Plasmon analyses of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs

Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years

The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.

The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization, Comparative Analysis, Phylogenomics and Time Divergence

The mechanism and course of Triticum plastome evolution is currently unknown; thus, it remains unclear how Triticum plastomes evolved during recent polyploidization. Here, we report the complete plastomes of two polyploid wheat species, Triticum sphaerococcum (AABBDD) and Triticum turgidum subsp. durum (AABB), and compare them with 19 available and complete Triticum plastomes to create the first map of genomic structural variation. Both T. sphaerococcum and T. turgidum subsp. durum plastomes were found to have a quadripartite structure, with plastome lengths of 134,531 bp and 134,015 bp, respectively. Furthermore, diploid (AA), tetraploid (AB, AG) and hexaploid (ABD, AGA^m) Triticum species plastomes displayed a conserved gene content and commonly harbored an identical set of annotated unique genes. Overall, there was a positive correlation between the number of repeats and plastome size. In all plastomes, the number of tandem repeats was higher than the number of palindromic and forward repeats. We constructed a Triticum phylogeny based on the complete plastomes and 42 shared genes from 71 plastomes. We estimated the divergence of Hordeum vulgare from wheat around 11.04-11.9 million years ago (mya) using a well-resolved plastome tree. Similarly, Sitopsis species diverged 2.8-2.9 mya before Triticum urartu (AA) and Triticum monococcum (AA). Aegilops speltoides was shown to be the maternal donor of polyploid wheat genomes and diverged ~0.2-0.9 mya. The phylogeny and divergence time estimates presented here can act as a reference framework for future studies of Triticum evolution.

Characterizing chloroplast genomes and inferring maternal divergence of the Triticum-Aegilops complex

The Triticum (wheat)-Aegilops (goatgrass) complex has been extensively studied, but the evolutionary history of polyploid wheats has not been fully elucidated. The chloroplast (cp) with maternal inheritance and homoplasy can simplify the sequence-based evolutionary inferences, but informative inferences would require a complete and accurate cp genome sequence. In this study, 16 cp genomes representing five Aegilops and 11 Triticum species and subspecies were sequenced, assembled and annotated, yielding five novel circular cp genome sequences. Analyzing the assembled cp genomes revealed no marked differences in genome structure and gene arrangement across the assayed species. A polymorphism analysis of 72 published cp genome sequences representing 10 Aegilops and 15 Triticum species and subspecies detected 1183 SNPs and 1881 SSRs. More than 80% SNPs detected resided on the downstream and upstream gene regions and only 2.78% or less SNPs were predicted to be deleterious. The largest nucleotide diversity was observed in the short single-copy genomic region. Relatively weak selection pressure on cp coding genes was detected. Different phylogenetic analyses confirmed that the maternal divergence of the Triticum-Aegilops complex had three deep lineages each representing a diploid species with nuclear A, B, or D genome. Dating the maternal divergence yielded age estimates of divergence that matched well with those reported previously. The divergence between emmer and bread wheats occurred at 8200-11,200 years ago. These findings are useful for further genomic studies, provide insight into cp genome evolvability and allow for better understanding of the maternal divergence of the Triticum-Aegilops complex.

The Independent Domestication of Timopheev's Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene

Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.

Development and deployment of KASP markers for multiple alleles of Lr34 in wheat

Heterogeneous Lr34 genes for leaf rust in winter wheat cultivar 'Duster' and KASP markers for allelic variation in exon 11 and exon 22 of Lr34. Wheat, Triticum aestivum (2n = 6x = 42, AABBDD), is a hexaploid species, and each of three homoeologous genomes A, B, and D should have one copy for a gene in its ancestral form if the gene has no duplication. Previously reported leaf rust resistance gene Lr34 has one copy on the short arm of chromosome 7D in hexaploid wheat, and allelic variation in Lr34 is in intron 4, exon 11, exon 12, or exon 22. In this study, we discovered that Oklahoma hard red winter wheat cultivar 'Duster' (PI 644,016) has two copies of the Lr34 gene, the resistance allele Lr34a and the susceptibility allele Lr34b. Both Lr34a and Lr34b were mapped in the same linkage group on chromosome 7D in a doubled-haploid population generated from a cross between Duster and a winter wheat cultivar 'Billings' which carries the susceptibility allele Lr34c. A chromosomal fragment including Lr34 and at least two neighboring genes on its proximal side but excluding genes on its distal side was duplicated in Duster. The Duster Lr34ab allele was associated with tip necrosis and increased resistance against leaf rust at adult plants in the Duster × Billings DH population tested in the field, demonstrating the function of the Duster Lr34ab allele in wheat. We have developed KASP markers for allelic variation in exon 11 and exon 22 of Lr34 in wheat. These markers can be utilized to accelerate the selection of Lr34 in wheat.

Evolutionary patterns of plastome uncover diploid-polyploid maternal relationships in Triticeae

To investigate the diploid-polyploid relationships and the role of maternal progenitors in establishment of polyploid richness in Triticeae, 35 polyploids representing almost all genomic constitutions together with 48 diploid taxa representing 20 basic genomes in the tribe were analyzed. Phylogenomic reconstruction, genetic distance matrix, and nucleotide diversity patterns of plastome sequences indicated that (1) The maternal donor of the annual polyploid species with the U- and D-genome are related to extant Ae. umbellulata and Ae. tauschii, respectively. The maternal donor to the annual polyploid species with the S-, G-, and B-genome originated from the species of Sitopsis section of the genus Aegilops. The annual species with the Xe-containing polyploids were donated by Eremopyrum as the female parent; (2) Pseudoroegneria and Psathyrostachys were the maternal donor of perennial species with the St- and Ns-containing polyploids, respectively; (3) The Lophopyrum, Thinopyrum and Dasypyrum genomes contributed cytoplasm genome to Pseudoroegneria species as a result of incomplete lineage sorting and/or chloroplast captures, and these lineages were genetically transmitted to the St-containing polyploid species via polyploidization; (4) There is a reticulate relationship among the St-containing polyploid species. It can be suggested that genetic heterogeneity might associate with the richness of the polyploids in Triticeae.

Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops

Background

Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops.

Results

Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and A^m-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.

Conclusions

RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L

Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. Chinese Spring (CS, 2n = 6x = 42, AABBDD). The synthesized library contains 27,392 oligos. Oligo painting using the probe library confirmed its specificity, shown by that only chromosome 4D could be painted in three wheat genotypes and CS nulli-tetrasomic line N4AT4D. Oligo painting was successfully used to define the 4D breakpoints in CS deletion lines involving 4D and two wheat-Haynaldia villosa 4D-4V translocation lines. Thirteen wheat relatives and a Triticum durum-H. villosa amphiploid were used for oligo painting. Except the 4D in two Aegilops tauschii accessions, the 4M in Ae. comosa and 4U in Ae. umbellulata could be painted. In tetraploid Ae. ventricosa, both 4D and 4M could be painted; however, the signal intensity of 4M was less compared with 4D. No painted chromosome was observed for the other alien species. This indicated that the relationship among D/M/U was closer than that among D/A/B as well as D with genomes H/R/S^s/S^c/Y/P/N/J. Our successful development of 4D-specific oligo probe library may serve as a model for developing oligo probes specific for other homoeologous chromosomes.

Nucleotide diversity patterns at the DREB1 transcriptional factor gene in the genome donor species of wheat (Triticum aestivum L)

Bread wheat (AABBDD) originated from the diploid progenitor Triticum urartu (AA), a relative of Aegilops speltoides (BB), and Ae. tauschii (DD). The DREB1 transcriptional factor plays key regulatory role in low-temperature tolerance. The modern breeding strategies resulted in serious decrease of the agricultural biodiversity, which led to a loss of elite genes underlying abiotic stress tolerance in crops. However, knowledge of this gene's natural diversity is largely unknown in the genome donor species of wheat. We characterized the dehydration response element binding protein 1 (DREB1) gene-diversity pattern in Ae. speltoides, Ae. tauschii, T. monococcum and T. urartu. The highest nucleotide diversity value was detected in Ae. speltoides, followed by Ae. tauschii and T. monococcum. The lowest nucleotide diversity value was observed in T. urartu. Nucleotide diversity and haplotype data might suggest no reduction of nucleotide diversity during T. monococcum domestication. Alignment of the 68 DREB1 sequences found a large-size (70 bp) insertion/deletion in the accession PI486264 of Ae. speltoides, which was different from the copy of sequences from other accessions of Ae. speltoides, suggesting a likely existence of two different ancestral Ae. speltoides forms. Implication of sequences variation of Ae. speltoides on origination of B genome in wheat was discussed.

Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops

Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.

Experimental evolutionary studies on the genetic autonomy of the cytoplasmic genome "plasmon" in the Triticum (wheat)-Aegilops complex

The term "plasmon" is used to indicate the whole cytoplasmic genetic system, whereas "genome" refers to the whole nuclear genetic system. Although maternal inheritance of the plasmon is well documented in angiosperms, its genetic autonomy from the coexisting nuclear genome still awaits critical examination. We tested this autonomy in two related studies: One was to determine the persistence of the genetic effect of the plasmon of Aegilops caudata (genome CC) on the phenotype of common wheat, Triticum aestivum strain "Tve" (genome AABBDD), during 63 y (one generation per year) of repeated backcrosses of Ae. caudata and its offspring with pollen of the same Tve wheat, and the second was to reconstruct an Ae. caudata strain from the genome of this strain and its plasmon that had been resident in Tve wheat for 50 generations, and to compare the phenotypic and organellar DNA characteristics between the native and reconstructed strains. Results indicated no change in the effect of Ae. caudata plasmon on Tve wheat during its stay in wheat for more than half a century, and no difference between the native and reconstructed caudata strains in their phenotype and simple sequence repeats in their organellar DNAs, thus demonstrating the prolonged genetic autonomy of the plasmon from the coexisting genomes of wheat and several other species that were used in the reconstruction of Ae. caudata The relationship between the proven genetic autonomy of the plasmon under changing nuclear conditions and its diversification during evolution of the Triticum-Aegilops complex is discussed.

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

BACKGROUND

Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited.

RESULTS

To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of Ae. tauschii and barley (Hordeum vulgare L.), which were regarded as virtual chromosomes of Ae. umbellulata. Interestingly, genetic diversity in Ae. umbellulata was higher than in Ae. tauschii, despite the narrow habitat of Ae. umbellulata. Comparative analyses of nucleotide polymorphisms between Ae. umbellulata and Ae. tauschii revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in Ae. umbellulata, with patterns clearly distinct from those in Ae. tauschii.

CONCLUSIONS

The anchored SNPs, covering all chromosomes, provide sufficient genetic markers between Ae. umbellulata accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in Ae. umbellulata.

Molecular cloning and functional characterization of two novel high molecular weight glutenin subunit genes in Aegilops markgrafii

The high molecular weight glutenin subunits (HMW-GS) in bread wheat are major determinants of the viscoelastic properties of dough and the end-use quality of wheat flour. Two novel HMW-GSs, 1Cx1.1 and 1Cy9.1, from the diploid species Aegilops markgrafii (CC) were identified in the present study. The corresponding open-reading frames of the genes of 1Cx1.1 and 1Cy9.1 were isolated and sequenced using allele-specific polymerase chain reaction. Sequence comparison demonstrated that the HMW-GSs from Ae. markgrafii possess a similar primary structure to the homologous proteins in wheat and related species. A tandem tripeptide exists in the central repetitive domain of 1Cx1.1, and this unique structure is very rare in the HMW-GSs of other genomes. To confirm the authenticity of these isolated endogenous HMW-GS, the heterologous proteins produced by removing the signal peptides expressed by E. coli exhibited the same electrophoretic mobility as the native proteins. Subsequently, the single protein was purified at a sufficient scale for incorporation into flour to performsodium dodecyl sulphate (SDS) sedimentation testing. Notably, the SDS sedimentation volume was less with the addition of 1Cx1.1 than it was with 1Cy9.1.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis

Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)₁₀ and (GTT)₉, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides _. The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)₁₀-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S^*-genomes. However, partial elimination of 45S rDNA repeats from 5S^* and 6S^* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the S^v-genome of Ae. vavilovii with the S^s genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

BACKGROUND

Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing.

RESULTS

The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago.

CONCLUSIONS

The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.

TaGW2, a Good Reflection of Wheat Polyploidization and Evolution

Hexaploid wheat consists of three subgenomes, namely, A, B, and D. These well-characterized ancestral genomes also exist at the diploid and tetraploid levels, thereby rendering wheat as a good model species for studying polyploidization. Here, we performed intra- and inter-species comparative analyses of wheat and its relatives to dissect polymorphism and differentiation of the TaGW2 genes. Our results showed that genetic diversity of TaGW2 decreased with progression from the diploids to tetraploids and hexaploids. The strongest selection occurred in the promoter regions of TaGW2-6A and TaGW2-6B. Phylogenetic trees clearly indicated that Triticum urartu and Ae. speltoides were the donors of the A and B genomes in tetraploid and hexaploid wheats. Haplotypes detected among hexaploid genotypes traced back to the tetraploid level. Fst and π values revealed that the strongest selection on TaGW2 occurred at the tetraploid level rather than in hexaploid wheat. This infers that grain size enlargement, especially increased kernel width, mainly occurred in tetraploid genotypes. In addition, relative expression levels of TaGW2s significantly declined from the diploid level to tetraploids and hexaploids, further indicating that these genes negatively regulate kernel size. Our results also revealed that the polyploidization events possibly caused much stronger differentiation than domestication and breeding.

Molecular evolution of Wcor15 gene enhanced our understanding of the origin of A, B and D genomes in Triticum aestivum

The allohexaploid bread wheat originally derived from three closely related species with A, B and D genome. Although numerous studies were performed to elucidate its origin and phylogeny, no consensus conclusion has reached. In this study, we cloned and sequenced the genes Wcor15-2A, Wcor15-2B and Wcor15-2D in 23 diploid, 10 tetraploid and 106 hexaploid wheat varieties and analyzed their molecular evolution to reveal the origin of the A, B and D genome in Triticum aestivum. Comparative analyses of sequences in diploid, tetraploid and hexaploid wheats suggest that T. urartu, Ae. speltoides and Ae. tauschii subsp. strangulata are most likely the donors of the Wcor15-2A, Wcor15-2B and Wcor15-2D locus in common wheat, respectively. The Wcor15 genes from subgenomes A and D were very conservative without insertion and deletion of bases during evolution of diploid, tetraploid and hexaploid. Non-coding region of Wcor15-2B gene from B genome might mutate during the first polyploidization from Ae. speltoides to tetraploid wheat, however, no change has occurred for this gene during the second allopolyploidization from tetraploid to hexaploid. Comparison of the Wcor15 gene shed light on understanding of the origin of the A, B and D genome of common wheat.

The chloroplast view of the evolution of polyploid wheat

Polyploid wheats comprise four species: Triticum turgidum (AABB genomes) and T. aestivum (AABBDD) in the Emmer lineage, and T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m) A(m) ) in the Timopheevi lineage. Genetic relationships between chloroplast genomes were studied to trace the evolutionary history of the species. Twenty-five chloroplast genomes were sequenced, and 1127 plant accessions were genotyped, representing 13 Triticum and Aegilops species. The A. speltoides (SS genome) diverged before the divergence of T. urartu (AA), A. tauschii (DD) and the Aegilops species of the Sitopsis section. Aegilops speltoides forms a monophyletic clade with the polyploid Emmer and Timopheevi wheats, which originated within the last 0.7 and 0.4 Myr, respectively. The geographic distribution of chloroplast haplotypes of the wild tetraploid wheats and A. speltoides illustrates the possible geographic origin of the Emmer lineage in the southern Levant and the Timopheevi lineage in northern Iraq. Aegilops speltoides is the closest relative of the diploid donor of the chloroplast (cytoplasm), as well as the B and G genomes to Timopheevi and Emmer lineages. Chloroplast haplotypes were often shared by species or subspecies within major lineages and between the lineages, indicating the contribution of introgression to the evolution and domestication of polyploid wheats.

Analysis of ATP6 sequence diversity in the Triticum-Aegilops species group reveals the crucial role of rearrangement in mitochondrial genome evolution

Mutation and chromosomal rearrangements are the two main forces of increasing genetic diversity for natural selection to act upon, and ultimately drive the evolutionary process. Although genome evolution is a function of both forces, simultaneously, the ratio of each can be varied among different genomes and genomic regions. It is believed that in plant mitochondrial genome, rearrangements play a more important role than point mutations, but relatively few studies have directly addressed this phenomenon. To address this issue, we isolated and sequenced the ATP6-1 and ATP6-2 genes from 46 different euplasmic and alloplasmic wheat lines. Four different ATP6-1 orthologs were detected, two of them reported for the first time. Expression analysis revealed that all four orthologs are transcriptionally active. Results also indicated that both point mutation and genomic rearrangement are involved in the evolution of ATP6. However, rearrangement is the predominant force that triggers drastic variation. Data also indicated that speciation of domesticated wheat cultivars were simultaneous with the duplication of this gene. These results directly support the notion that rearrangement plays a significant role in driving plant mitochondrial genome evolution.

A comparison of the levels of hydroxamic acids in Aegilops speltoides and a hexaploid wheat and effects on Rhopalosiphum padi behaviour and fecundity

Hydroxamic acids (HAs) are plant secondary metabolites produced by certain cereals, which have been found to be toxic to pest aphids in artificial diet assays. Previous studies have shown that tetraploid and hexaploid wheat varieties, the leaf tissues of which contained higher levels of these compounds than used in artificial diets, did not reduce aphid settling or fecundity. This current study reports findings on a high HA producing B genome accession of the diploid ancestor of wheat, Aegilops speltoides. We found that this accession does have a negative impact on aphid host selection and substantially reduces nymph production. Whole leaf tissue assays showed very high levels of HAs, well in excess of the toxic level determined in the artificial diet assays. Extraction of the apoplast fluid (AF) from this accession showed that the HA level is much lower than that of the whole tissue, but is still close to the artificial diet toxic level. Furthermore the HA level in the AF increases in response to aphid feeding. These observations could explain why hexaploid wheat remains susceptible to aphids, despite having whole leaf tissue HA levels in excess of the toxic levels determined in artificial diets.

Sequence variations of the partially dominant DELLA gene Rht-B1c in wheat and their functional impacts

Rht-B1c, allelic to the DELLA protein-encoding gene Rht-B1a, is a natural mutation documented in common wheat (Triticum aestivum). It confers variation to a number of traits related to cell and plant morphology, seed dormancy, and photosynthesis. The present study was conducted to examine the sequence variations of Rht-B1c and their functional impacts. The results showed that Rht-B1c was partially dominant or co-dominant for plant height, and exhibited an increased dwarfing effect. At the sequence level, Rht-B1c differed from Rht-B1a by one 2kb Veju retrotransposon insertion, three coding region single nucleotide polymorphisms (SNPs), one 197bp insertion, and four SNPs in the 1kb upstream sequence. Haplotype investigations, association analyses, transient expression assays, and expression profiling showed that the Veju insertion was primarily responsible for the extreme dwarfing effect. It was found that the Veju insertion changed processing of the Rht-B1c transcripts and resulted in DELLA motif primary structure disruption. Expression assays showed that Rht-B1c caused reduction of total Rht-1 transcript levels, and up-regulation of GATA-like transcription factors and genes positively regulated by these factors, suggesting that one way in which Rht-1 proteins affect plant growth and development is through GATA-like transcription factor regulation.

A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence–absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.

Synthesis and characterization of advanced durum wheat hybrids and addition lines with thinopyrum chromosomes

Durum wheat (Triticum turgidum L., 2n = 4x = 28; AABB genomes) is a natural hybrid-an allotetraploid between 2 wild species, Triticum urartu Tumanian (AA genome) and Aegilops speltoides Tausch (BB genome). Even at the allotetraploid level, durum wheat can tolerate chromosomal imbalance, for example, addition of alien chromosome 1E of diploid wheatgrass, Lophopyrum elongatum. Therefore, one way to broaden its genetic base is to add a desirable chromosome(s) from diploid wild relatives. We attempted chromosomal engineering with chromosomes of a diploid wheatgrass, Thinopyrum bessarabicum-a source of resistance to some diseases including Fusarium head blight. Several advanced hybrids and alien addition lines were studied using traditional cytology, multicolor fluorescent genomic in situ hybridization, and molecular markers. Hybrid derivatives varied in chromosome number from F1 to F8 generations and in backcross generations. In advanced generations, we exercised selection against 28-chromosome plants and in favor of 30-chromosome plants that helped recover 14 addition lines in the F8 generation, as indicated by the absence of segregation for 29-chromosome plants. Disomic additions showed regular meiosis with 15 bivalents, 14 of durum wheat, and 1 of Th. bessarabicum. The addition lines will facilitate further chromosome engineering work on durum wheat for broadening its genetic base.

Variations and classification of toxic epitopes related to celiac disease among α-gliadin genes from four Aegilops genomes

The α-gliadins are associated with human celiac disease. A total of 23 noninterrupted full open reading frame α-gliadin genes and 19 pseudogenes were cloned and sequenced from C, M, N, and U genomes of four diploid Aegilops species. Sequence comparison of α-gliadin genes from Aegilops and Triticum species demonstrated an existence of extensive allelic variations in Gli-2 loci of the four Aegilops genomes. Specific structural features were found including the compositions and variations of two polyglutamine domains (QI and QII) and four T cell stimulatory toxic epitopes. The mean numbers of glutamine residues in the QI domain in C and N genomes and the QII domain in C, N, and U genomes were much higher than those in Triticum genomes, and the QI domain in C and N genomes and the QII domain in C, M, N, and U genomes displayed greater length variations. Interestingly, the types and numbers of four T cell stimulatory toxic epitopes in α-gliadins from the four Aegilops genomes were significantly less than those from Triticum A, B, D, and their progenitor genomes. Relationships between the structural variations of the two polyglutamine domains and the distributions of four T cell stimulatory toxic epitopes were found, resulting in the α-gliadin genes from the Aegilops and Triticum genomes to be classified into three groups.

Genetic Fingerprinting of Wheat and Its Progenitors by Mitochondrial Gene orf256

orf256 is a wheat mitochondrial gene associated with cytoplasmic male sterility (CMS) that has different organization in various species. This study exploited the orf256 gene as a mitochondrial DNA marker to study the genetic fingerprint of Triticum and Aegilops species. PCR followed by sequencing of common parts of the orf256 gene were employed to determine the fingerprint and molecular evolution of Triticum and Aegilops species. Although many primer pairs were used, two pairs of orf256 specific primers (5:-94/C: 482, 5:253/C: 482), amplified DNA fragments of 576 bp and 230 bp respectively in all species were tested. A common 500 bp of nine species of Triticum and Aegilops were aligned and showed consistent results with that obtained from other similar chloroplast or nuclear genes. Base alignment showed that there were various numbers of base substitutions in all species compared to S. cereal (Sc) (the outgroup species). Phylogenetic relationship revealed similar locations and proximity on phylogenetic trees established using plastid and nuclear genes. The results of this study open a good route to use unknown function genes of mitochondria in studying the molecular relationships and evolution of wheat and complex plant genomes.

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.

Phylogenetic analysis of C, M, N, and U genomes and their relationships with Triticum and other related genomes as revealed by LMW-GS genes at Glu-3 loci

Phylogenetic relationships between the C, U, N, and M genomes of Aegilops species and the genomes of common wheat and other related species were investigated by using three types of low-molecular-weight glutenin subunit (LMW-GS) genes at Glu-3 loci. A total of 20 LMW-GS genes from Aegilops and Triticum species were isolated, including 11 LMW-m type and 9 LMW-i type genes. Particularly, four LMW-m type and three LMW-i type subunits encoded by the genes on the C, N, and U genomes possessed an extra cysteine residue at conserved positions, which could provide useful information for understanding phylogenetic relationships among Aegilops and Triticum genomes. Phylogenetic trees constructed by using either LMW-i or the combination of LMW-m and LMW-s, as well as analysis of all the three types of LMW-GS genes together, demonstrated that the C and U genomes were closely related to the A genome, whereas the N and M genomes were closely related to the D genome. Our results support previous findings that the A genome was derived from Triticum uratu, the B genome was from Aegilops speltoides, and the D genome was from Aegilops tauschii. In addition, phylogenetic relationships among different genomes analysed in this study support the concept that Aegilops is not monophyletic.

Tandem repeats on an eco-geographical scale: outcomes from the genome of Aegilops speltoides

The chromosomal pattern of tandem repeat fractions of repetitive DNA is one of the most important characteristics of a species. In the present research, we aimed to detect and evaluate the level of intraspecific variability in the chromosomal distribution of species-specific Spelt 1 and Aegilops-Triticum-specific Spelt 52 tandem repeats in Aegilops speltoides and in closely related diploid and polyploid species. There is a distinct eco-geographical gradient in Spelt 1 and Spelt 52 blocks abundance in Ae. speltoides. In marginal populations, the number of Spelt 1 chromosomal blocks could be 12-14 times lower than in the center of the species distribution. Also, in related diploid species, the abundance of Spelt 52 correlates with evolutionary proximity to Ae. speltoides. Finally, the B- and G-genomes of allopolyploid wheats have Spelt 1 chromosomal distribution patterns similar to those of the types of Ae. speltoides with poor and rich contents of Spelt 1, respectively. The observed changes in numbers of blocks of Spelt 1 and Spelt 52 tandem repeats along the eco-geographical gradient may due to their depletion in the marginal populations as a result of increased recombination frequency under stressful conditions. Alternatively, it may be accumulation of tandem repeats in conducive climatic/edaphic environments in the center of the species' geographical distribution. Anyway, we observe a bidirectional shift of repetitive DNA genomic patterns on the population level leading to the formation of population-specific chromosomal patterns of tandem repeats. The appearance of a new chromosomal pattern is considered an important factor in promoting the emergence of interbreeding barriers.

Population genetic analysis of safflower (Carthamus tinctorius; Asteraceae) reveals a Near Eastern origin and five centers of diversity

Analyses of genetic variation in crop gene pools are a powerful tool for investigating the origin and early evolution of crop lineages. Such analyses also have the potential to identify unique genetic resources for continued crop improvement. The oilseed crop safflower (Carthamus tinctorius) is believed to have been domesticated in the Fertile Crescent region, but up to 10 geographic centers of similarity throughout the world have been proposed based on morphology. Nuclear microsatellite analysis of accessions from each of the 10 proposed centers of similarity, as well as individuals of the progenitor species, suggested the presence of five genetic clusters (1, Europe; 2, Turkey-Iran-Iraq-Afghanistan; 3, Israel-Jordan-Syria; 4, Egypt-Ethiopia; and 5, the Far East-India-Pakistan). North American accessions, products of a secondary introduction from the native range, suggest that a subset of the native accessions harbor unique genetic diversity that could be useful in future breeding efforts. Overall, a Near Eastern origin of safflower was confirmed based on the genetic similarity between the progenitor and the Near Eastern safflower accessions, as well as previous archaeological finds. Genetic differentiation between geographical clusters of accessions is evident, although not to the degree proposed based on morphology.

Genetic structure of Aegilops cylindrica Host in its native range and in the United States of America

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae. markgrafii (Greuter) Hammer. and Ae. tauschii Coss. presumably along the Fertile Crescent, where the geographic distributions of its diploid progenitors overlap. However, the center of genetic diversity of this species now encompasses a larger area including northern Iraq, eastern Turkey, and Transcaucasia. Although the majority of accessions of Ae. cylindrica (87%) had D-type plastomes derived from Ae. tauschii, accessions with C-type plastomes (13%), derived from Ae. markgrafii, were also observed. This corroborates a previous study suggesting the dimaternal origin of Ae. cylindrica. Model-based and genetic distance-based clustering using both chloroplast and nuclear markers indicated that Ae. tauschii ssp. tauschii contributed one of its D-type plastomes and its D genome to Ae. cylindrica. Analysis of genetic structure using nuclear markers suggested that Ae. cylindrica accessions could be grouped into three subpopulations (arbitrarily named N-K1, N-K2, and N-K3). Members of the N-K1 subpopulation were the most numerous in its native range and members of the N-K2 subpopulation were the most common in the USA. Our analysis also indicated that Ae. cylindrica accessions in the USA were derived from a few founder genotypes. The frequency of Ae. cylindrica accessions with the C-type plastome in the USA (approximately 24%) was substantially higher than in its native range of distribution (approximately 3%) and all C-type Ae. cylindrica in the USA except one belonged to subpopulation N-K2. The high frequency of the C-type plastome in the USA may reflect a favorable nucleo-cytoplasmic combination.

Multiple origins promote the ecological amplitude of allopolyploid Aegilops (Poaceae)

Polyploidy has been ubiquitous in plant evolution and is thought to be an important engine of biodiversity that facilitates speciation, adaptation, and range expansion. Polyploid species can exhibit higher ecological tolerance than their progenitor species. For allotetraploid species, this higher tolerance is often attributed to the existence of heterosis resulting from entire genome duplication. However, multiple origins of allopolyploid species may further promote their ecological success by providing genetic variability in ecological traits underlying local adaptation and range expansion. Here we show in a group of allopolyploid species in the genus Aegilops that range size and abundance are correlated with the number of inferred origins. We found that allopolyploid Aegilops spp. contain multiple chloroplast haplotypes, each identical to haplotypes of the diploid progenitor species, indicating multiple origins as the major source of variation. The number of inferred origins in each allopolyploid species was correlated to the total area occupied by the allopolyploid and the tendency for the species to be common. Additionally, we found differences in ecological tolerance among independent origins in Aegilops triuncialis. These results strongly support the hypothesis that the introduction of genetic variability by multiple origins can increase the ecological amplitude and evolutionary success of allopolyploid species.

Development of Triticum turgidum subsp. durum--Aegilops longissima amphiploids with high iron and zinc content through unreduced gamete formation in F1 hybrids

Four different interspecific hybrids involving three different accessions of Aegilops longissima Schweinf. & Muschl. with high grain iron and zinc content and three Triticum turgidum L. subsp. durum (Desf.) Husn. cultivars with low micronutrient content were made for durum wheat biofortification and investigated for chromosome pairing, fertility, putative amphiploidy, and micronutrient content. The chromosome pairing in the 21-chromosome F1 hybrids (ABSl) consisted of 0-6 rod bivalents and occasionally 1 trivalent. All the F1 hybrids, however, unexpectedly showed partial but variable fertility. The detailed meiotic investigation indicated the simultaneous occurrence of two types of aberrant meiotic divisions, namely first-division restitution and single-division meiosis, leading to regular dyads and unreduced gamete formation and fertility. The F2 seeds, being putative amphiploids (AABBSlSl), had nearly double the chromosome number (40-42) and regular meiosis and fertility. The F1 hybrids were intermediate between the two parents for different morphological traits. The putative amphiploids with bold seed size had higher grain ash content and ash iron and zinc content than durum wheat cultivars, suggesting that Ae. longissima possesses a better genetic system(s) for uptake and seed sequestration of iron and zinc, which could be transferred to elite durum and bread wheat cultivars and exploited.

Molecular evidence for a natural primary triple hybrid in plants revealed from direct sequencing

BACKGROUND AND AIMS

Molecular evidence for natural primary hybrids composed of three different plant species is very rarely reported. An investigation was therefore carried out into the origin and a possible scenario for the rise of a sterile plant clone showing a combination of diagnostic morphological features of three separate, well-defined Potamogeton species.

METHODS

The combination of sequences from maternally inherited cytoplasmic (rpl20-rps12) and biparentally inherited nuclear ribosomal DNA (ITS) was used to identify the exact identity of the putative triple hybrid.

KEY RESULTS

Direct sequencing showed ITS variants of three parental taxa, P. gramineus, P. lucens and P. perfoliatus, whereas chloroplast DNA identified P. perfoliatus as the female parent. A scenario for the rise of the triple hybrid through a fertile binary hybrid P. gramineus x P. lucens crossed with P. perfoliatus is described.

CONCLUSIONS

Even though the triple hybrid is sterile, it possesses an efficient strategy for its existence and became locally successful even in the parental environment, perhaps as a result of heterosis. The population investigated is the only one known of this hybrid, P. x torssanderi, worldwide. Isozyme analysis indicated the colony to be genetically uniform. The plants studied represented a single clone that seems to have persisted at this site for a long time.

Meiotic restitution in wheat polyhaploids (amphihaploids): a potent evolutionary force

Polyploidy is well recognized as a major force in plant speciation. Among the polyploids in nature, allopolyploids are preponderant and include important crop plants like bread wheat, Triticum aestivum L. (2n = 6x = 42; AABBDD genomes). Allopolyploidy must result through concomitant or sequential events that entail interspecific or intergeneric hybridization and chromosome doubling in the resultant hybrids. To gain insight into the mechanism of evolution of wheat, we extracted polyhaploids of 2 cultivars, Chinese Spring (CS) and Fukuhokomugi (Fuko), of bread wheat by crossing them with maize, Zea mays L. ssp. mays. The derived Ph1-polyhaploids (2n = 3x = 21; ABD) showed during meiosis mostly univalents, which produced first-division restitution (FDR) nuclei that in turn gave rise to unreduced (2n) male gametes with 21 chromosomes. The haploids on maturity set some viable seed. The mean number of seeds per spike was 1.45 +/- 0.161 in CS and 2.3 +/- 0.170 in Fuko. Mitotic chromosome preparations from root tips of the derived plantlets revealed 2n = 42 chromosomes, that is, twice that of the parental polyhaploid, which indicated that they arose by fusion of unreduced male and female gametes formed by the polyhaploid. The Ph1-induced univalency must have produced 2n gametes and hence bilateral sexual polyploidization and reconstitution of disomic bread wheat. These findings highlight the quantum jump by which bread wheat evolved from durum wheat in nature. Thus, bread wheat offers an excellent example of rapid evolution by allopolyploidy. In the induced polyhaploids (ABD) that are equivalent of amphihaploids, meiotic phenomena such as FDR led to regeneration of parental bread wheat, perhaps a simulation of the evolutionary steps that occurred in nature at the time of the origin of hexaploid wheat.

Independent Wheat B and G Genome Origins in Outcrossing Aegilops Progenitor Haplotypes

The origin of modern wheats involved alloploidization among related genomes. To determine if Aegilops speltoides was the donor of the B and G genomes in AABB and AAGG tetraploids, we used a 3-tiered approach. Using 70 amplified fragment length polymorphism (AFLP) loci, we sampled molecular diversity among 480 wheat lines from their natural habitats encompassing all S genome Aegilops, the putative progenitors of wheat B and G genomes. Fifty-nine Aegilops representatives for S genome diversity were compared at 375 AFLP loci with diploid, tetraploid, and 11 nulli-tetrasomic Triticum aestivum wheat lines. B genome-specific markers allowed pinning the origin of the B genome to S chromosomes of A. speltoides, while excluding other lineages. The outbreeding nature of A. speltoides influences its molecular diversity and bears upon inferences of B and G genome origins. Haplotypes at nuclear and chloroplast loci ACC1, G6PDH, GPT, PGK1, Q, VRN1, and ndhF for approximately 70 Aegilops and Triticum lines (0.73 Mb sequenced) reveal both B and G genomes of polyploid wheats as unique samples of A. speltoides haplotype diversity. These have been sequestered by the AABB Triticum dicoccoides and AAGG Triticum araraticum lineages during their independent origins.

Microsatellite mapping of the genes for brittle rachis on homoeologous group 3 chromosomes in tetraploid and hexaploid wheats

The brittle rachis character, which causes spontaneous shattering of spikelets, has an adaptive value in wild grass species. The loci Br1 and Br2 in durum wheat (Triticum durum Desf.) and Br3 in hexaploid wheat (T. aestivum L.) determine disarticulation of rachides above the junction of the rachilla with the rachis such that a fragment of rachis is attached below each spikelet. Using microsatellite markers, the loci Br1, Br2 and Br3 were mapped on the homoeologous group 3 chromosomes. The Br2 locus was located on the short arm of chromosome 3A and linked with the centromeric marker, Xgwm32, at a distance of 13.3 cM. The Br3 locus was located on the short arm of chromosome 3B and linked with the centromeric marker, Xgwm72 (at a distance of 14.2 cM). The Br1 locus was located on the short arm of chromosome 3D. The distance of Br1 from the centromeric marker Xgdm72 was 25.3 cM. Mapping the Br1, Br2 and Br3 loci of the brittle rachis suggests the homoeologous origin of these 3 loci for brittle rachides. Since the genes for brittle rachis have been retained in the gene pool of durum wheat, the more closely linked markers with the brittle rachis locus are required to select against brittle rachis genotypes and then to avoid yield loss in improved cultivars.

Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops revealed by nucleotide sequence analysis

The second largest BamHI fragment (B2) of the chloroplast DNA in Triticum (wheat) and Aegilops contains a highly variable region (a hotspot), resulting in four types of B2 of different size, i.e. B2l (10.5kb), B2m (10.2kb), B2 (9.6kb) and B2s (9.4kb). In order to gain a better understanding of the molecular nature of the variations in length and explain unexpected identity among B2 of Ae. ovata, Ae. speltoides and common wheat (T. aestivum), the nucleotide sequence between a stop codon of rbcL and a HindIII site in cemA in the hotspot was determined for Ae. ovata, Ae. speltoides, Ae. caudata and Ae. mutica. The total number of nucleotides in the region was 2808, 2810, 3302, and 3594 bp, for Ae. speltoides, Ae. ovata, Ae. caudata and Ae. mutica, respectively, and the sequences were compared with the corresponding ones of Ae. crassa 4x, T. aestivum and Ae. squarrosa. Compared with the largest B2l fragment of Ae. mutica, a 791bp and a 793 bp deletion were found in Ae. speltoides and Ae. ovata, respectively, and the possible site of deletion in the two species is the same as that of T. aestivum. However, a deleted segment in Ae. ovata is 2 bp longer than that of Ae. speltoides (and T. aestivum), demonstrating that recurrent deletions had occurred in the chloroplast genomes of both species. Comparison of the sequences from Ae. caudata and Ae. crassa 4x with that of Ae. mutica revealed a 289 bp and a 61 bp deletion at the same site in Ae. caudata and Ae. crassa 4x, respectively. Sequence comparison using wild Aegilops plants showed that the large length variations in a hotspot are fixed to each species. A considerable number of polymorphisms are observed in a loop in the 3' of rbcL. The study reveals the relative importance of the large and small indels and minute inversions to account for variations in the chloroplast genomes among closely related species.

Multiple origins of U genome in two UM genome tetraploid Aegilops species, Ae. columnaris and Ae. triaristata, revealed based on the polymorphism of a genome-specific PCR fragment

To elucidate the evolutionary mode of the formation of species via polyploidization, we conducted phylogenetic analysis of the U genome of the UM genome tetraploid Aegilops species, Ae. columnaris and Ae. triaristata. Using the genome-specific PCR primer set U31, we investigated the variation of the U genome of 48 accessions each of Ae. columnaris and Ae. triaristata and 72 accessions of their diploid ancestor Ae. umbellulata. As a result, three alleles were distinguishable by amplified length and CAPS polymorphisms, namely, allele I = normal size with an MspI site, allele II = normal size without an MspI site, and allele III = shorter size caused by a 123bp deletion. All three alleles were detected both in diploid and tetraploid accessions. Sequence comparison indicated the inheritance of alleles I and III from the diploid to the tetraploids, suggesting multiple origins of the U genome of the tetraploids. Regarding allele II, however, the sequence comparison indicated that parallel mutations at the MspI site produced allele II several times. The phylogenetic tree based on the sequences of the U31 region demonstrated the presence of a third lineage of the U genome from Ae. umbellulata to Ae. columnaris. Consequently, we concluded that the U genome had at least three origins in Ae. columnaris, and at least two, probably more, in Ae. triaristata.

Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes

A total of 137 loci were mapped in Aegilops speltoides, the closest extant relative of the wheat B genome, using two F(2) mapping populations and a set of wheat-Ae. speltoides disomic addition (DA) lines. Comparisons of Ae. speltoides genetic maps with those of Triticum monococcum indicated that Ae. speltoides conserved the gross chromosome structure observed across the tribe Triticeae. A putative inversion involving the short arm of chromosome 2 was detected in Ae. speltoides. A translocation between chromosomes 2 and 6, present in the wheat B genome, was absent. The ligustica/aucheri spike dimorphism behaved as allelic variation at a single locus, which was mapped in the centromeric region of chromosome 3. The genetic length of each chromosome arm was about 50 cM, irrespective of its physical length. Compared to T. monococcum genetic maps, recombination was virtually eliminated from the proximal 50-100 cM and was localized in short distal regions, which were often expanded compared to the T. monococcum maps. The wheat B genome and the genome of Ae. longissima, a close relative of Ae. speltoides, do not show the extreme localization of crossovers observed in Ae. speltoides.

Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica

Aegilops cylindrica Host (2n = 4x = 28, genome CCDD) is an allotetraploid formed by hybridization between the diploid species Ae. tauschii Coss. (2n = 2x = 14, genome DD) and Ae. markgrafii (Greuter) Hammer (2n = 2x = 14, genome CC). Previous research has shown that Ae. tauschii contributed its cytoplasm to Ae. cylindrica. However, our analysis with chloroplast microsatellite markers showed that 1 of the 36 Ae. cylindrica accessions studied, TK 116 (PI 486249), had a plastome derived from Ae. markgrafii rather than Ae. tauschii. Thus, Ae. markgrafii has also contributed its cytoplasm to Ae. cylindrica. Our analysis of chloroplast and nuclear microsatellite markers also suggests that D-type plastome and the D genome in Ae. cylindrica were closely related to, and were probably derived from, the tauschii gene pool of Ae. tauschii. A determination of the likely source of the C genome and the C-type plastome in Ae. cylindrica was not possible.

Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor

Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species.

High-resolution organellar genome analysis of Triticum and Aegilops sheds new light on cytoplasm evolution in wheat

We have utilised polymorphic chloroplast microsatellites to analyse cytoplasmic relationships between accessions in the genera Triticum and Aegilops. Sequencing of PCR products revealed point mutations and insertions/deletions in addition to the standard repeat length expansion/contraction which most likely represent ancient synapomorphies. Phylogenetic analyses revealed three distinct groups of accessions. One of these contained all the non- Aegilops speltoides S-type cytoplasm species, another comprised almost exclusively A, C, D, M, N, T and U cytoplasm-type accessions and the third contained the polyploid Triticum species and all the Ae. speltoides accessions, further confirming that Ae. speltoides or a closely related but now extinct species was the original B-genome donor of cultivated polyploid wheat. Successive decreases in levels of genetic diversity due to domestication were also observed. Finally, we highlight the importance of elucidating longer-term evolutionary processes operating at microsatellite repeat loci.