Expression of high zinc efficiency of Aegilops tauschii and Triticum monococcum in synthetic hexaploid wheats

The effect of varied zinc (Zn) supply on shoot and root dry matter production, severity of Zn deficiency symptoms and Zn tissue concentrations was studied in two Triticum turgidum (BBAA) genotypes and three synthetic hexaploid wheat genotypes by growing plants in a Zn-deficient calcareous soil under greenhouse conditions with (+Zn=5 mg kg^-1 soil) and without (−Zn) Zn supply. Two synthetic wheats (BBAADD) were derived from two different Aegilops tauschii (DD) accessions using same Triticum turgidum (BBAA), while one synthetic wheat (BBAAAA) was derived from Triticum turgidum (BBAA) and Triticum monococcum (AA). Visible symptoms of Zn deficiency, such as occurrence of necrotic patches on leaves and reduction in shoot elongation developed more rapidly and severely in tetraploid wheats than in synthetic hexaploid wheats. Correspondingly, decreases in shoot and root dry matter production due to Zn deficiency were higher in tetraploid wheats than in synthetic hexaploid wheats. Transfer of the DD genome from Aegilops tauschii or the AA genome from Triticum monococcum to tetraploid wheat greatly improved root and particularly shoot growth under Zn-deficient, but not under Zn-sufficient conditions. Better growth and lesser Zn deficiency symptoms in synthetic hexaploid wheats than in tetraploid wheats were not accompanied by increases in Zn concentration per unit dry weight, but related more to the total amount of Zn per shoot, especially in the case of synthetic wheats derived from Aegilops tauschii. This result indicates higher Zn uptake capacity of synthetic wheats. The results demonstrated that the genes for high Zn efficiency from Aegilops tauschii (DD) and Triticum monococcum (AA) are expressed in the synthetic hexaploid wheats. These wheat relatives can be used as valuable sources of genes for improvement of Zn efficiency in wheat. This revised version was published online in June 2006 with corrections to the Cover Date.     

Genome‐wide sequence information reveals recurrent hybridization among diploid wheat wild relatives

Many conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome‐wide sequence information, independent data were obtained from genotyping‐by‐sequencing and a target‐enrichment experiment that returned 244 low‐copy nuclear loci. The data were analyzed using Bayesian, likelihood and coalescent‐based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat‐group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species except Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa except Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat‐group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case for tetraploid and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.     

Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution

Transposable elements (TEs) account for up to 80% of the wheat genome and are considered one of the main drivers of wheat genome evolution. However, the contribution of TEs to the divergence and evolution of wheat genomes is not fully understood. In this study, we have developed 55 miniature inverted-repeat transposable element (MITE) markers that are based on the presence/absence of an element, with over 60% of these 55 MITE insertions associated with wheat genes. We then applied these markers to assess genetic diversity among Triticum and Aegilops species, including diploid (AA, BB and DD genomes), tetraploid (BBAA genome) and hexaploid (BBAADD genome) species. While 18.2% of the MITE markers showed similar insertions in all species indicating that those are fossil insertions, 81.8% of the markers showed polymorphic insertions among species, subspecies, and accessions. Furthermore, a phylogenetic analysis based on MITE markers revealed that species were clustered based on genus, genome composition, and ploidy level, while 47.13% genetic divergence was observed between the two main clusters, diploids versus polyploids. In addition, we provide evidence for MITE dynamics in wild emmer populations. The use of MITEs as evolutionary markers might shed more light on the origin of the B-genome of polyploid wheat.     

Salt Tolerance in the Triticeae: K/Na Discrimination in Synthetic Hexaploid Wheats

Ion concentrations were measured in the leaves of synthetichexaploid wheats and their parents growing in saline hydroponicculture. The synthetic hexaploids contained genomes from a tetraploidwheat (Triticum diccocum, T. durum, T. araraticum or T. timopheevi)and from a diploid species (T. monococcum, T. urartu, T. boeoticumor Aegilops squarrosa). Leaf Na concentrations were low, andK concentrations high, in Ae. squarrosa, T. araraticum and allof the synthetic hexaploids, but high in T. dicoccum and T.durum. At low salinities leaf Na concentrations were particularlyhigh in T. durum in comparison with the other species. Theseresults suggest that the enhanced K/Na discrimination character,originally found in Ae. squarrosa and BBAADD genome hexaploidwheats, is also present in diploid wheat and in GGAA genometetraploid wheats. It is suggested that this character has beenlost in the evolution of the BBAA genome tetraploid wheats. Key words: Salt, ion transport, A genome, Triticum spp     

Uptake and retranslocation of leaf-applied cadmium (109Cd) in diploid, tetraploid and hexaploid wheats

Uptake and retranslocation of leaf-applied radiolabeled cadmium (109Cd) was studied in three diploid (Triticum monococcum, AA), four tetraploid (Triticum turgidum, BBAA) and two hexaploid (Triticum aestivum, BBAADD) wheat genotypes grown for 9 d under controlled environmental conditions in nutrient solution. Among the tetraploid wheats, two genotypes were primitive (ssp. dicoccum) and two genotypes modern wheats (ssp. durum). Radiolabelled Cd was applied by immersing the tips (3 cm) of mature leaf into a 109Cd radiolabelled solution. There was a substantial variation in the uptake and export of 109Cd among and within wheat species. On average, diploid wheats (AA) absorbed and translocated more 109Cd than other wheats. The largest variation in 109Cd uptake was found within tetraploid wheats (BBAA). Primitive tetraploid wheats (ssp. dicoccum) had a greater uptake capacity for 109Cd than modern tetraploid wheats (ssp. durum). In all wheats studied, the amount of the 109Cd exported from the treated leaf into the roots and the remainder of the shoots was poorly related to the total absorption. For example, bread wheat cultivars were more or less similar in total absorption, but differed greatly in the amount of 109Cd retranslocated. The diploid wheat genotype 'FAL-43' absorbed the lowest amount of 109Cd, but retranslocated the greatest amount of 109Cd in roots and remainder of shoots. The results indicate the existence of substantial genotypic variation in the uptake and retranslocation of leaf-applied 109Cd. This variation is discussed in terms of potential genotypic differences in binding of Cd to cell walls and the composition of phloem sap ligands possibly affecting Cd transport into sink organs.     

Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes

To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, low-copy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.     

Phytosiderophore release in Aegilops tauschii and Triticum species under zinc and iron deficiencies.

Using three diploid (Triticum monococcum, AA), three tetraploid (Triticum turgidum, BBAA), two hexaploid (Triticum aestivum and Triticum compactum, BBAADD) wheats and two Aegilops tauschii (DD) genotypes, experiments were carried out under controlled environmental conditions in nutrient solution (i) to study the relationships between the rates of phytosiderophore (PS) release from the roots and the tolerance of diploid, tetraploid, and hexaploid wheats and AE: tauschii to zinc (Zn) and iron (Fe) deficiencies, and (ii) to assess the role of different genomes in PS release from roots under different regimes of Zn and Fe supply. Phytosiderophores released from roots were determined both by measurement of Cu mobilized from a Cu-loaded resin and identification by using HPLC analysis. Compared to tetraploid wheats, diploid and hexaploid wheats were less affected by Zn deficiency as judged from the severity of leaf symptoms. Aegilops tauschii showed very slight Zn deficiency symptoms possibly due to its slower growth rate. Under Fe-deficient conditions, all wheat genotypes used were similarly chlorotic; however, development of chlorosis was first observed in tetraploid wheats. Correlation between PS release rate determined by Cu-mobilization test and HPLC analysis was highly significant. According to HPLC analysis, all genotypes of Triticum and AE: tauschii species released only one PS, 2'-deoxymugineic acid, both under Fe and Zn deficiency. Under Zn deficiency, rates of PS release in tetraploid wheats averaged 1 micromol x (30 plants)(-1) x (3 h)(-1), while in hexaploid wheats rate of PS release was around 14 micromol x (30 plants)(-1) x (3 h)(-1). Diploid wheats and AE: tauschii accessions behaved similarly in their capacity to release PS and intermediate between tetraploid and hexaploid wheats regarding the PS release capacity. All Triticum and Aegilops species released more PS under Fe than Zn deficiency, particularly when the rate of PS release was expressed per unit dry weight of roots. On average, the rates of PS release under Fe deficiency were 3.0, 5.7, 8.4, and 16 micromol x (30 plants)(-1) x (3 h)(-1) for AE: tauschii, diploid, tetraploid and hexaploid wheats, respectively. The results of the present study show that the PS release mechanism in wheat is expressed effectively when three genomes, A, B and D, come together, indicating complementary action of the corresponding genes from A, B and D genomes to activate biosynthesis and release of PS.     

Shaping polyploid wheat for success: Origins,domestication, and the genetic improvement of agronomic traits

Bread wheat (Triticum aestivum L., AABBDD, 2n = 6x = 42), which accounts for most of the cultivated wheat crop worldwide, is a typical allohexaploid with a genome derived from three diploid wild ancestors. Bread wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of domestication. Today, cultivated allohexaploid bread wheat has numerous advantageous traits, including adaptive plasticity, favorable yield traits, and extended end-use quality, which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food crop. In the past decade, rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid crop. Here, we summarize recent advances in characterizing major genetic factors underlying the origin, evolution, and improvement of polyploid wheats. We end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding.     

Evolution and origin of bread wheat

Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500–9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat’s large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.

We describe the evolution of bread wheat in nature and under human selection with an emphasis on the donors of its subgenomes, evolution under polyploidy, and the “where when and how” of its domestication.     

Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee

Allopolyploidization is widespread and has played a major role in flowering plant diversification. Genomic changes are common consequences of allopolyploidization, but their mechanisms of occurrence and dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen as a model to investigate genetic changes in allopolyploid using an approach that exploits next‐generation sequencing technologies. Genes affected by putative homoeolog loss were inferred by comparing the numbers of single‐nucleotide polymorphisms detected using RNA‐seq in individual accessions of C. arabica, and between accessions of its two diploid progenitor species for common sequence positions. Their physical locations were investigated and clusters of genes exhibiting homoeolog loss were identified. To validate these results, genome sequencing data were generated from one accession of C. arabica and further analyzed. Genomic rearrangements involving homoeologous exchanges appear to occur in C. arabica and to be a major source of genetic diversity. At least 5% of the C. arabica genes were inferred to have undergone homoeolog loss. The detection of a large number of homoeologous exchange events (HEEs) shared by all accessions of C. arabica strongly reinforces the assumption of a single allopolyploidization event. Furthermore, HEEs were specific to one or a few accessions, suggesting that HEE accumulates gradually. Our results provide evidence for the important role of HEE in allopolyploid genome evolution.     

Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co‐evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn‐over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n = 4x = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3–6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.     

Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure

The physical map of the hexaploid wheat chromosome 3B was screened using centromeric DNA probes. A 1.1‐Mb region showing the highest number of positive bacterial artificial chromosome (BAC) clones was fully sequenced and annotated, revealing that 96% of the DNA consisted of transposable elements, mainly long terminal repeat (LTR) retrotransposons (88%). Estimation of the insertion time of the transposable elements revealed that CRW (also called Cereba) and Quinta are the youngest elements at the centromeres of common wheat (Triticum spp.) and its diploid ancestors, with Quinta being younger than CRW in both diploid and hexaploid wheats. Chromatin immunoprecipitation experiments revealed that both CRW and Quinta families are targeted by the centromere‐specific histone H3 variant CENH3. Immuno colocalization of retroelements and CENH3 antibody indicated that a higher proportion of Quinta than CRWs was associated with CENH3, although CRWs were more abundant. Long arrays of satellite repeats were also identified in the wheat centromere regions, but they lost the ability to bind with CENH3. In addition to transposons, two functional genes and one pseudogene were identified. The gene density in the centromere appeared to be between three and four times lower than the average gene density of chromosome 3B. Comparisons with related grasses also indicated a loss of microcollinearity in this region. Finally, comparison of centromeric sequences of Aegilops tauschii (DD), Triticum boeoticum (AA) and hexaploid wheat revealed that the centromeres in both the polyploids and diploids are still undergoing dynamic changes, and that the new CRWs and Quintas may have undertaken the core role in kinetochore formation.     

The presence of the enhanced K/Na discrimination trait in diploid Triticum species

Summary A number of accessions of the three species of diploid wheat, Triticum boeoticum, T. monococcum, and T. urartu, were grown in 50 mol m^-3 NaCl+2.5 mol m^-3 CaCl₂. Sodium accumulation in the leaves was low and potassium concentrations remained high. This was not the case in T. durum grown under the same conditions, and indicates the presence in diploid wheats of the enhanced K/Na discrimination character which has previously been found in Aegilops squarrosa and hexaploid wheat. None of the accessions of diploid wheat showed poor K/Na discrimination, which suggests that if the A genome of modern tetraploid wheats was derived from a diploid Triticum species, then the enhanced K/Na discrimination character became altered after the formation of the original allopolyploid. Another possibility is that a diploid wheat that did not have the enhanced K/Na discrimination character was involved in the hybridization event which produced tetraploid wheat, and that this diploid is now extinct or has not yet been discovered.     

Faithful inheritance of cytosine methylation patterns in repeated sequences of the allotetraploid tobacco correlates with the expression of DNA methyltransferase gene families from both parental genomes

The widespread occurrence of epigenetic alterations in allopolyploid species deserves scrutiny that DNA methylation systems may be perturbed by interspecies hybridization and polyploidization. Here we studied the genes involved in DNA methylation in Nicotiana tabacum (tobacco) allotetraploid containing S and T genomes inherited from Nicotiana sylvestris and Nicotiana tomentosiformis progenitors. To determine the inheritance of DNA methyltransferase genes and their expression patterns we examined three major DNA methyltransferase families (MET1, CMT3 and DRM) from tobacco and the progenitor species. Using Southern blot hybridization and PCR-based methods (genomic CAPS), we found that the parental loci of these gene families are retained in tobacco. Homoeologous expression was found in all tissues examined (leaf, root, flower) suggesting that DNA methyltransferase genes were probably not themselves targets of uniparental epigenetic silencing for over thousands of generations of allotetraploid evolution. The level of CG and CHG methylation of selected high-copy repeated sequences was similar and high in tobacco and its diploid progenitors. We speculate that natural selection might favor additive expression of parental DNA methyltransferase genes maintaining high levels of DNA methylation in tobacco, which has a repeat-rich heterochromatic genome. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AM946602–AM946620 and FM872474–FM872476.     

The Genome of Bread Wheat <Emphasis Type="Italic">Triticum aestivum</Emphasis> L.: Unique Structural and Functional Properties

Polyploidy is the major mechanism of speciation in flowering plants. All genomes of ancient species that are the progenitors of extant plant species experienced polyploidization. Three consecutive stages of polyploidization, i.e., ancient polyploidization, tetra-, and hexaploidization, resulted in the emergence of modern allohexaploid bread wheat Triticum aestivum L. with the BBAADD genome. Polyploidization and subsequent stabilization of the polyploid genome of T. aestivum led, on one hand, to cytological diploidization and, on the other hand, to structural and functional asymmetry of its three subgenomes. In recent years, there has been a sharp increase in the data accumulation on the origin and structure of the bread wheat genomes a result of analysis of genomes and transcripomes of natural and synthetic wheats using modern mapping and sequencing methods. This review provides up-to-date information on the peculiarities of the T. aestivum genome reorganization, which affected its structure and functioning.