Tribe Triticeae Research Articles

Rubisco catalytic properties of wild and domesticated relatives provide scope for improving wheat photosynthesis.

Rubisco is a major target for improving crop photosynthesis and yield, yet natural diversity in catalytic properties of this enzyme is poorly understood. Rubisco from 25 genotypes of the Triticeae tribe, including wild relatives of bread wheat (Triticum aestivum), were surveyed to identify superior enzymes for improving photosynthesis in this crop. In vitro Rubisco carboxylation velocity (V c), Michaelis-Menten constants for CO2 (K c) and O2 (K o) and specificity factor (S c/o) were measured at 25 and 35 °C. V c and K c correlated positively, while V c and S c/o were inversely related. Rubisco large subunit genes (rbcL) were sequenced, and predicted corresponding amino acid differences analysed in relation to the corresponding catalytic properties. The effect of replacing native wheat Rubisco with counterparts from closely related species was analysed by modelling the response of photosynthesis to varying CO2 concentrations. The model predicted that two Rubisco enzymes would increase photosynthetic performance at 25 °C while only one of these also increased photosynthesis at 35 °C. Thus, under otherwise identical conditions, catalytic variation in the Rubiscos analysed is predicted to improve photosynthetic rates at physiological CO2 concentrations. Naturally occurring Rubiscos with superior properties amongst the Triticeae tribe can be exploited to improve wheat photosynthesis and crop productivity.

Phylogenetic analysis of the genus Pseudoroegneria and the Triticeae tribe using the rbcL gene

The Pseudoroegneria species are perennial grasses in the Triticeae tribe, whose St genome has been linked to several important polyploid species. Due to frequent hybridization and complex genetic mechanism, the relationships within Pseudoroegneria, and within the Triticeae have been heavily disputed. Using the chloroplast rbcL gene we estimated the nucleotide diversity of 8 Pseudoroegneria species. We also examined the phylogenetic relationships within Pseudoroegneria and of Pseudoroegneria within the Triticeae. The estimates of nucleotide diversity indicated that Pseudoroegneria tauri and Pseudoroegneria spicata species had the highest diversity, while Pseudoroegneria gracillima had the lowest diversity. The phylogenetic analysis of Pseudoroegneria placed all P. spicata species into a clade separate from the other Pseudoroegneria species, while the relationship of the other Pseudoroegneria species could not be determined. Due to the groupings of Pseudoroegneria with the polyploid Elymus, our results strongly supported Pseudoroegneria as the maternal genome donor to Elymus. There was also weak support that P. spicata may be the maternal donor to the StH Elymus species.

Variability of breeding system, caryopsis microstructure and germination in annual and perennial species of the genus Brachypodium P. Beauv.

The basis of any patterns of variation in plant populations is the breeding system they express. In the genus Brachypodium, the breeding system ranges from autogamy in facultatively chasmogamic Brachypodium distachyon to allogamy in obligatory chasmogamic B. pinnatum. B. distachyon and B. sylvaticum appeared to be extremes with respect to dormancy and germination behaviour. Winter and facultatively biennial forms of the annual B. distachyon expressed an intermediate dormancy behaviour towards perennial species. Perennial species such as B. pinnatum, B. phoenicoides, B. rupestre and B. sylvaticum demonstrated allogamic behaviour and were highly dormant. The storage potential of hemicelluloses in endosperm cell walls and suberin-phenolic synthesis in testa and pigment strand differ distinctly between annuals and perennials. The suberized glumellae base and caryopsis attachment restrict the growth of coleorhiza and can change growth relationships between root and coleoptile. Coleorhizal hairs facilitating water capillary adhesion to an embryo are developed in both types of Brachypodium species, but in perennial types they are less efficient. The pattern of development of coleorhizal hairs distinguishes Brachypodium species from members of the tribe Triticeae. The coleorhizal hairs are less developed in Triticeae. This trait is variable at the populational level, especially in heterozygous populations (B. phoenicoides). Both extremes in terms of dormancy, i.e. B. distachyon and B. sylvaticum, revealed inter- and intrapopulational variability of germination.

The Genetic Basis of Composite Spike Form in Barley and 'Miracle-Wheat'.

Inflorescences of the tribe Triticeae, which includes wheat (Triticum sp. L.) and barley (Hordeum vulgare L.) are characterized by sessile spikelets directly borne on the main axis, thus forming a branchless spike. ‘Compositum-Barley’ and tetraploid ‘Miracle-Wheat’ (T. turgidum convar. compositum (L.f.) Filat.) display noncanonical spike-branching in which spikelets are replaced by lateral branch-like structures resembling small-sized secondary spikes. As a result of this branch formation ‘Miracle-Wheat’ produces significantly more grains per spike, leading to higher spike yield. In this study, we first isolated the gene underlying spike-branching in ‘Compositum-Barley,’ i.e., compositum 2 (com2). Moreover, we found that COM2 is orthologous to the branched headt (bht) locus regulating spike branching in tetraploid ‘Miracle-Wheat.’ Both genes possess orthologs with similar functions in maize BRANCHED SILKLESS 1 (BD1) and rice FRIZZY PANICLE/BRANCHED FLORETLESS 1 (FZP/BFL1) encoding AP2/ERF transcription factors. Sequence analysis of the bht locus in a collection of mutant and wild-type tetraploid wheat accessions revealed that a single amino acid substitution in the DNA-binding domain gave rise to the domestication of ‘Miracle-Wheat.’ mRNA in situ hybridization, microarray experiments, and independent qRT-PCR validation analyses revealed that the branch repression pathway in barley is governed through the spike architecture gene Six-rowed spike 4 regulating COM2 expression, while HvIDS1 (barley ortholog of maize INDETERMINATE SPIKELET 1) is a putative downstream target of COM2. These findings presented here provide new insights into the genetic basis of spike architecture in Triticeae, and have disclosed new targets for genetic manipulations aiming at boosting wheat’s yield potential.

Biological and ecological features of display Anisoplia austriaca Hrbst. in phytocenoses from of representatives of the tribe Triticeae

Biological and ecological features of display Anisoplia austriaca Hrbst. in phytocenoses from of representatives of the tribe Triticeae

Genome constitution of Elymus tangutorum (Poaceae: Triticeae) inferred from meiotic pairing behavior and genomic in situ hybridization

AbstractElymus tangutorum (Nevski) Hand.‐Mazz (2n = 6x = 42) is a perennial species in the tribe Triticeae, which distributes in Nepal and north and northwest China. However, the genome constitution of E. tangutorum is controversial and its taxonomic status is not clear. Hybridizations of E. tangutorum were carried out with E. wawawaiensis J. R. Carlson & Barkworth (StH), Roegneria grandis Keng (StY), and E. dahuricus Turcz. ex Griseb. (StYH). Meiotic pairing in the hybrids E. tangutorum × E. wawawaiensis (StH), E. tangutorum × R. grandis (StY), and E. tangutorum × E. dahuricus (StYH) averaged 10.48, 11.12, and 20.92 bivalents per cell, respectively. The results suggested that E. tangutorum is an allohexaploid and contains the StYH genomes. Results of genomic in situ hybridization analysis strongly supported the chromosome pairing data. Therefore, E. tangutorum should be treated as Campeiostachys dahurica var. tangutorum (Nevski) B. R. Baum, J. L. Yang & C. Yen. Intergenomic rearrangements of E. tangutorum may be affected by environmental factors.

De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat

Agropyron cristatum is a wild grass of the tribe Triticeae that is widely grown in harsh environments. As a wild relative of wheat, A. cristatum carries many resistance genes that could be used to broaden the genetic diversity of wheat. Here, we report the transcriptome sequencing of the flag leaf and young spike tissues of a representative tetraploid A. cristatum. More than 90 million reads from the two tissues were assembled into 73,664 unigenes. All unigenes were functionally annotated against the KEGG, COG, and Gene Ontology databases and predicted long non-coding RNAs. Pfam prediction demonstrates that A. cristatum carries an abundance of stress resistance genes. The extent of specific genes and rare alleles make A. cristatum a vital genetic reservoir for the improvement of wheat. Altogether, the available gene resources in A. cristatum facilitate efforts to harness the genetic diversity of wild relatives to enhance wheat.

Proteome response of wild wheat relativeKengyilia thoroldianato drought stress

Yang, S., Li, X., Ma, Y., Sun, X., Yang, Y. and Yang, Y. 2015. Proteome response of wild wheat relative Kengyilia thoroldiana to drought stress. Can. J. Plant Sci. 95: 237–249. Wild relatives of crops provide plant breeders with a broad pool of potentially useful genetic sources. The genus Kengyilia, being a member of the tribe Triticeae, is related to wheat, barley, and other cereals and forage grasses. We studied proteomic changes in K. thoroldiana seedlings in response to drought stress after withholding water for 0, 3, 6, 9 and 15 d. To determine the proteomic changes that occurred in leaves of K. thoroldiana under drought stress, two-dimensional gel electrophoresis (2-DE) and mass spectrometry were performed to identify protein expression changes. Seventy proteins showing reproducible and significant expression changes were identified. Among them, 28 proteins were up-regulated, whereas seven proteins were down-regulated. Based on database-annotated functions, these 70 proteins were categorized as energy metabolism, stress response, antioxidative enzyme, transcript and signal transduction, predicted proteins, and chloroplast-related proteins. Cluster analysis further showed that the up-regulated proteins were mainly stress response proteins and antioxidative enzymes. These results suggest that K. thoroldiana may resist drought stress by increasing the expression of stress response proteins and by producing antioxidative enzymes to remove reactive oxygen species. We conclude that the K. thoroldiana drought stress response mechanism could represent a useful genetic resource for related studies in wheat.

Improving Crop Adaptation to Climate Change through Strategic Crossing of Stress Adaptive Traits

Crossing programs based on phenomics have resulted in a new generation of drought adapted wheat lines based on strategic crossing of complementary physiological traits (PT) that have been included in CIMMYT's international distribution system since 2010. New PT lines have shown superior performance over conventional material in most international environments. For example, in the 17th SAWYT the average yield of PT lines was larger than the group of conventionally bred lines at 75% of international sites. This ongoing effort has involved broadening the genetic base of conventional wheat genepools through extensive use of genetic resources, including landraces and products of inter-specific hybridization with members of the Triticeae tribe. One of the prerequisites for successful application of phenomics in breeding is the establishment of reliable screening tools and platforms that can precisely measure expression of physiological traits in realistic field environments. Genetic gains associated with selection for canopy temperature and spectral water indices have shown that such remotely sensed traits can serve as proxies that reliably estimate water relations characteristics impacting on yield. The first aerial remote sensing platforms for large scale genetic resource screening was developed at CIMMYT in Mexico and more than half of the accessions of the World Wheat Collection have been screened. These high throughput field phenotyping tools have application in gene discovery and QTL for both drought and heat adaptive traits have been identified on 4 different chromosomes of the Seri/Babax RILs population, showing for the first time a common genetic basis for these key abiotic stresses. Similarly the phenology- controlled ‘Wheat Association Mapping Initiative’ panel has been used for gene discovery work. To define the best constellation of traits for application in breeding -and determine priorities for genetic understanding- it is necessary to develop conceptual models of adaptive traits that highlight wheat's genetic limitations under water limitation; pre-breeding serves as a practical tool to test different models.

World food security and the tribe Triticeae (Poaceae): Genetic resources of cultivated, wild, and weedy taxa for crop improvement

World food security and the tribe Triticeae (Poaceae): Genetic resources of cultivated, wild, and weedy taxa for crop improvement Bao‐Rong LU Norman ELLSTRAND (Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Handan Road 220, Shanghai 200433, China) (Department of Botany and Plant Sciences, Center for Conservation Biology and Center for Invasive Species Research, University of California, Riverside, CA 92521‐0124, USA)

Characterization of Thinopyrum Species for Wheat Stem Rust Resistance and Ploidy Level

ABSTRACTIn the tribe Triticeae, several Thinopyrum species have been used as sources of resistance to stem rust (caused by Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. & E. Henn., abbreviated as Pgt) and other wheat (Triticum aestivum L.) diseases. To identify novel sources of resistance to Pgt race TTKSK (Ug99), we evaluated and characterized the stem rust resistance of 242 accessions belonging to five Thinopyrum species, including beach wheatgrass [Th. bessarabicum (Savul. & Rayss) A. Löve], diploid tall wheatgrass [Th. elongatum (Host) D.R. Dewey], intermediate wheatgrass [Th. intermedium (Host) Barkworth & D. R. Dewey], sand cough or sea wheatgrass [Th. junceum (L.) A. Löve], and decaploid tall wheatgrass [Th. ponticum (Podp.) Barkworth & D.R. Dewey]. These accessions were evaluated for seedling reactions to nine Pgt races (TTKSK, TTTTF, TRTTF, RTQQC, QFCSC, TCMJC, TPMKC, TMLKC, and TPPKC), genotyped with molecular markers linked to four stem rust resistance genes (Sr24, Sr25, Sr26, and Sr43) derived from Thinopyrum species, and examined for ploidy levels. All accessions but one (Th. elongatum PI 531718) were resistant to all or most races. Most of the Th. elongatum and Th. ponticum accessions showed near‐immunity to all of the races while the accessions of the other three species (Th. bessarabicum, Th. intermedium, and Th. junceum) had varied levels of resistance ranging from near immunity to moderate resistance. Molecular marker analysis showed that most of the markers appeared to be species‐ or genus‐specific rather than linked to a gene of interest, and thus genotyping analysis was of limited value. Comparisons of infection types of accessions based on ploidy level suggested that higher ploidy level was associated with higher levels of stem rust resistance. The results from this study substantiate that the Thinopyrum species are a rich source of stem rust resistance.

Biochemical specialization and evolution in the Triticeae Dum. Tribe (Poaceae)

The problems of evolution and specialization of the tribe Triticeae are considered from the standpoint of the evolution of a seed protein complex and amino acid composition. The potential for using biochemical indices for the assessment of advances in the evolution and specialization of grasses are discussed. The degree of specialization was assessed for 98 taxa of the tribe Triticeae using the index of remoteness from a hypothetic ancestor of grasses (IR). Within the Poaceae family, Triticeae is shown to be a tribe with an extremely high level of specialization. Henrardia and Leymus are distinguished as the most specialized genera in the tribe. Species and genera of the tribe—second diploids—were first found to be characterized by a lower IR as compared to donors of simple genomes. This fact is interpreted as a reflection of the biochemical despecialization of the taxon. The extremely low specialization of Pascopyrum smithii (IR 19.0) can be regarded as a demonstration of the highest degree of the despecialization in tribe.

Evolutionary history of Methyltransferase 1 genes in hexaploid wheat.

BackgroundPlant and animal methyltransferases are key enzymes involved in DNA methylation at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in the hexaploid wheat Triticum aestivum (TaMET1).ResultsNine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7, indicating that group 2 homoeologous genes are predominant at the transcriptional level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous group 5 and 7, but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1.ConclusionsWe retraced the evolutionary history of MET1 genes in wheat, explaining the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-922) contains supplementary material, which is available to authorized users.

Isolation and characterization of novel Glu-St1 alleles from Pseudoroegneria spicata and Pd. strigosa.

Pseudoroegneria is a small genus of the Triticeae tribe; its St genome is present in over half of allopolyploid Triticeae species. The high molecular weight (HMW) subunits of glutenin (GS) encoded by the St genome are not well described. In this paper, we report the characterization of fourteen alleles of HMW-GS genes from the two species Pd. spicata and Pd. strigosa. Analysis shows that all fourteen sequences possess a typical primary structure shared by other known HMW-GS, but with some unique modifications. All fourteen Glu-St1 alleles are significantly smaller than normal Glu-1 genes due to fewer repeat motifs in a repetitive region with no indication of large deletion in other conserved regions. Thus, the small size is a common feature of HMW-GS encoded by Glu-St1 loci of Pseudoroegneria species. Sequence analysis indicated that all fourteen Glu-St1 alleles were intermediate type between x- and y-type, which represent an intermediate stage in the evolutionary divergence of x- and y-type subunits.

Phylogenetic relationships between Leymus and related diploid Triticeae species revealed by ISSR markers

To investigate the genetic diversity and phylogenetic relationships between polyploid Leymus and related diploid species of the Triticeae tribe, inter-simple sequence repeats (ISSR) markers was used to analyze 41 Leymus accessions representing 22 species and 2 subspecies, together with Pseudoroegneria stipifolia (St), Psathyrostachys fragilis (Ns), Australopyrum retrofractum (W), Hordeum bogdanii, H. chilense (H) and Lophopyrum elongatum (Ee). A total of 376 clear and reproducible DNA fragments were amplified by 29 ISSR primers, among which 368 (97.87%) fragments were found to be polymorphic. 8–18 polymorphic bands were amplified by each polymorphic primer, with an average of 12.69 bands. The data of 376 ISSR bands were used to generate Nei’s similarity coefficients and to construct a dendrogram by means of UPGMA. The similarity coefficients data suggested great genetic diversity in genus Leymus and related diploid Triticeae species, the genetic diversity among the different species more abundant than that of the different accessions. The dendrogram and principal coordinate analysis showed explicit interspecific relationships and demonstrated close phylogenetic relationships between Leymus species and Psathyrostachys.

Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

This study presents a phylogenetic analysis of the selected representatives of the Triticeae tribe and the assessment of possibilities of species identification on the basis of sequence variation in the three regions from the chloroplast DNA (matK, rbcL and trnH-psbA). The analysis included diploid and polyploid species of the following genomic compositions: E b , E e , H, I, Ns, St, Ta, Xu, NsXm, XoXr, XuXu, E b E e , E b E b E e , E b E e St, StH, StStH. The obtained matK and rbcL sequences revealed three well-supported clades: (1) Elymus, Lopophyrum, Pseudoroegneria, Thinopyrum (genomes E b , E e , St, StH, E b E e , E b E b E e , E b E e St, StStH); (2) Leymus, Hordelymus, Psathyrostachys (genomes Ns, NsXm, XoXr); (3) Hordeum (genomes H, I, Xu). This results support the view that the analyzed Elymus species (E. caninus, E. repens) acquired the Pseudoroegneria St genome maternally. They also indicate that Hordelymus europaeus carries the Ns genome from Psathyrostachys and point at the maternal origin of this component. Moreover, the presented results confirm the contribution of Psathyrostachys in the origin of Leymus as well as indicate the maternal character of this input. Differentiation observed within the Hordeum clade aligns with the alleged genome composition of the analyzed species. The DNA barcoding potential of the analyzed sequences was low. Nevertheless, several informative polymorphisms were found like e.g. the matK substitution specific for Thinopyrum bessarabicum, the trnH-psbA substitution differentiating Leymus arenarius from Psathyrostachys juncea and the group of species-specific deletions within trnH-psbA. In the DNA barcoding context we have also demonstrated negative importance of the high frequency cpDNA inversion leading to intraspecific variation.

Comparison of Acetyl-CoA carboxylase 1 (Acc-1) gene diversity among different Triticeae genomes

It has widely been documented that life form and mating system have significant influences on genetic diversity. In the tribe Triticeae, several genera contain both annual and perennial species, whereas other genera comprise strictly annual or perennial species. It was suggested that Triticeae annuals have originated from Triticeae perennials. The present study aims to analyze nucleotide diversity of Acc-1 gene among different Triticeae genomes, and attempts to link effects of life history (annuals and perennials) and mating systems. The nucleotide diversity of 364 Acc-1 sequences in Triticeae species was characterized. The highest estimates of nucleotide diversity values (π=0.01919, θ=0.03515) were found for the Ns genome among the genomes analyzed. Nucleotide diversities in the D genome and Ns genome of polyploids are higher than those in respective genomes of diploids, while in the St genome of polyploids, it is lower than that in the St genome of diploids. The averaged π value (0.013705) in the genomes of perennials is more than twice of the value (0.00508) in the genomes of annuals. The averaged π value (0.01323) in the genomes of outcrossing species is two-fold of the value (0.005664) in the genomes of selfer. Our results suggested that the evolutionary history and mating system may play an important role in determining nucleotide diversity of Acc-1 gene in each genome.

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.

Mutualistic fungal endophytes in the Triticeae - survey and description.

Grasses of the tribe Triticeae were screened to determine the presence of mutualistic epichloae fungal endophytes. Over 1500 accessions, from more than 250 species, encompassing 22 genera within the Triticeae were screened using immunodetection and direct staining/microscopy techniques. Only two genera, Elymus and Hordeum, were identified as harbouring epichloae endophytes with accessions native to a range of countries including Canada, China, Iran, Kazakhstan, Kyrgyzstan, Mongolia, Russia and the USA. Genetic analysis based on simple sequence repeat data revealed that the majority of endophytes cluster according to geographical regions rather than to host species; many strains isolated from Hordeum grouped with those derived from Elymus, and amongst the Elymus-derived strains, there was no clear correspondence between clustering topology and host species. This is the first detailed survey demonstrating the genetic diversity of epichloae endophytes within the Triticeae and highlights the importance of germplasm centres for not only preserving the genetic diversity of plant species but also the beneficial microorganisms they may contain.

Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae

Key message A cytogenetic map of wheat was constructed using FISH with cDNA probes. FISH markers detected homoeology and chromosomal rearrangements of wild relatives, an important source of genes for wheat improvement. To transfer agronomically important genes from wild relatives to bread wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) by induced homoeologous recombination, it is important to know the chromosomal relationships of the species involved. Fluorescence in situ hybridization (FISH) can be used to study chromosome structure. The genomes of allohexaploid bread wheat and other species from the Triticeae tribe are colinear to some extent, i.e., composed of homoeoloci at similar positions along the chromosomes, and with genic regions being highly conserved. To develop cytogenetic markers specific for genic regions of wheat homoeologs, we selected more than 60 full-length wheat cDNAs using BLAST against mapped expressed sequence tags and used them as FISH probes. Most probes produced signals on all three homoeologous chromosomes at the expected positions. We developed a wheat physical map with several cDNA markers located on each of the 14 homoeologous chromosome arms. The FISH markers confirmed chromosome rearrangements within wheat genomes and were successfully used to study chromosome structure and homoeology in wild Triticeae species. FISH analysis detected 1U-6U chromosome translocation in the genome of Aegilops umbellulata, showed colinearity between chromosome A of Ae. caudata and group-1 wheat chromosomes, and between chromosome arm 7S#3L of Thinopyrum intermedium and the long arm of the group-7 wheat chromosomes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-013-2253-z) contains supplementary material, which is available to authorized users.