Mechanism of haploidy-dependent unreductional meiotic cell division in polyploid wheat

Enrichment and Diversification of the Wheat Genome via Alien Introgression

Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome's polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.

Behavior of Centromeres during Restitution of the First Meiotic Division in a Wheat–Rye Hybrid

In first division restitution (FDR)-type meiosis, univalents congregate on the metaphase I plate and separate sister chromatids in an orderly fashion, producing dyads with somatic chromosome numbers. The second meiotic division is abandoned. The separation of sister chromatids requires separation of otherwise fused sister centromeres and a bipolar attachment to the karyokinetic spindle. This study analyzed packaging of sister centromeres in pollen mother cells (PMCs) in a wheat–rye F₁ hybrid with a mixture of standard reductional meiosis and FDR. No indication of sister centromere separation before MI was observed; such separation was clearly only visible in univalents placed on the metaphase plate itself, and only in PMCs undergoing FDR. Even in the FDR, PMCs univalents off the plate retained fused centromeres. Both the orientation and configuration of univalents suggest that some mechanism other than standard interactions with the karyokinetic spindle may be responsible for placing univalents on the plate, at which point sister centromeres are separated and normal amphitelic interaction with the spindle is established. At this point it is not clear at all what univalent delivery mechanism may be at play in the FDR.

Genomic and Meiotic Changes Accompanying Polyploidization

Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.

Asynapsis and unreduced gamete formation in a Trifolium interspecific hybrid

BACKGROUND

Unreduced gametes, a driving force in the widespread polyploidization and speciation of flowering plants, occur relatively frequently in interspecific or intergeneric hybrids. Studies of the mechanisms leading to 2n gamete formation, mainly in the wheat tribe Triticeae have shown that unreductional meiosis is often associated with chromosome asynapsis during the first meiotic division. The present study explored the mechanisms of meiotic nonreduction leading to functional unreduced gametes in an interspecific Trifolium (clover) hybrid with three sub-genomes from T. ambiguum and one sub-genome from T. occidentale.

RESULTS

Unreductional meiosis leading to 2n gametes occurred when there was a high frequency of asynapsis during the first meiotic division. In this hybrid, approximately 39% of chromosomes were unpaired at metaphase I. Within the same cell at anaphase I, sister chromatids of univalents underwent precocious separation and formed laggard chromatids whereas paired chromosomes segregated without separation of sister chromatids as in normal meiosis. This asynchrony was frequently accompanied by incomplete or no movement of chromosomes toward the poles and restitution leading to unreduced chromosome constitutions. Reductional meiosis was restored in progeny where asynapsis frequencies were low. Two progeny plants with approximately 5 and 7% of unpaired chromosomes at metaphase I showed full restoration of reductional meiosis.

CONCLUSIONS

The study revealed that formation of 2n gametes occurred when asynapsis (univalent) frequency at meiosis I was high, and that normal gamete production was restored in the next generation when asynapsis frequencies were low. Asynapsis-dependent 2n gamete formation, previously supported by evidence largely from wheat and its relatives and grasshopper, is also applicable to hybrids from the dicotyledonous plant genus Trifolium. The present results align well with those from these widely divergent organisms and strongly suggest common molecular mechanisms involved in unreduced gamete formation.

Partitioning and physical mapping of wheat chromosome 3B and its homoeologue 3E in Thinopyrum elongatum by inducing homoeologous recombination

We performed homoeologous recombination-based partitioning and physical mapping of wheat chromosome 3B and Th. elongatum chromosome 3E, providing a unique physical framework of this homoeologous pair for genome studies. The wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) and Thinopyrum elongatum (2n = 2x = 14, EE) genomes can be differentiated from each other by fluorescent genomic in situ hybridization (FGISH) as well as molecular markers. This has facilitated homoeologous recombination-based partitioning and engineering of their genomes for physical mapping and alien introgression. Here, we constructed a special wheat genotype, which was double monosomic for wheat chromosome 3B and Th. elongatum chromosome 3E and homozygous for the ph1b mutant, to induce 3B-3E homoeologous recombination. Totally, 81 3B-3E recombinants were recovered and detected in the primary, secondary, and tertiary homoeologous recombination cycles by FGISH. Comparing to the primary recombination, the secondary and tertiary recombination shifted toward the proximal regions due to the increase in homology between the pairing partners. The 3B-3E recombinants were genotyped by high-throughput wheat 90-K single nucleotide polymorphism (SNP) arrays and their recombination breakpoints physically mapped based on the FGISH patterns and SNP results. The 3B-3E recombination physically partitioned chromosome 3B into 38 bins, and 429 SNPs were assigned to the distinct bins. Integrative analysis of FGISH and SNP results led to the construction of a composite bin map for chromosome 3B. Additionally, we developed 22 SNP-derived semi-thermal asymmetric reverse PCR markers specific for chromosome 3E and constructed a comparative map of homoeologous chromosomes 3E, 3B, 3A, and 3D. In summary, this work provides a unique physical framework for further studies of the 3B-3E homoeologous pair and diversifies the wheat genome for wheat improvement.

An Update of Recent Use of Aegilops Species in Wheat Breeding

Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.

Cloning and characterization of the homoeologous genes for the Rec8-like meiotic cohesin in polyploid wheat

BACKGROUND

Meiosis is a specialized cell division critical for gamete production in the sexual reproduction of eukaryotes. It ensures genome integrity and generates genetic variability as well. The Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiotic cell division. The Rec8-like genes and cohesins have been cloned and characterized in diploid models, but not in polyploids. The present study aimed to clone the homoeologous genes (homoeoalleles) for Rec8-like cohesin in polyploid wheat, an important food crop for humans, and to characterize their structure and function under a polyploid condition.

RESULTS

We cloned two Rec8-like homoeoalleles from tetraploid wheat (TtRec8-A1 and TtRec8-B1) and one from hexaploid wheat (TaRec8-D1), and performed expression and functional analyses of the homoeoalleles. Also, we identified other two Rec8 homoeoalleles in hexaploid wheat (TaRec8-A1 and TaRec8-B1) and the one in Aegilops tauschii (AetRec8-D1) by referencing the DNA sequences of the Rec8 homoeoalleles cloned in this study. The coding DNA sequences (CDS) of these six Rec8 homoeoalleles are all 1,827 bp in length, encoding 608 amino acids. They differed from each other primarily in introns although single nucleotide polymorphisms were detected in CDS. Substantial difference was observed between the homoeoalleles from the subgenome B (TtRec8-B1 and TaRec8-B1) and those from the subgenomes A and D (TtRec8-A1, TaRec8-A1, and TaRec8-D1). TtRec8-A1 expressed dominantly over TtRec8-B1, but comparably to TaRec8-D1, in polyploid wheat. In addition, we developed the antibody against wheat Rec8 and used the antibody to detect Rec8 cohesin in the Western blotting and subcellular localization analyses.

CONCLUSIONS

The Rec8 homoeoalleles from the subgenomes A and D are transcriptionally more active than the one from the subgenome B in polyploid wheat. The structural variation and differential expression of the Rec8 homoeoalleles indicate a unique cross-genome coordination of the homoeologous genes in polyploid wheat, and imply the distinction of the wheat subgenome B from the subgenomes A and D in the origin and evolution.

Chromosomal structural changes and microsatellite variations in newly synthesized hexaploid wheat mediated by unreduced gametes

Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate chromosome level variation and microsatellite level variation of newly synthesized hexaploid wheat have been rarely reported. Here, unreduced gametes were applied to develop synthesized hexaploid wheat, NA0928, population by crossing T. turgidum ssp. dicoccum MY3478 and Ae. tauschii SY41, and further S0-S3 generations of NA0928 were assayed by sequential cytological and microsatellite techniques. We demonstrated that plentiful chromosomal structural changes and microsatellite variations emerged in the early generations of newly synthesized hexaploid wheat population NA0928, including aneuploidy with whole-chromosome loss or gain, aneuploidy with telosome formation, chromosome-specific repeated sequence elimination (indicated by fluorescence in situ hybridization) and microsatellite sequence elimination (indicated by sequencing), and many kinds of variations have not been previously reported. Additionally, we reported a new germplasm, T. turgidum accession MY3478 with excellent unreduced gametes trait, and then succeeded to transfer powdery mildew resistance from Ae. tauschii SY41 to synthesized allohexaploid wheat population NA0928, which would be valuable resistance resources for wheat improvement.

Sister chromatid separation and monopolar spindle organization in the first meiosis as two mechanisms of unreduced gametes formation in wheat-rye hybrids

KEY MESSAGE

Unreduced gametes. The absence of a strict pachytene checkpoint in plants presents an opportunity to study meiosis in polyhaploid organisms. In the present study, we demonstrate that meiosis is coordinated in hybrids between disomic wheat-rye substitution lines 1Rv(1A), 2R(2D), 5R(5D), 6R(6A) and rye (Triticum aestivum L. × Secale cereale L., 4x = 28, ABDR). By using in situ hybridization with a centromere pAet6-09 probe and immunostaining with H3Ser10ph-, CENH3-, and α-tubulin-specific antibodies, we distinguished four chromosome behaviour types. The first one is a mitotic-like division that is characterized by mitotic centromere architecture, robust bipolar spindle, one-step loss of arm and centromere cohesion, and sister chromatid separation in the first and only meiotic division. The second type involves a monopolar spindle formation, which appears as a hat-shaped group of chromosomes moving in one direction, wherein MT bundles are co-oriented polewards. It prevents chromosome segregation in meiosis I, with a bipolar spindle distributing sister chromatids to the poles in meiosis II. These events subsequently result in the formation of unreduced microspores. The other two meiotic-like chromosome segregation patterns known as reductional and equational plus reductional represent stand-alone types of cell division rather than intermediate steps of meiosis I. Only sterile pollen is produced as a result of such meiotic-like chromosome behaviours. Slightly variable meiotic phenotypes are reproducibly observed in hybrids under different growth conditions. The 2R(2D)xR genotype tends to promote reductional division. In contrast, the genotypes 1Rv(1A)xR, 5R(5D)xR, and 6R(6A)xR promote equational chromosome segregation and monopolar spindle formation in addition to reductional and equational plus reductional division types.

Unreduced gamete formation in wheat × Aegilops spp. hybrids is genotype specific and prevented by shared homologous subgenomes

The presence of homologous subgenomes inhibited unreduced gamete formation in wheat × Aegilops interspecific hybrids. Unreduced gamete rates were under the control of the wheat nuclear genome. Production of unreduced gametes is common among interspecific hybrids, and may be affected by parental genotypes and genomic similarity. In the present study, five cultivars of Triticum aestivum and two tetraploid Aegilops species (i.e. Ae. triuncialis and Ae. cylindrica) were reciprocally crossed to produce 20 interspecific hybrid combinations. These hybrids comprised two different types: T. aestivum × Aegilops triuncialis; 2n = ABDU(t)C(t) (which lack a common subgenome) and T. aestivum × Ae. cylindrica; 2n = ABDD(c)C(c) (which share a common subgenome). The frequency of unreduced gametes in F1 hybrids was estimated in sporads from the frequency of dyads, and the frequency of viable pollen, germinated pollen and seed set were recorded. Different meiotic abnormalities recorded in the hybrids included precocious chromosome migration to the poles at metaphase I and II, laggards in anaphase I and II, micronuclei and chromosome stickiness, failure in cell wall formation, premature cytokinesis and microspore fusion. The mean frequency of restitution meiosis was 10.1 %, and the mean frequency of unreduced viable pollen was 4.84 % in T. aestivum × Ae. triuncialis hybrids. By contrast, in T. aestivum × Ae. cylindrica hybrids no meiotic restitution was observed, and a low rate of viable gametes (0.3 %) was recorded. This study present evidence that high levels of homologous pairing between the D and D(c) subgenomes may interfere with meiotic restitution and the formation of unreduced gametes. Variation in unreduced gamete production was also observed between T. aestivum × Ae. triuncialis hybrid plants, suggesting genetic control of this trait.

Meiosis, unreduced gametes, and parthenogenesis: implications for engineering clonal seed formation in crops

Meiosis and unreduced gametes. Sexual flowering plants produce meiotically derived cells that give rise to the male and female haploid gametophytic phase. In the ovule, usually a single precursor (the megaspore mother cell) undergoes meiosis to form four haploid megaspores; however, numerous mutants result in the formation of unreduced gametes, sometimes showing female specificity, a phenomenon reminiscent of the initiation of gametophytic apomixis. Here, we review the developmental events that occur during female meiosis and megasporogenesis at the light of current possibilities to engineer unreduced gamete formation. We also provide an overview of the current understanding of mechanisms leading to parthenogenesis and discuss some of the conceptual implications for attempting the induction of clonal seed production in cultivated plants.

QTug.sau-3B is a major quantitative trait locus for wheat hexaploidization

Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division restitution, which exhibited prolonged cell division during meiosis I, was responsible for unreduced gamete formation. A major quantitative trait locus (QTL) for this trait, named QTug.sau-3B, was detected on chromosome 3B in two T. turgidum×Ae. tauschii haploid populations. This QTL is situated between markers Xgwm285 and Xcfp1012 and covered a genetic distance of 1 cM in one population. QTug.sau-3B is a haploid-dependent QTL because it was not detected in doubled haploid populations. Comparative genome analysis indicated that this QTL was close to Ttam-3B, a collinear homolog of tam in wheat. Although the relationship between QTug.sau-3B and Ttam requires further study, high frequencies of unreduced gametes may be related to reduced expression of Ttam in wheat.

Development and discrimination of 12 double ditelosomics in tetraploid wheat cultivar DR147

As an important group in Triticum, tetraploid wheat plays a significant role in the research of wheat evolution. Several complete aneuploid sets of common wheat have provided valuable tools for genetic and breeding studies, while similar aneuploids of tetraploid wheat are still not well developed. Here, 12 double ditelosomics developed in Triticum turgidum L. var. durum cultivar DR147 (excluding dDT2B and dDT3A) were reported. Hybrids between DR147 and the original double-ditelosomic dDT2B of Langdon lost vigor and died prematurely after the three-leaf stage; therefore, the dDT2B line was not obtained. The cytogenetic behaviors and phenotypic characteristics of each line were detailedly described. To distinguish the entire chromosome complement of tetraploid wheat, the DR147 karyotype was established by fluorescence in situ hybridization (FISH), using the Aegilops tauschii clone pAsl and the barley clone pHvG38 as probes. FISH using a cereal-specific centromere repeat (6C6) probe suggested that all the lines possessed four telosomes, except for 4AS of double-ditelosomic dDT4A, which carried a small segment of the long arm. On the basis of the idiogram of DR147, these lines were successfully discriminated by FISH using the probes pAsl and pHvG38 and were then accurately designated.

The origin of unusual chromosome constitutions among newly formed allopolyploids

PREMISE OF THE STUDY

Wide hybridization followed by spontaneous chromosome doubling of the resulting hybrids plays an important role in plant speciation. Such chromosome doubling is usually accomplished via unreduced gametes produced by altered meiosis, the so-called 'meiotic restitution'. Unreduced gametes are expected to carry somatic chromosome numbers and constitutions. However, it has been shown recently that new allopolyploids often carry unusual chromosome constitutions which include compensating and noncompensating nulli-tetrasomies and monotrisomies, and translocations of homoeologues.

METHODS

We have reanalyzed meiotic divisions in a wheat-rye hybrid by in situ probing with labeled DNA focusing on deviations from the standard pattern of meiotic restitution.

KEY RESULTS

In a typical first division restitution in a wide hybrid, there is no chromosome pairing, univalents separate sister chromatids in anaphase I, and there is no meiosis II. Here we illustrate that occasional pairing of homoeologous chromosomes in metaphase I, combined with separation of sister chromatids of univalents, generates diads with compensating nulli-disomies and associated translocations of homoeologues. Similarly, precocious metaphase I migration to the poles of some undivided univalents generates a wide range of noncompensating simple and complex nulli-disomies in the gametes.

CONCLUSIONS

Both alterations to the standard pattern of meiotic restitution tend to maintain the somatic chromosome numbers in the gametes; chromosome constitutions are variable but mostly genetically balanced. This source of variation among progeny may be an important factor contributing to greater success of natural allopolyploids.

Genetic mechanisms of allopolyploid speciation through hybrid genome doubling: novel insights from wheat (Triticum and Aegilops) studies

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

Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species

The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome), namely Triticumturgidum L. (AABB genome) and Aegilopstauschii Coss. (DD genome). An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL) analysis showed that (1) production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2) first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3) six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii's ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated that the genetic mechanisms for hybrid genome doubling could be studied based on the intrinsic natural variation that exists in the parental species.

Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification

The evolution of the polyploid Triticum wheats is distinctive in that domestication, natural hybridization and allopolyploid speciation have all had significant impacts on their diversification. In this review, I outline the phylogenetic relationships of cultivated wheats and their wild relatives and provide an overview of the recent progress and remaining issues in understanding the genetic and ecological factors that favored their evolution. An attempt is made to view the evolution of the polyploid Triticum wheats as a continuous process of diversification that was initiated by domestication of tetraploid emmer wheat and driven by various natural events ranging from interploidy introgression via hybridization to allopolyploid speciation of hexaploid common wheat, instead of viewing it as a group of discrete evolutionary processes that separately proceeded at the tetraploid and hexaploid levels. This standpoint underscores the important role of natural hybridization in the reticulate diversification of the tetraploid-hexaploid Triticum wheat complex and highlights critical, but underappreciated, issues that concern the allopolyploid speciation of common wheat.