and mammals. In inter-specific hybrids between A. thaliana and A. arenosa or between A. thaliana and A. lyrata, the A. thaliana-derived rRNA gene is silenced [11,26,149,150]. The involvement of epigenetic regulation is indicated by the de-repression of silencing by treatment with the DNA methyltransferase inhibitor 5-azaC (5 azacytidine) or the histone deacetylase inhibitor, TSA (trichostatin A), in Arabidopsis, Brassica, and Triticale hybrids [151,152]. Treatment with both 5-azaC and TSA showed no additional effects, indicating DNA methylation and histone deacetylation work in the same pathway [152]. The silenced A. thaliana-derived rRNA gene is enriched with repressive epigenetic marks such as DNA methylation and H3K9 di-methylation, whereas the active A. arenosa-derived gene is enriched with active epigenetic marks like H3K4 tri-methylation [153]. This epigenetic silencing is established during early postembryonic growth, and the A. thaliana-derived gene is progressively associated with silent modifications [154]. Factors required for nucleolar dominance, such as histone deacetylase; HDA6 (Histone deacetylase 6) and HDT1 (Histone deacetylase 1), de novo DNA methyltransferase DRM2 (Domains rearranged methyltransferase 2), RNA-directed DNA methylation pathway components; RDR2 (RNA-dependent RNA polymerase 2) and DCL3 (Dicer-like 3), and methylcytosine binding proteins; MBD6 (Methyl-CpG-binding domain 6) and MBD10, were identified from RNAi screening [153,155,156]. Knockdown of these genes showed de-repression of silencing of the A. thaliana-derived rRNA gene, and this activation was associated with increased active histone modification of the A. thaliana-derived copy.

Small RNAs may have important roles in allotetraploid formation, as changes in expression/accumulation of small RNAs are observed in inter-specific hybrids [157,158]. Ha et al. [157] analyzed small RNA accumulation in A. thaliana, A. arenosa, a natural allotetraploid A. suecica, and a re-synthesized allotetraploid between A. thaliana and A. arenosa (F1 and F7 plants). A. thaliana-derived repeat- and transposon-associated siRNAs (small interfering RNAs), which are important for silencing of these sequences, were reduced in F1, but many siRNAs that disappeared in F1 were restored in F7 and their accumulation was similar to A. suecica [157]. These data suggest that repeat-associated siRNA functions as a genetic buffer in allotetraploid formation: reduced repeat-associated siRNA causes instability of re-synthesized allotetraploid plants, and siRNA-maintained plants form stable allotetraploid plants (Figure 5a) [157]. Expression of other classes of small RNAs, such as miRNAs (microRNA) and tasiRNAs (trans-acting siRNA), are changed as well in the inter-specific hybrid between A. thaliana and A. arenosa, and in the natural allotetraploid A. suecica. Many miRNA-targeted genes are differentially expressed in allotetraploids, indicating that a change of miRNA expression would induce phenotypic diversity in allotetraploids (Figure 5b) [157]. In fact for example, Ng et al. [159] suggest that the changed expression of miR163 induces variation in defense response by changing the amount of target transcripts of miR163 and secondary metabolites in allotetraploids.

6. Changes in Homoeologous Gene Expression

Some crops are allopolyploids, and it is important to understand the interaction and contribution of the homoeologs to the phenotype, and apply the knowledge for potential agronomical improvements. Allopolyploid formation is generally accompanied by gene expression change and, in synthetic wheat allohexaploids, the homoeologous gene expression changes established in early generations are similar to those in the natural allohexaploid [160]. Thus, it is important to understand the processes involved in the immediate genomic changes that occur in allopolyploids, not only to apply the knowledge for improvement of recently or artificially formed allopolyploid crops but to understand the evolutionary history of ancient allopolyploids.

Gene expression analyses between parental lines and synthetic allopolyploids have revealed changes in the context of additive (gene expression being equal to the average of the parental gene expression level) and non-additive (gene expression being different to the average of the parental gene expression level) gene expression, and the homoeologous expression changes can be meta-stable or stably inherited over generations. One of the interesting gene expression changes observed in allopolyploids is parental-biased gene expression. Parental-biased gene expression change refers to biased expression of homoeologous genes (up- or down-regulated) depending on the parent-of-origin. Strong parental-biased expression has been reported in newly synthesized allohexaploid wheat [21,30,35,161,162] and allotetraploid cotton [36,163166]. In allotetraploid cotton (AADD, G. hirsutum) fiber cells, 30% of homoeolog expression was biased to either the A- or the D-ancestral genome [163]. Biased homoeolog expression in cotton has also been shown by microarray [36,164] and there are evidences for biased homoeolog expression of the D-genome over the A-genome [163,165,166]. Biased homoeologous expression has been shown in other allopolyploid species such as Arabidopsis, wheat, sugarcane, and C x hytivus [21,28,167,168]. Organ-specific and biotic/abiotic stress-related bias of homoeologous expression has been observed in allotetraploid cotton [31,169,170], Nicotiana [171], and Tragopogon [172], demonstrating that polyploid genome expression can be flexible, even soon after polyploid formation.

Change in homoeolog expression is expected to affect protein expression, and ultimately phenotype. Study on re-synthesized allotetraploid B. napus revealed that 2/3 of the investigated additive homoeologs exhibited non-additive protein expression [173]. Another study on synthesized B. napus followed protein expression changes across four generations (F1–F4) and reported stochastic changes in protein level across generations that were silenced in one generation and reactivated in another [174]. These stochastic changes suggest a potential relationship between small RNAs that are involved in epigenetic regulation of genes at early generations of allopolyploid formation, and translational regulation of proteins by small RNAs.

In the long-term, stably inherited homoeologous genes can experience sub-functionalization (if the homoeologs complement each other to retain the original gene function), neo-functionalization (acquiring new function), or pseudo-functionalization (homoeolog loses its original function) [1]. These evolutionary fates of homoeologous genes are gradual processes that follow immediate genomic changes after an allopolyploidization event. In A. thaliana x A. arenosa hybrid plants, 0.4% of genes were silenced immediately after polyploidization, but expression variation between A. thaliana and A. arenosa that diverged 1.5 million years ago, show 2.5% gene expression difference [28]. In newly synthesized allohexaploid wheat and allotetraploid cotton, 5% of genes are silenced within several generations after polyploidization [21,30,31]. In natural allotetraploid cotton, which has experienced polyploidization 1–2 million years ago, 25% of assessed homoeologous genes were silenced or biased in their expression [169]. In a recently formed allopolyploid species, Tragopogon, possible sub-functionalization was reported occurring within 80 years (or 40 generations) [172]. A recent study of gene expression changes in allohexaploid wheat suggests that half of the duplicated genes are structurally (chromosomal rearrangements) and functionally (sub-functionalization and neo-functionalization) altered within 10 million years, and the pseudo-functionalization process is completed within 45–50 million years [175]. Rice is another plant that has experienced polyploidization events [176], and expression divergence between paleoduplicates of rice, has shown 88–96% gene expression divergence within 50–70 million years [177]. The degree and speed of homoeolog expression divergence after polyploidization can vary depending on the species, but it is evident that homoeologous expression divergence occurs immediately after polyploidization and gene silencing can continue through evolution.

7. Conclusion

It is indubitable that allopolyploids have selective advantages. Allopolyploidy can cause dynamic changes in gene expression due to functional homoeologous copies interacting with each other, to changes in selective pressure on one of the homoeologous copies, and/or to epigenetic changes, which require orchestration of the genes for the plant to survive the “genome shock”. Interaction of homoeologs plays a key role in creating new phenotypes, and synthetic allopolyploids have helped us understand many genomic changes associated with polyploidization. With the success of RNAi technologies in down-regulating homoeologs in polyploids, demonstrated in sugarcane and Arabidopsis [178,179], it will be of interest to create polyploid crops that lack expression of genes involved in epigenetic regulation to investigate the involvement of epigenetics in homoeologous gene expression and their agronomical traits. Development of methods to synthesize allopolyploids and high-throughput sequencing technologies are expected to accelerate research on different allopolyploid plants. Combined analyses of phenotype, proteome, epigenome, transcriptome, and small RNAs in allopolyploid species will allow us to understand the mechanism of reproductive barriers, hybrid incompatibility, and allopolyploid gene regulation, and may provide insights into enhancing, manipulating, or controlling agronomical performance in allopolyploid crops.

Acknowledgments

This work was supported in part by a grant-in-aid for Scientific Research on Innovative Areas (24113509) and by Grant for Promotion of Niigata University Research Projects (23C024) to R. Fujimoto.

References

  1. Adams, K.L.; Wendel, J.F. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol 2005, 8, 135–141.
  2. Chen, Z.J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol 2007, 58, 377–406.
  3. Ramsey, J.; Schemske, D.W. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst 1998, 29, 467–501.
  4. Yamauchi, A.; Hosokawa, A.; Nagata, H.; Shimoda, M. Triploid bridge and role of parthenogenesis in the evolution of autopolyploidy. Am. Nat 2004, 164, 101–112.
  5. Soltis, D.E.; Soltis, P.S. Molecular data and the dynamic nature of polyploidy. Crit. Rev. Plant Sci 1993, 12, 243–273.
  6. Griffiths, S.; Sharp, R.; Foote, T.N.; Bertin, I.; Wanous, M.; Reader, S.; Colas, I.; Moore, G. Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 2006, 439, 749–752.
  7. Comai, L. The advantages and disadvantages of being polyploid. Nat. Rev. Genet 2005, 6, 836–846.
  8. Osborn, T.C.; Pires, J.C.; Birchler, J.A.; Auger, D.L.; Chen, Z.J.; Lee, H.S.; Comai, L.; Madlung, A.; Doerge, R.W.; Colot, V.; et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet 2003, 19, 141–147.
  9. Chen, Z.J. Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 2010, 15, 57–71.
  10. Nasrallah, M.E.; Yogeeswaran, K.; Snyder, S.; Nasrallah, J.B. Arabidopsis species hybrids in the study of species differences and evolution of amphiploidy in plants. Plant Physiol 2000, 124, 1605–1614.
  11. Fujimoto, R.; Taylor, J.M.; Sasaki, T.; Kawanabe, T.; Dennis, E.S. Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis. Plant Mol. Biol 2011, 77, 419–431.
  12. Ni, Z.; Kim, E.D.; Ha, M.; Lackey, E.; Liu, J.; Zhang, Y.; Sun, Q.; Chen, Z.J. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 2009, 457, 327–331.
  13. Guo, M.; Davis, D.; Birchler, J.A. Dosage effects on gene expression in a maize ploidy series. Genetics 1996, 142, 1349–1355.
  14. Ha, M.; Kim, E.D.; Chen, Z.J. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc. Natl. Acad. Sci. USA 2009, 106, 2295–2300.
  15. Okamoto, S.; Odashima, M.; Fujimoto, R.; Sato, Y.; Kitashiba, H.; Nishio, T. Self-compatibility in Brassica napus is caused by independent mutations in S-locus genes. Plant J 2007, 50, 391–400.
  16. Dubcovsky, J.; Dvorak, J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 2007, 316, 1862–1866.
  17. Matsuoka, Y. Evolution of polyploid Triticum wheats under cultivation: The role of domestication, natural hybridization and allopolyploid speciation in their diversification. Plant Cell Physiol 2011, 52, 750–764.
  18. Wendel, J.F.; Cronn, R.C. Polyploidy and the evolutionary history of cotton. Adv. Agron 2003, 78, 139–186.
  19. Lee, J.J.; Woodward, A.W.; Chen, Z.J. Gene expression changes and early events in cotton fibre development. Ann. Bot 2007, 100, 1391–1401.
  20. Nagaharu, N. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot 1935, 7, 389–452.
  21. Kashkush, K.; Feldman, M.; Levy, A.A. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 2002, 160, 1651–1659.
  22. Gaeta, R.T.; Pires, J.C.; Iniguez-Luy, F.; Leon, E.; Osborn, T.C. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 2007, 19, 3403–3417.
  23. Madlung, A.; Tyagi, A.P.; Watson, B.; Jiang, H.; Kagochi, T.; Doerge, R.W.; Martienssen, R.; Comai, L. Genomic changes in synthetic Arabidopsis polyploids. Plant J 2005, 41, 221–230.
  24. Madlung, A.; Masuelli, R.W.; Watson, B.; Reynolds, S.H.; Davison, J.; Comai, L. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 2002, 129, 733–746.
  25. Lukens, L.N.; Pires, J.C.; Leon, E.; Vogelzang, R.; Oslach, L.; Osborn, T. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol 2006, 140, 336–348.
  26. Beaulieu, J.; Jean, M.; Belzile, F. The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants. Mol. Genet. Genomics 2009, 281, 421–435.
  27. Parisod, C.; Alix, K.; Just, J.; Petit, M.; Sarilar, V.; Mhiri, C.; Ainouche, M.; Chalhoub, B.; Glandbastien, M.A. Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 2010, 186, 37–45.
  28. Comai, L.; Tyagi, A.P.; Winter, K.; Holmes-Davis, R.; Reynolds, S.H.; Stevens, Y.; Byers, B. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 2000, 12, 1551–1568.
  29. Kashkush, K.; Feldman, M.; Levy, A.A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet 2003, 33, 102–106.
  30. He, P.; Friebe, B.R.; Gill, B.S.; Zhou, J.M. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol. Biol 2003, 52, 401–414.
  31. Adams, K.L.; Percifield, R.; Wendel, J.F. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 2004, 168, 2217–2226.
  32. Albertin, W.; Balliau, T.; Brabant, P.; Chèvre, A.M.; Eber, F.; Malosse, C.; Thiellement, H. Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 2006, 173, 1101–1113.
  33. Wang, J.; Tian, L.; Lee, H.S.; Wei, N.E.; Jiang, H.; Watson, B.; Madlung, A.; Osborn, T.C.; Doerge, R.W.; Comai, L.; Chen, Z.J. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 2006, 172, 507–517.
  34. Gaeta, R.T.; Yoo, S.Y.; Pires, J.C.; Doerge, R.W.; Chen, Z.J.; Osborn, T.C. Analysis of gene expression in resynthesized Brassica napus allopolyploids using Arabidopsis 70mer oligo microarrays. PLoS One 2009, 4, e4760.
  35. Pumphrey, M.; Bai, J.; Laudencia-Chingcuanco, D.; Anderson, O.; Gill, B.S. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 2009, 181, 1147–1157.
  36. Rapp, R.A.; Udall, J.A.; Wendel, J.F. Genomic expression dominance in allopolyploids. BMC Biol 2009, 7, 18.
  37. Mejía-Jiménez, A.; Muñoz, C.; Jacobsen, H.J.; Roca, W.M.; Singh, S.P. Interspecific hybridization between common and tepary beans: Increased hybrid embryo growth, fertility, and efficiency of hybridization through recurrent and congruity backcrossing. Theor. Appl. Genet 1994, 88, 324–331.
  38. Akbar, M.A. Chromosomal stability and performance of resynthesized Brassica napus produced for gain in earliness and short-day response. Hereditas 1989, 111, 247–253.
  39. Van Eijk, J.P.; van Raamsdonk, L.W.D.; Eikelboom, W.; Bino, R.J. Interspecific crosses between Tulipa gesneriana cultivars and wild Tulipa species: A survey. Sex. Plant Reprod 1991, 4, 1–5.
  40. Murfett, J.; Strabala, T.J.; Zurek, D.M.; Mou, B.; Beecher, B.; McClure, B.A. S RNase and interspecific pollen rejection in the genus Nicotiana: Multiple pollen-rejection pathways contribute to unilateral incompatibility between self-Incompatible and self-compatible species. Plant Cell 1996, 8, 943–958.
  41. Asano, Y. Studies on crosses between distantly related species of lilies IV. The culture of immature hybrid embryos 0.3–0.4 mm long. J. Jpn. Soc. Hort. Sci 1980, 49, 114–118.
  42. Kho, Y.O.; Baër, J. Incompatibility problems in species crosses of tulips. Euphytica 1971, 20, 30–35.
  43. Franken, J.; Custers, J.B.M.; Bino, R.J. Effects of temperature on pollen tube growth and fruit set in reciprocal crosses between Cucumis sativus and C. metuliferus. Plant Breed 1988, 100, 150–153.
  44. Watts, V.M. Influence of intrastylar pollination on seed set in lilies. Proc. Am. Soc. Hort. Sci 1967, 91, 660–663.
  45. Asano, Y.; Myodo, H. Studies on crosses between distantly related species of lilies I. For the intrastylar pollination technique. J. Jpn. Soc. Hort. Sci 1977, 46, 59–65.
  46. Stettler, R.F. Irradiated mentor pollen: Its use in remote hybridization of black cottonwood. Nature 1968, 219, 746–747.
  47. Dayton, D.F. Overcoming self-incompatibility in plants with killed compatible pollen. J. Am. Soc. Hort. Sci 1974, 99, 190–192.
  48. Den Nijs, A.P.M.; Oost, E.H. Effects of mentor pollen on pollen-pistil incongruities among species of Cucumis L. Euphytica 1980, 29, 267–271.
  49. Visser, T. Pollen and pollination experiments IV. Mentor pollen and pioneer pollen techniques regarding incompatibility and incongruity in apple and pear. Euphytica 1981, 31, 305–312.
  50. Emsweller, S.L.; Stuart, N.W. Use of growth regulating substances to overcome incompatibilities in Lilium. Proc. Am. Soc. Hort. Sci 1948, 51, 581–589.
  51. Raghavan, V.; Srivastava, P.S. Embryo culture. In Experimental Embryology of Vascular Plants; Johri, B.M., Ed.; Springer-Verlag: Berlin, Germany, 1982; pp. 195–230.
  52. Williams, E.G.; Maheswaran, G.; Hutchinson, J.F. Embryo and ovule culture in crop improvement. Plant Breed. Rev 1987, 5, 181–236.
  53. Iwai, S.; Kishi, C.; Nakata, K.; Kawashima, N. Production of Nicotiana tabacum x Nicotiana acuminata hybrid by ovule culture. Plant Cell Rep 1986, 5, 403–404.
  54. Chen, B.Y.; Heneen, W.K.; Jonsson, R. Resynthesis of Brassica napus L. through interspecific hybridization between B. alboglabra Bailey and B. campestris L. with special emphasis on seed colour. Plant Breed 1986, 101, 52–59.
  55. Asano, Y.; Myodo, H. Studies on crosses between distantly related species of lilies II. The culture of immature hybrid embryos. J. Jpn. Soc. Hort. Sci 1977, 46, 267–273.
  56. Okazaki, K.; Asano, Y.; Oosawa, K. Interspecific hybrids between Lilium ‘Oriental’ hybrid and L. ‘Asiatic’ hybrid produced by embryo culture with revised media. Breed. Sci 1994, 44, 59–64.
  57. Gangadevi, T.; Rao, P.N.; Rao, B.H.; Satyanarayana, K.V. A study of morphology, cytology and sterility in interspecific hybrids and amphidiploids of Nicotiana knightiana × N. umbratica. Theor. Appl. Genet 1985, 70, 330–332.
  58. Poysa, V. The development of bridge lines for interspecific gene transfer between Lycopersicon esculentum and L. peruvianum. Theor. Appl. Genet 1990, 79, 187–192.
  59. Choudhary, B.R.; Joshi, P.; Ramarao, S. Interspecific hybridization between Brassica carinata and Brassica rapa. Plant Breed 2000, 119, 417–420.
  60. Asano, Y. Overcoming interspecific hybrid sterility in Lilium. J. Jpn. Soc. Hort. Sci 1982, 51, 75–81.
  61. Bretagnolle, F.; Thompson, J.D. Gametes with the somatic chromosome number: Mechanisms of their formation and role in the evolution of autopolyploid plants. New Phytol 1995, 129, 1–22.
  62. Lim, K.B.; Chung, J.D.; Kronenburg, B.C.E.; Ramanna, M.S.; de Jong, J.H.; Jacobsen, E.; van Tuyl, J.M. Introgression of Lilium rubellum Baker chromosomes into L. Longiflorum Thunb.: A genome painting study of the F1 hybrid, BC1 and BC2 progenies. Chromosome Res 2000, 8, 119–125.
  63. Nimura, M.; Kato, J.; Horaguchi, H.; Mii, M.; Sakai, K.; Katoh, T. Induction of fertile amphidiploids by artificial chromosome-doubling in interspecific hybrid between Dianthus caryophyllus L. and D. japonicus Thunb. Breed. Sci 2006, 56, 303–310.
  64. Jensen, C.J. Chromosome Doubling Techniques in Haploids. In Haploids in Higher Plants: Advances and Potential; Kasha, K.J., Ed.; University of Guelph: Guelph, ON, Canada, 1974; pp. 153–190.
  65. Van Tuyl, J.M.; Meijer, B.; van Diën, M.P. The use of oryzalin as an alternative for colchicine in in-vitro chromosome doubling of Lilium and Nerine. Acta Hort 1992, 352, 625–630.
  66. Kermani, M.J.; Sarasan, V.; Roberts, A.V.; Yokoya, K.; Wentworth, J.; Sieber, V.K. Oryzalin-induced chromosome doubling in Rosa and its effect on plant morphology and pollen fertility. Theor. Appl. Genet 2003, 107, 1195–1200.
  67. Burge, G.K.; Morgan, E.R.; Eason, J.R.; Clark, G.E.; Catley, J.L.; Seelye, J.F. Sandersonia aurantiaca: Domestication of a new ornamental crop. Sci. Hort 2008, 118, 87–99.
  68. Sree Ramulu, K.; Verhoeven, H.A.; Dijkhuis, P. Mitotic blocking, micronucleation, and chromosome doubling by oryzalin, amiprophos-methyl, and colchicine in potato. Protoplasma 1991, 160, 65–73.
  69. Dvorak, J.; Harvey, B.L.; Coulman, B.E. The use of nitrous oxide for producing euploids and aneuploids in wheat and barley. Can. J. Genet. Cytol 1973, 15, 205–214.
  70. Kato, A. Chromosome doubling of haploid maize seedling using nitrous oxide gas at the flower primordial stage. Plant Breed 2002, 121, 370–377.
  71. Okazaki, K.; Kurimoto, K.; Miyajima, I.; Enami, A.; Mizuochi, H.; Matsumoto, Y.; Ohya, H. Induction of 2n pollen in tulips by arresting meiotic process with nitrous oxide gas. Euphytica 2005, 143, 101–114.
  72. Akutsu, M.; Kitamura, S.; Toda, R.; Miyajima, I.; Okazaki, K. Production of 2n pollen of Asiatic hybrid lilies by nitrous oxide treatment. Euphytica 2007, 155, 143–152.
  73. Nukui, S.; Kitamura, S.; Hioki, T.; Ootsuka, H.; Miyoshi, K.; Satou, T.; Takatori, U.; Oomiya, T.; Okazaki, K. N2O induces mitotic polyploidization in anther somatic cells and restores fertility in sterile interspecific hybrid lilies. Breed. Sci 2011, 61, 327–337.
  74. Kitamura, S.; Akutsu, M.; Okazaki, K. Mechanism of action of nitrous oxide gas applied as a polyploidizing agent during meiosis in lilies. Sex. Plant Reprod 2009, 22, 9–14.
  75. Barba-Gonzalez, R.; Miller, C.T.; Ramanna, M.S.; van Tuyl, J.M. Nitrous oxide (N2O) induces 2n gametes in sterile F1 hybrids between Oriental × Asiatic lily (Lilium) hybrids and leads to intergenomic recombination. Euphytica 2006, 148, 308–309.
  76. Karpechenko, G.D. The production of polyploidy gametes in hybrids. Hereditas 1927, 9, 349–368.
  77. Veilleux, R. Diploid and polyploid gametes in crop plants: Mechanisms of formation and utilization in plant breeding. Plant Breed. Rev 1983, 3, 253–288.
  78. Ramanna, M.S.; Jacobsen, E. Relevance of sexual polyploidization for crop improvement—A review. Euphytica 2003, 113, 3–18.
  79. Barba-Gonzalez, R.; Lim, K.B.; Zhou, S.; Ramanna, M.S.; van Tuyl, J.M. Interspecific hybridization in lily: The use of 2n gametes in interspecific lily hybrids. Floric. Ornam. Plant Biotech 2008, 5, 138–145.
  80. Lim, K.B.; Ramanna, M.S.; de Jong, J.H.; Jacobsen, E.; van Tuyl, J.M. Indeterminate meiotic restitution (IMR): A novel type of meiotic nuclear restitution mechanism detected in interspecific lily hybrids by GISH. Theor. Appl. Genet 2001, 103, 219–230.
  81. Asano, Y. Fertility of a hybrid between distantly related species in Lilium. Cytologia 1984, 49, 447–456.
  82. Van Tuyl, J.M.; Lim, K.B. Interspecific hybridization and polyploidization as tools in Ornamental plant breeding. Acta Hort 2003, 612, 13–22.
  83. Barba-Gonzalez, R.; Lokker, A.C.; Lim, K.B.; Ramanna, M.S.; van Tuyl, J.M. Use of 2n gametes for the production of sexual polyploids from sterile Oriental × Asiatic hybrids of lilies (Lilium). Theor. Appl. Genet 2004, 109, 1125–1132.
  84. Khan, N.; Zhou, S.; Ramanna, M.S.; Arens, P.; Herrera, J.; Visser, R.G.F.; van Tuyl, J.M. Potential for analytic breeding in allopolyploids: An illustration from Longiflorum × Asiatic hybrid lilies (Lilium). Euphytica 2009, 166, 399–409.
  85. Rieseberg, L.H.; Blackman, B.K. Speciation genes in plants. Ann. Bot 2010, 106, 439–455.
  86. Mayfield, D.; Chen, Z.J.; Pires, J.C. Epigenetic regulation of flowering time in polyploids. Curr. Opin. Plant Biol 2011, 14, 174–178.
  87. Nishiyama, I.; Yabuno, T. Causal relationships between the polar nuclei in double fertilization and interspecific cross-incompatibility in Avena. Cytologia 1978, 43, 453–466.
  88. Johnston, S.A.; Hanneman, R.E., Jr. Manipulations of endosperm balance number overcome crossing barriers between diploid solanum species. Science 1982, 217, 446–448.
  89. Kinoshita, T. Reproductive barrier and genomic imprinting in the endosperm of flowering plants. Genes Genet. Syst 2007, 82, 177–186.
  90. Martienssen, R.A. Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytol 2010, 186, 46–53.
  91. Köhler, C.; Mittelsten Scheid, O.; Erilova, A. The impact of the triploid block on the origin and evolution of polyploidy plants. Trends Genet 2010, 26, 142–148.
  92. Hanson, M.R.; Bentolila, S. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 2004, 16, S154–S169.
  93. Leino, M.; Landgren, M.; Glimelius, K. Alloplasmic effects on mitochondrial transcriptional activity and RNA turnover result in accumulated transcripts of Arabidopsis orfs in cytoplasmc male-sterile Brassica napus. Plant J 2005, 42, 469–480.
  94. Köhler, C.; Wolff, P.; Spillane, C. Epigenetic mechanisms underlying genomic imprinting in plants. Annu. Rev. Plant Biol 2012, 63, 331–352.
  95. Kinoshita, T.; Yadegari, R.; Harada, J.J.; Goldberg, R.B.; Fischer, R.L. Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 1999, 11, 1945–1952.
  96. Jullien, P.E.; Kinoshita, T.; Ohad, N.; Berger, F. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 2006, 18, 1360–1372.
  97. Köhler, C.; Page, D.R.; Gagliardini, V.; Grossniklaus, U. The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat. Genet 2005, 37, 28–30.
  98. Haig, D.; Westoby, M. Genomic imprinting in endosperm: Its effect on seed development in crosses between species, and between different ploidies of the same species, and its implications for the evolution of apomixis. Phil. Trans. R. Soc. Lond. B 1991, 333, 1–13.
  99. Costa, L.M.; Yuan, J.; Rouster, J.; Paul, W.; Dickinson, H.; Gutierrez-Marcos, J.F. Maternal control of nutrient allocation in plant seeds by genomic imprinting. Curr. Biol 2012, 22, 160–165.
  100. Josefsson, C.; Dilkes, B.; Comai, L. Parent-dependent loss of gene silencing during interspecies hybridization. Curr. Biol 2006, 16, 1322–1328.
  101. Erilova, A.; Brownfield, L.; Exner, V.; Rosa, M.; Twell, D.; Mittelsten Scheid, O.; Hennig, L.; Köhler, C. Imprinting of the polycomb group gene MEDEA serves as a ploidy sensor in Arabidopsis. PLoS Genet 2009, 5, e1000663.
  102. Walia, H.; Josefsson, C.; Dilkes, B.; Kirkbride, R.; Harada, J.; Comai, L. Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr. Biol 2009, 19, 1128–1132.
  103. de Folter, S.; Immink, R.G.; Kieffer, M.; Parenicová, L.; Henz, S.R.; Weigel, D.; Busscher, M.; Kooiker, M.; Colombo, L.; Kater, M.M.; et al. Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell 2005, 17, 1424–1433.
  104. Kang, I.H.; Steffen, J.G.; Portereiko, M.F.; Lloyd, A.; Drews, G.N. The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis. Plant Cell 2008, 20, 635–647.
  105. Ishikawa, R.; Ohnishi, T.; Kinoshita, Y.; Eiguchi, M.; Kurata, N.; Kinoshita, T. Rice interspecies hybrids show precocious or delayed developmental transitions in the endosperm without change to the rate of syncytial nuclear division. Plant J 2011, 65, 798–806.
  106. Kubo, T.; Newton, K.J. Angiosperm mitochondrial genomes and mutations. Mitochondrion 2008, 8, 5–14.
  107. Schnable, P.S.; Wise, R.P. The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 1998, 3, 175–180.
  108. Schmitz-Linneweber, C.; Small, I. Pentatricopeptide repeat proteins: A socket set for organelle gene expression. Trends Plant Sci 2008, 13, 663–670.
  109. Bentolila, S.; Alfonso, A.A.; Hanson, M.R. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc. Natl. Acad. Sci. USA 2002, 99, 10887–10892.
  110. Brown, G.G.; Formanova, N.; Jin, H.; Wargachuk, R.; Dendy, C.; Patil, P.; Laforest, M.; Zhang, J.; Cheung, W.Y.; Landry, B.S. The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. Plant J 2003, 35, 262–272.
  111. Koizuka, N.; Imai, R.; Fujimoto, H.; Hayakawa, T.; Kimura, Y.; Kohno-Murase, J.; Sakai, T.; Kawasaki, S.; Imamura, J. Genetic characterization of a pentatricopeptide repeat protein gene, orf687, that restores fertility in the cytoplasmic male-sterile Kosena radish. Plant J 2003, 34, 407–415.
  112. Kazama, T.; Toriyama, K. A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice. FEBS Lett 2003, 544, 99–102.
  113. Klein, R.R.; Klein, P.E.; Mullet, J.E.; Minx, P.; Rooney, W.L.; Schertz, K.F. Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12. Theor. Appl. Genet 2005, 111, 994–1012.
  114. Wang, Z.; Zou, Y.; Li, X.; Zhang, Q.; Chen, L.; Wu, H.; Su, D.; Chen, Y.; Guo, J.; Luo, D.; et al. Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. Plant Cell 2006, 18, 676–687.
  115. Gillman, J.D.; Bentolila, S.; Hanson, M.R. The petunia restorer of fertility protein is part of a large mitochondrial complex that interacts with transcripts of the CMS-associated locus. Plant J 2007, 49, 217–227.
  116. Kazama, T.; Nakamura, T.; Watanabe, M.; Sugita, M.; Toriyama, K. Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein in BT-type cytoplasmic male sterile rice. Plant J 2008, 55, 619–628.
  117. Uyttewaal, M.; Arnal, N.; Quadrado, M.; Martin-Canadell, A.; Vrielynck, N.; Hiard, S.; Gherbi, H.; Bendahmane, A.; Budar, F.; Mireau, H. Characterization of Raphanus sativus pentatricopeptide repeat proteins encoded by the fertility restorer locus for Ogura cytoplasmic male sterility. Plant Cell 2008, 20, 3331–3345.
  118. Cui, X.; Wise, R.P.; Schnable, P.S. The rf2 nuclear restorer gene of male-sterile T-cytoplasm maize. Science 1996, 272, 1334–1336.
  119. Fujii, S.; Toriyama, K. Suppressed expression of Retrograde-Regulated Male Sterility restores pollen fertility in cytoplasmic male sterile rice plants. Proc. Natl. Acad. Sci. USA 2009, 106, 9513–9518.
  120. Itabashi, E.; Iwata, N.; Fujii, S.; Kazama, T.; Toriyama, K. The fertility restorer gene, Rf2, for Lead Rice-type cytoplasmic male sterility of rice encodes a mitochondrial glycine-rich protein. Plant J 2011, 65, 359–367.
  121. Liu, F.; Cui, X.; Horner, H.; Weiner, H.; Schnable, P.S. Mitochondrial aldehyde dehydrogenase activity is requires for male fertility in maize. Plant Cell 2001, 13, 1063–1078.
  122. Fujii, S.; Kazama, T.; Yamada, M.; Toriyama, K. Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes. BMC Genomics 2010, 11, 209.
  123. Fujii, S.; Toriyama, K. Genome barriers between nuclei and mitochondria exemplified by cytoplasmic male sterility. Plant Cell Physiol 2008, 49, 1484–1494.
  124. Takayama, S.; Isogai, A. Self-incompatibility in plants. Annu. Rev. Plant Biol 2005, 56, 467–489.
  125. Fujimoto, R.; Nishio, T. Self-incompatibility. Adv. Bot. Res 2007, 45, 139–154.
  126. Shiba, H.; Kakizaki, T.; Iwano, M.; Tarutani, Y.; Watanabe, M.; Isogai, A.; Takayama, S. Dominance relationships between self-incompatibility alleles controlled by DNA methylation. Nat. Genet 2006, 38, 297–299.
  127. Tarutani, Y.; Shiba, H.; Ito, T.; Kakizaki, T.; Suzuki, G.; Watanabe, M.; Isogai, A.; Takayama, S. Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility. Nature 2010, 466, 983–986.
  128. Tochigi, T.; Udagawa, H.; Li, F.; Kitashiba, H.; Nishio, T. The self-compatibility mechanism in Brassica napus L. is applicable to F1 hybrid breeding. Theor. Appl. Genet. 2011, 123, 475–482.
  129. Kimura, R.; Sato, K.; Fujimoto, R.; Nishio, T. Recognition specificity of self-incompatibility maintained after the divergence of Brassica oleracea and Brassica rapa. Plant J 2002, 29, 215–223.
  130. Fujimoto, R.; Sugimura, T.; Fukai, E.; Nishio, T. Suppression of gene expression of a recessive SP11/SCR allele by an untranscribed SP11/SCR allele in Brassica self-incompatibility. Plant Mol. Biol 2006, 61, 577–587.
  131. Nasrallah, J.B.; Liu, P.; Sherman-Broyles, S.; Schmidt, R.; Nasrallah, M.E. Epigenetic mechanisms for breakdown of self-incompatibility in interspecific hybrids. Genetics 2007, 175, 1965–1973.
  132. Goldberg, E.E.; Kohn, J.R.; Lande, R.; Robertson, K.A.; Smith, S.A.; Igic, B. Species selection maintains self-incompatibility. Science 2010, 330, 493–495.
  133. Shaked, H.; Kashkush, K.; Ozkan, H.; Feldman, M.; Levy, A.A. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 2001, 13, 1749–1759.
  134. Mestiri, I.; Chagué, V.; Tanguy, A.M.; Huneau, C.; Huteau, V.; Belcram, H.; Coriton, O.; Chalhoub, B.; Jahier, J. Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol 2010, 186, 86–101.
  135. Song, K.; Lu, P.; Tang, K.; Osborn, T.C. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 1995, 92, 7719–7723.
  136. Xiong, Z.; Gaeta, R.T.; Pires, J.C. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc. Natl. Acad. Sci. USA 2011, 108, 7908–7913.
  137. Szadkowski, E.; Eber, F.; Huteau, V.; Lodé, M.; Huneau, C.; Belcram, H.; Coriton, O.; Manzanares-Dauleux, M.J.; Delourme, R.; King, G.J.; et al. The first meiosis of resynthesized Brassica napus, a genome blender. New Phytol 2010, 186, 102–112.
  138. Szadkowski, E.; Eber, F.; Huteau, V.; Lodé, M.; Coriton, O.; Jenczewski, E.; Chévre, A.M. Polyploid formation pathways have an impact on genetic rearrangements in resynthesized Brassica napus. New Phytol 2011, 191, 884–894.
  139. Cifuentes, M.; Grandont, L.; Moore, G.; Chévre, A.M.; Jenczewski, E. Genetic regulation of meiosis in polyploid species: New insights into an old question. New Phytol 2010, 186, 29–36.
  140. Pontes, O.; Neves, N.; Silva, M.; Lewis, M.S.; Madlung, A.; Comai, L.; Viegas, W.; Pikaard, C.S. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc. Natl. Acad. Sci. USA 2004, 101, 18240–18245.
  141. McClintock, B. The significance of responses of the genome to challenge. Science 1984, 226, 792–801.
  142. Wang, J.; Tian, L.; Madlung, A.; Lee, H.S.; Chen, M.; Lee, J.J.; Watson, B.; Kagochi, T.; Comai, L.; Chen, Z.J. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 2004, 167, 1961–1973.
  143. Xu, Y.; Zhong, L.; Wu, X.; Fang, X.; Wang, J. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta 2009, 229, 471–483.
  144. Kakutani, T. Epi-alleles in plants: Inheritance of epigenetic information over generations. Plant Cell Physiol 2002, 43, 1106–1111.
  145. Fujimoto, R.; Sasaki, T.; Inoue, H.; Nishio, T. Hypomethylation and transcriptional reactivation of retrotransposon-like sequences in ddm1 transgenic plants of Brassica rapa. Plant Mol. Biol 2008, 66, 463–473.
  146. Tsukahara, S.; Kobayashi, A.; Kawabe, A.; Mathieu, O.; Miura, A.; Kakutani, T. Bursts of retrotransposition reproduced in Arabidopsis. Nature 2009, 461, 423–426.
  147. Sasaki, T.; Fujimoto, R.; Kishitani, S.; Nishio, T. Analysis of target sequences of DDM1s in Brassica rapa by MSAP. Plant Cell Rep 2011, 30, 81–88.
  148. Preuss, S.; Pikaard, C.S. rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch. Biochim. Biophys. Acta 2007, 1769, 383–392.
  149. Chen, Z.J.; Comai, L.; Pikaard, C.S. Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc. Natl. Acad. Sci. USA 1998, 95, 14891–14896.
  150. Lewis, M.S.; Pikaard, D.J.; Nasrallah, M.; Doelling, J.H.; Pikaard, C.S. Locus-specific ribosomal RNA gene silencing in nucleolar dominance. PLoS One 2007, 2, e815.
  151. Neves, N.; Heslop-Harrison, J.S.; Viegas, W. rRNA gene activity and control of expression mediated by methylation and imprinting during embryo development in wheat x rye hybrids. Theor. Appl. Genet 1995, 91, 529–533.
  152. Chen, Z.J.; Pikaard, C.S. Epigenetic silencing of RNA polymerase I transcription: A role for DNA methylation and histone modification in nucleolar dominance. Genes Dev 1997, 11, 2124–2136.
  153. Lawrence, R.J.; Earley, K.; Pontes, O.; Silva, M.; Chen, Z.J.; Neves, N.; Viegas, W.; Pikaard, C.S. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol. Cell 2004, 13, 599–609.
  154. Pontes, O.; Lawrence, R.J.; Silva, M.; Preuss, S.; Costa-Nunes, P.; Earley, K.; Neves, N.; Viegas, W.; Pikaard, C.S. Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance. PLoS One 2007, 2, e1157.
  155. Earley, K.; Lawrence, R.J.; Pontes, O.; Reuther, R.; Enciso, A.J.; Silva, M.; Neves, N.; Gross, M.; Viegas, W.; Pikaard, C.S. Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev 2006, 20, 1283–1293.
  156. Preuss, S.B.; Costa-Nunes, P.; Tucker, S.; Pontes, O.; Lawrence, R.J.; Mosher, R.; Kasschau, K.D.; Carrington, J.C.; Baulcombe, D.C.; Viegas, W.; et al. Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol. Cell 2008, 32, 673–684.
  157. Ha, M.; Lu, J.; Tian, L.; Ramachandran, V.; Kasschau, K.D.; Chapman, E.J.; Carrington, J.C.; Chen, X.; Wang, X.J.; Chen, Z.J. Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 2009, 106, 17835–17840.
  158. Kenan-Eichler, M.; Leshkowitz, D.; Tal, L.; Noor, E.; Melamed-Bessudo, C.; Feldman, M.; Levy, A.A. Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 2011, 188, 263–272.
  159. Ng, D.W.; Zhang, C.; Miller, M.; Palmer, G.; Whiteley, M.; Tholl, D.; Chen, Z.J. cis- and trans-regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allotetraploids. Plant Cell 2011, 23, 1729–1740.
  160. Chague, V.; Just, J.; Mestri, I.; Balzergue, S.; Tanguy, A.M.; Huneau, C.; Huteau, V.; Blacramm, H.; Coriton, O.; Jahier, J.; Chalhoub, B. Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol 2010, 187, 1181–1194.
  161. Akhunova, A.R.; Matnivazov, R.T.; Liang, H.; Akhunov, E.D. Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics 2010, 11, 505.
  162. Qi, B.; Huang, W.; Zhu, B.; Zhong, X.; Guo, J.; Zhao, N.; Xu, C.; Zhang, H.; Pang, J.; Han, F.; Liu, B. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biol 2012, 10, 3.
  163. Hovav, R.; Udall, J.A.; Chaudhary, B.; Rapp, R.; Flagel, L.; Wendel, J.F. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc. Natl. Acad. Sci. USA 2008, 105, 6191–6195.
  164. Udall, J.A.; Swanson, J.M.; Nettleton, D.; Percifield, R.J.; Wendel, J.F. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 2006, 173, 1823–1827.
  165. Flagel, L.; Udall, J.; Nettleton, D.; Wendel, J. Duplicated gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol 2008, 6, 16.
  166. Flagel, L.E.; Wendel, J.F. Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol 2010, 186, 184–193.
  167. Zhuang, Y.; Chen, J.F. Changes of gene expression in early generations of the synthetic allotetraploid Cucumis x hytivus Chen et Kirkbride. Genet. Resour. Crop Evol 2009, 56, 1071–1076.
  168. Mudge, S.R.; Osabe, K.; Casu, R.E.; Bonnett, G.D.; Manners, J.M.; Birch, R.G. Efficient silencing of reporter transgenes coupled to known functional promoters in sugarcane, a highly polyploid crop species. Planta 2009, 229, 549–558.
  169. Adams, K.L.; Cronn, R.; Percifield, R.; Wendel, J.F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 2003, 100, 4649–4654.
  170. Dong, S.W.; Adams, K.L. Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids. New Phytol 2011, 190, 1045–1057.
  171. Anssour, S.; Baldwin, I.T. Variation in antiherbivore defense responses in synthetic Nicotiana allopolyploids correlates with changes in uniparental patterns of gene expression. Plant Physiol 2010, 153, 1907–1918.
  172. Buggs, R.J.; Elliott, N.M.; Zhang, L.; Koh, J.; Viccini, L.F.; Soltis, D.E.; Soltis, P.S. Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus. New Phytol 2010, 186, 175–183.
  173. Marmagne, A.; Brabant, P.; Thiellement, H.; Alix, K. Analysis of gene expression in resynthesized Brassica napus allotetraploids: Transcriptional changes do not explain differential protein regulation. New Phytol 2010, 186, 216–227.
  174. Kong, F.; Mao, S.; Jiang, J.; Wang, J.; Fang, X.; Wang, Y. Proteomic changes in newly synthesized Brassica napus allotetraploids and their early generations. Plant Mol. Biol. Rep 2011, 29, 927–935.
  175. Pont, C.; Murat, F.; Confolent, C.; Balzergue, S.; Salse, J. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol 2011, 12, R119.
  176. Zhang, Y.; Xu, G.H.; Guo, X.Y.; Fan, L.J. Two ancient rounds of polyploidy in rice genome. J. Zhejiang Univ. Sci. B 2005, 6, 87–90.
  177. Throude, M.; Bolot, S.; Bosio, M.; Pont, C.; Sarda, X.; Quraishi, U.M.; Bourgis, F.; Lessard, P.; Rogowsky, P.; Ghesquiere, A.; et al. Structure and expression analysis of rice paleo duplications. Nucleic Acids Res 2009, 37, 1248–1259.
  178. Lackey, E.; Ng, D.W.K.; Chen, Z.J. RNAi-mediated down-regulation of DCL1 and AGO1 induces developmental changes in resynthesized Arabidopsis allotetraploids. New Phytol 2010, 186, 207–215.
  179. Osabe, K.; Mudge, S.R.; Graham, M.W.; Birch, R.G. RNAi mediated down-regulation of PDS gene expression in Sugarcane (Saccharum), a highly polyploid crop. Trop. Plant Biol 2009, 2, 143–148.
Ijms 13 08696f1 200
Figure 1. Procedures and technical remarks of making synthetic allopolyploids.

Click here to enlarge figure

Figure 1. Procedures and technical remarks of making synthetic allopolyploids.
Ijms 13 08696f1 1024
Ijms 13 08696f2 200
Figure 2. Imprinting of maize Meg1 gene and its role on maternal nutrient allocation. Meg1 imprinting limits the differentiation of transfer tissue and therefore nutrient allocation and seed size is affected when regulation of imprinting is disrupted. Nutrient allocation is shown by the size of arrows. T: Transfer tissue, EM: Embryo, EN: Endosperm, M: Maternal tissue.

Click here to enlarge figure

Figure 2. Imprinting of maize Meg1 gene and its role on maternal nutrient allocation. Meg1 imprinting limits the differentiation of transfer tissue and therefore nutrient allocation and seed size is affected when regulation of imprinting is disrupted. Nutrient allocation is shown by the size of arrows. T: Transfer tissue, EM: Embryo, EN: Endosperm, M: Maternal tissue.
Ijms 13 08696f2 1024
Ijms 13 08696f3 200
Figure 3. Hypothetical retrograde signals from mitochondria involved in cytoplasmic male sterility (CMS)/restoration of fertility systems. (a) Retrograde signals from CMS mitochondria, which are enhanced by CMS-associated gene products, disturb the expression of a certain nuclear-encoded gene essential for pollen development. Such imbalance leads male sterility. (b) A PPR-type RF protein is imported into mitochondria and suppresses the expression of the CMS-associated gene and recovers the mitochondrial state to normal, which reduces the retrograde signals and restores the expression of a nuclear-encoded gene essential for pollen development. (c) Non-PPR type RF protein is imported into mitochondria and functions to improve the mitochondrial metabolic state. Although the CMS associated gene products still exist in mitochondria, retrograde signals and fertility are restored.

Click here to enlarge figure

Figure 3. Hypothetical retrograde signals from mitochondria involved in cytoplasmic male sterility (CMS)/restoration of fertility systems. (a) Retrograde signals from CMS mitochondria, which are enhanced by CMS-associated gene products, disturb the expression of a certain nuclear-encoded gene essential for pollen development. Such imbalance leads male sterility. (b) A PPR-type RF protein is imported into mitochondria and suppresses the expression of the CMS-associated gene and recovers the mitochondrial state to normal, which reduces the retrograde signals and restores the expression of a nuclear-encoded gene essential for pollen development. (c) Non-PPR type RF protein is imported into mitochondria and functions to improve the mitochondrial metabolic state. Although the CMS associated gene products still exist in mitochondria, retrograde signals and fertility are restored.
Ijms 13 08696f3 1024
Ijms 13 08696f4 200
Figure 4. Two types of mutation cause self-compatibility in B. napus. (a) Class-I SP11 lost its function by mutation (blue cross), while expression of class-II SP11 is suppressed by dominant relationship in pollen (green cross). (b) Class-I SRK lost its function by mutation (blue cross), and class-II SP11 is silenced by dominant relationship (green cross).

Click here to enlarge figure

Figure 4. Two types of mutation cause self-compatibility in B. napus. (a) Class-I SP11 lost its function by mutation (blue cross), while expression of class-II SP11 is suppressed by dominant relationship in pollen (green cross). (b) Class-I SRK lost its function by mutation (blue cross), and class-II SP11 is silenced by dominant relationship (green cross).
Ijms 13 08696f4 1024
Ijms 13 08696f5 200
Figure 5. Roles of small RNA in allotetraploid formation. In allotetraploid formation, expression of small RNAs is changed. (a) Reduced repeat-associated siRNA would cause genomic instability and such re-synthesized F1 would be unviable. On the other hand, F1 with enriched siRNA would form stable allotetraploid. (b) Changes of miRNAs expression in F1 would induce diversity of the accumulation of target mRNAs. These transcriptional changes would induce phenotypic diversity in allotetraploid [157].

Click here to enlarge figure

Figure 5. Roles of small RNA in allotetraploid formation. In allotetraploid formation, expression of small RNAs is changed. (a) Reduced repeat-associated siRNA would cause genomic instability and such re-synthesized F1 would be unviable. On the other hand, F1 with enriched siRNA would form stable allotetraploid. (b) Changes of miRNAs expression in F1 would induce diversity of the accumulation of target mRNAs. These transcriptional changes would induce phenotypic diversity in allotetraploid [157].
Ijms 13 08696f5 1024
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert