Domestication and nearly eight thousand years of cultivation have resulted in a narrow genetic base, which hinders the identification of effective allele combinations and hampers breeding progress under changing environmental conditions. The gene portfolio can be extended using a crossing strategy providing favourable conditions for the formation of wheat × alien chromosome addition, substitution and translocation lines. To utilize the gene pool of Aegilops comosa, the present study applied durum wheat–Ae. comosa amphiploids top-crossed (TC) by hexaploid wheat (Mv9kr1ph1b), a strategy exploiting monosomic conditions of D- and M-genomes in TC1 to form cytogenetic stocks. While the expected genome structure of amphiploid and TC1 generations was confirmed, consecutive in situ hybridization using D- and M-genomic, as well as DNA repeat probes on 52 TC2F1 lines, showed significant elimination of not only M- but also D-genome chromosomes. Differences in the elimination frequency seemed to be related to chromosome size, with an opposite tendency for the two genomes, as shorter M chromosomes (1M, 4M, 6M) were retained more frequently, while the shorter D chromosomes (1D, 4D) were predominantly eliminated. D–M rearrangements within group 1, 3, 4, and 6 chromosomes were dominantly homoeologous, with 5D/5M recombinations observed at the highest frequency. Besides monosomic introgressions, disomic substitutions 2M(2D) and 7M(7D), addition 6M, and translocation T6MS·6ML-6D were selected. Morphological characterization and yield components indicated the good compensation ability of these Ae. comosa chromosomes for the loss of those of wheat. Relationships between chromosomes size and their elimination from wheat × alien hybrid progenies were discussed. Based on the high level of homoeologous recombinations and substitutions, top-crossing has proven to be an effective strategy for transferring alien chromosome segments from closely related diploid species into wheat. The newly developed wheat–Ae. comosa prebreeding materials represent potentially valuable genetic resources for wheat improvement.

In addition to wild relatives, cultivated Triticeae species such as barley can also serve as an excellent gene source to improve the agronomic traits of bread wheat. The Asakaze-Manas addition lines previously developed in Martonvásár exhibit low fertility and unstable inheritance; nonetheless, they could serve as ’bridge materials’ for the incorporation of barley chromatin into the wheat genome. By leveraging the centric breakage-fusion mechanism of unpaired chromosomes and the gametocidal effect of chromosome 2C from Aegilops cylindrica, the 4H and 6H addition lines were used to develop genetically stable translocation genotypes. In situ hybridization and molecular marker analyses were applied to identify the wheat and barley chromosome arms in the compensatory translocations, designated as T6HS.6BL, T6BS.6HL and T4BS.4HL. These results were confirmed by GBS read coverage analysis, which revealed a putative pericentric inversion in the barley chromosome arms involved in the T6HS.6BL and T6BS.6HL. The comparable agronomic performance of the centric fusion lines indicates that these chromosomal rearrangements had minimal, if any, negative impact relative to the parental wheat varieties. The newly developed translocation lines had an increased amount of minerals such as iron, suggesting that they could serve as promising genetic material for the biofortification of hexaploid wheat. Molecular marker analysis and in situ hybridization techniques, combined with genotyping-by-sequencing, enable the selection of stable wheat-barley translocation lines, leading to chromosome-mediated improvement in grain quality.

Triticum timopheevii (2n = 4x = 28, GGAtAt) is a valuable wild wheat relative for improving disease resistance and agronomic performance in bread wheat, although the detection of introgressed chromosomal segments remains challenging due to close genomic similarity. A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Multiple large-scale chromosomal rearrangements were identified, most frequently involving wheat chromosome 2B and T. timopheevii chromosome 2G, involving the replacement of a ~625 Mb wheat segment with a ~526 Mb T. timopheevii segment. Additional rearrangements included a 6A–6At translocation, a nullisomic 6B genotype, and widespread 1B.1R rye introgressions. These findings were confirmed by fluorescence in situ hybridization. Phenotyping of plant-pathogen interactions showed that some lines carrying 2G introgressions displayed reduced disease symptoms against individual leaf or yellow rust isolates. Several genotypes also showed favorable yield-component traits, including increased spikelet and grain number. Our results demonstrate that GBS-based read coverage analysis combined with cytogenetic validation is an effective approach for dissecting genome structure and identifying candidate introgressions with potential breeding relevance. The recurrent involvement of specific chromosomes highlights preferential homoeologous recombination patterns and supports the targeted utilization of T. timopheevii genetic diversity for wheat improvement.

Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F2 individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1Mb could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the Mb sub-genome (425 markers) and the Ub sub-genome (495 markers). Chromosomes of the Mb sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the Ub sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1Ub, 3Ub, and 5Ub retaining a substantial level of collinearity with Triticum aestivum, while 2Ub, 4Ub, 6Ub, and 7Ub show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3Mb, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.

The stable 3St(3D) substitution line offers promising genetic potential for improving drought tolerance in wheat during critical reproductive stages. The flowering stage is highly susceptible to drought, which significantly reduces wheat grain yield globally. Low genetic diversity in wheat further limits the discovery of optimal gene variants for breeding climate-resilient varieties. The substitution of chromosome 3D by a group 3 chromosome pair from Thinopyrum intermedium × Th. ponticum artificial hybrid was identified using in situ hybridization and genotyping-by-sequencing. This homoeologous substitution showed good functional compensation for grain yield and fertility, similar to the wheat parents ('Mv9kr1' and 'Mv Karizma') in field and greenhouse trials. The substitution line exhibits a semidwarf phenotype due to the Rht8 and Rht2 dwarfing alleles. Automated shoot phenotyping after a 10-day water withdrawal at flowering revealed efficient water preservation allowing to maintain photosynthetic functions, sustained photosynthetic activity, and less chlorophyll degradation, indicated by Normalized Difference Vegetation Index (NDVI) and modified Normalized Difference Index (mND705) values and moderate level of protective functions shown by the expression of stress-related genes. Compared to the wheat parents, the substitution line developed thicker roots with increased volume under drought, resulting in a lower surface-to-volume ratio. This may enhance water storage efficiency and help reduce yield loss under drought conditions.

Wild wheat relative Aegilops biuncialis offers valuable traits for crop improvement through interspecific hybridization. However, gene transfer from Aegilops has been hampered by difficulties in detecting introgressed Ub- and Mb-genome chromatin in the wheat background at high resolution. The present study applied DArTseq technology to genotype two backcrossed populations (BC382, BC642) derived from crosses of wheat line Mv9kr1 with Ae. biuncialis accession, MvGB382 (early flowering and drought-tolerant) and MvGB642 (leaf rust-resistant). A total of 11,952 Aegilops-specific Silico-DArT markers and 8,998 wheat-specific markers were identified. Of these, 7,686 markers were assigned to Ub-genome chromosomes and 4,266 to Mb-genome chromosomes and were ordered using chromosome scale reference assemblies of hexaploid wheat and Ae. umbellulata. Ub-genome chromatin was detected in 5.7

Some species of the genus Aegilops, a wild relative of wheat, carry chromosomes that after introducing to wheat exhibit preferential transmission to progeny. Their selective retention is a result of the abortion of gametes lacking them due to induced chromosomal aberrations. These chromosomes are termed Gametocidal (Gc) and, based on their effects, they are categorized into three types: mild, intense or severe, and very strong. Gc elements within the same homoeologous chromosome groups of Aegilops (II, III, or IV) demonstrate similar Gc action. This review explores the intriguing dynamics of Gc chromosomes and encompasses comprehensive insights into their source species, behavioral aspects, mode of action, interactions, suppressions, and practical applications of the Gc system in wheat breeding. By delving into these areas, this work aims to contribute to the development of novel plant genetic resources for wheat breeding. The insights provided herein shed light on the utilization of Gc chromosomes to produce chromosomal rearrangements in wheat and its wild relatives, thereby facilitating the generation of chromosome deletions, translocations, and telosomic lines. The Gc approach has significantly advanced various aspects of wheat genetics, including the introgression of novel genes and alleles, molecular markers and gene mapping, and the exploration of homoeologous relationships within Triticeae species. The mystery lies in why gametes possessing Gc genes maintain their normality while those lacking Gc genes suffer abnormalities, highlighting an unresolved research gap necessitating deeper investigation.

Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael , a perennial hybrid of Thinopyrum intermedium and Th. ponticum , was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, J st , J vs , J r , and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA) 7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6J vs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm’s high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and ‘Mv Karizma.’ Moreover, the introgressed 6J vs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA) 7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding.

Aegilops species, wild relatives of wheat, offer valuable traits for wheat improvement through interspecific hybridization. Despite many Ae. biuncialis accessions maintained in gene banks, only a few have been utilized in wheat breeding. Gene transfer from Aegilops has been hampered by difficulties in detecting introgressed Ub- and Mb-genome chromatin at high resolution in the wheat background. The present study applied DArTseq technology, to genotype two backcrossed populations (BC382, BC642) derived from crosses of a wheat line Mv9kr1 with Ae. biuncialis accession, MvGB382 (earlyflowering and drought tolerant) and MvGB642 (leaf rust-resistant). 11,952 Aegilops specific Silico-DArT markers were obtained, while 8998 markers were specific to wheat. Using the results obtained on diploid progenitors and wheat-Aegilops addition lines, 7686 markers were assigned to the Ub-genome chromosomes and 4266 for Mb-genome chromosomes and ordered by the use of chromosome assemblies of hexaploid wheat and Ae. umbellulata. In the BC3 populations, 5.7% of BC382 and 22.7% of BC642 lines contained Ub-genome chromatin, while Mb-genome chromatin was detected in 88.5% of BC382 and 84% of BC642 lines. Notably, chromosomes 4Mb and 5Mb were frequently present in both populations, whereas chromosomes 3Mb and 6Mb were rarer. A Mv9kr1-Ae. biuncialis MvGB382 4Mb and 5Mb disomic addition lines were identified together with a new 5DS.5DL-5MbL recombination. Moreover, previously developed Mv9kr1-MvGB642 introgression lines were identified more precisely by DArTseq. A possible effect of the 5MbL distal region on seed length has been also observed and discussed. The new cytogenetic stocks represent valuable genetic resources for wheat improvement.

Cultivated and wild species of the genus rye (Secale) are important but underexploited gene sources for increasing the genetic diversity of bread wheat. Gene transfer is possible via bridge genetic materials derived from intergeneric hybrids. During this process, it is essential to precisely identify the rye chromatin in the wheat genetic background. In the present study, backcross generation BC2F8 from a cross between Triticum aestivum (Mv9kr1) and S. cereanum ('Kriszta,' a cultivar from the artificial hybrid of S. cereale and S. strictum) was screened using in-situ hybridization (GISH and FISH) and analyzed by DArTseq genotyping in order to select potentially agronomically useful genotypes for prebreeding purposes. Of the 329,267 high-quality short sequence reads generated, 27,822 SilicoDArT and 8,842 SNP markers specific to S. cereanum 1R-7R chromosomes were identified. Heatmaps of the marker densities along the 'Lo7' rye reference pseudomolecules revealed subtle differences between the FISH- and DArTseq-based results. This study demonstrates that the "exotic" rye chromatin of S. cereanum introgressed into wheat can be reliably identified by high-throughput DArTseq genotyping. The Mv9kr1-'Kriszta' addition and translocation lines presented here may serve as valuable prebreeding genetic materials for the development of stress-tolerant or disease-resistant wheat varieties.

GBS read coverage analysis identified a Robertsonian chromosome from two Thinopyrum subgenomes in wheat, conferring leaf and stripe rust resistance, drought tolerance, and maintaining yield stability. Agropyron glael (GLAEL), a Thinopyrum intermedium × Th. ponticum hybrid, serves as a valuable genetic resource for wheat improvement. Despite its potential, limited knowledge of its chromosome structure and homoeologous relationships with hexaploid wheat (Triticum aestivum) has restricted the full exploitation of GLAEL's genetic diversity in breeding programs. Here, we present the development of a 44-chromosome wheat/GLAEL addition line (GLA7). Multicolor genomic in situ hybridization identified one chromosome arm from the St subgenome of Th. intermedium, while the other arm remained unclassified. Genotyping-by-sequencing (GBS) read coverage analysis revealed a unique Robertsonian translocation between two distinct Thinopyrum subgenomes, identified as 4StS·1JvsS. The GLA7 line demonstrated strong adult plant resistance to both leaf rust and stripe rust under natural and artificial infection conditions. Automated phenotyping of shoot morphological parameters together with leaf relative water content and yield components showed that the GLA7 line exhibited elevated drought tolerance compared to parental wheat genotypes. Three years of field trials showed that GLA7 exhibits similar agronomic performance and yield components to the wheat parents. This unique addition line holds promise for enhancing wheat's tolerance to multiple stresses through the introduction of new resistance genes, as well as its ability to mitigate the effects of temporary water limitation during flowering, all without negatively impacting wheat performance.

The annual goatgrass, Aegilops biuncialis is a rich source of genes with considerable agronomic value. This genetic potential can be exploited for wheat improvement through interspecific hybridization to increase stress resistance, grain quality and adaptability. However, the low throughput of cytogenetic selection hampers the development of alien introgressions. Using the sequence of flow-sorted chromosomes of diploid progenitors, the present study enabled the development of chromosome-specific markers. In total, 482 PCR markers were validated on wheat (Mv9kr1) and Ae. biuncialis (MvGB642) crossing partners, and 126 on wheat-Aegilops additions. Thirty-two markers specific for U- or M-chromosomes were used in combination with GISH and FISH for the screening of 44 Mv9kr1 × Ae. biuncialis BC3F3 genotypes. The predominance of chromosomes 4M and 5M, as well as the presence of chromosomal aberrations, may indicate that these chromosomes have a gametocidal effect. A new wheat-Ae. biuncialis disomic 4U addition, 4M(4D) and 5M(5D) substitutions, as well as several introgression lines were selected. Spike morphology and fertility indicated that the Aegilops 4M or 5M compensated well for the loss of 4D and 5D, respectively. The new cytogenetic stocks represent valuable genetic resources for the introgression of key genes alleles into wheat.

Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the Pairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of the Ph1 locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the original ph1b mutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, the ph1b mutation was transferred from two CSph1b mutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1 ph1b/ph1b exhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. The ph1b mutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialis F1 hybrids, predominantly with the Mb-genome chromosomes of Aegilops relative to those of the Ub genome. High frequency of wheat-Aegilops chromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialis amphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1b mutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.

Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass Aegilops biuncialis has high β-glucan content, which makes it an attractive gene source to develop wheat lines with modified fiber composition. In order to support introgression breeding, this work examined genetic variability in grain β-glucan, pentosan, and protein content in a collection of Ae. biuncialis. A large variation in grain protein and edible fiber content was revealed, reflecting the origin of Ae. biuncialis accessions from different eco-geographical habitats. Association analysis using DArTseq-derived SNPs identified 34 QTLs associated with β-glucan, pentosan, water-extractable pentosan, and protein content. Mapping the markers to draft chromosome assemblies of diploid progenitors of Ae. biuncialis underlined the role of genes on chromosomes 1Mb, 4Mb, and 5Mb in the formation of grain β-glucan content, while other QTLs on chromosome groups 3, 6, and 1 identified genes responsible for total- and water-extractable pentosan content. Functional annotation of the associated marker sequences identified fourteen genes, nine of which were identified in other monocots. The QTLs and genes identified in the present work are attractive targets for chromosome-mediated gene transfer to improve the health-promoting properties of wheat-derived foods.

Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. Development of alien introgression lines of wheat may be facilitated by the knowledge of DNA sequences of Aegilops chromosomes. As the Aegilops genomes are complex, sequencing relevant Aegilops chromosomes purified by flow cytometric sorting offers an attractive route forward. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Hybridization of FITC-conjugated GAA oligonucleotide probe to chromosomes suspensions of the two species allowed the application of bivariate flow karyotyping and sorting some individual chromosomes. Bivariate flow karyotype FITC vs. DAPI of Ae. biuncialis consisted of nine chromosome-populations, but their chromosome content determined by microscopic analysis of flow sorted chromosomes indicated that only 7Mb and 1Ub could be sorted at high purity. In the case of Ae. geniculata, fourteen chromosome-populations were discriminated, allowing the separation of nine individual chromosomes (1Mg, 3Mg, 5Mg, 6Mg, 7Mg, 1Ug, 3Ug, 6Ug, and 7Ug) out of the 14. To sort the remaining chromosomes, a partial set of wheat-Ae. biuncialis and a whole set of wheat-Ae. geniculata chromosome addition lines were also flow karyotyped, revealing clear separation of the GAA-rich Aegilops chromosomes from the GAA-poor A- and D-genome chromosomes of wheat. All of the alien chromosomes represented by individual addition lines could be isolated at purities ranging from 74.5% to 96.6% and from 87.8% to 97.7%, respectively. Differences in flow karyotypes between Ae. biuncialis and Ae. geniculata were analyzed and discussed. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat.

Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning.

Understanding the genetic diversity of Aegilops biuncialis, a valuable source of agronomical useful genes, may significantly facilitate the introgression breeding of wheat. The genetic diversity and population structure of 86 Ae. biuncialis genotypes were investigated by 32700 DArT markers with the simultaneous application of three statistical methods- neighbor-joining clustering, Principal Coordinate Analysis, and the Bayesian approach to classification. The collection of Ae. biuncialis accessions was divided into five groups that correlated well with their eco-geographic habitat: A (North Africa), B (mainly from Balkans), C (Kosovo and Near East), D (Turkey, Crimea, and Peloponnese), and E (Azerbaijan and the Levant region). The diversity between the Ae. biuncialis accessions for a phenological trait (heading time), which is of decisive importance in the adaptation of plants to different eco-geographical environments, was studied over 3 years. A comparison of the intraspecific variation in the heading time trait by means of analysis of variance and principal component analysis revealed four phenotypic categories showing association with the genetic structure and geographic distribution, except for minor differences. The detailed exploration of genetic and phenologic divergence provides an insight into the adaptation capacity of Ae. biuncialis, identifying promising genotypes that could be utilized for wheat improvement.

Using COS markers, the study reveals homeologous relationships between tetraploid Agropyron cristatum and bread wheat to support alien introgression breeding of wheat. Crested wheatgrass (Agropyron cristatum L. Gaertn.) is a wild relative of wheat that possesses many genes that are potentially useful in wheat improvement. The species comprises a complex of diploid, tetraploid and hexaploid forms. In this study, wheat–A. cristatum chromosome, telosome and translocation lines were used to characterize syntenic relationships between tetraploid A. cristatum and bread wheat. Prior to mapping COS markers, the cytogenetic stock lines were characterized for fertility and by FISH and GISH for karyotype stability. Out of 328 COS markers selected for the study, 279 consistently amplified products in tetraploid A. cristatum, and, out of these, 139 were polymorphic between tetraploid crested wheatgrass and wheat. Sixty-nine markers were found to be suitable for the detection of tetraploid A. cristatum chromosomes 1P–6P in wheat, ranging from 6 to 17 markers per chromosome. BLASTn of the source ESTs resulted in significant hits for 67 markers on the wheat pseudomolecules. Generally, COS markers of the same homeologous group were detected on similar arms in both Agropyron and wheat. However, some intragenomic duplications and chromosome rearrangements were detected in tetraploid A. cristatum. These results provide new insights into the structure and evolution of the tetraploid A. cristatum genome and will facilitate the exploitation of the wild species for introgression breeding of bread wheat.

Chromosome pairing in meiosis usually starts in the vicinity of the telomere attachment to the nuclear membrane and congregation of telomeres in the leptotene bouquet is believed responsible for bringing homologue pairs together. In a heterozygote for an inversion of a rye (Secale cereale L.) chromosome arm in wheat, a distal segment of the normal homologue is capable of chiasmate pairing with its counterpart in the inverted arm, located near the centromere. Using 3D imaging confocal microscopy, we observed that some telomeres failed to be incorporated into the bouquet and occupied various positions throughout the entire volume of the nucleus, including the centromere pole. Rye telomeres appeared ca. 21 times more likely to fail to be included in the telomere bouquet than wheat telomeres. The frequency of the out-of-bouquet rye telomere position in leptotene was virtually identical to the frequency of telomeres deviating from Rabl's orientation in the nuclei of somatic cells, and was similar to the frequency of synapsis of the normal and inverted chromosome arms, but lower than the MI pairing frequency of segments of these two arms normally positioned across the volume of the nucleus. Out-of-position placement of the rye telomeres may be responsible for reduced MI pairing of rye chromosomes in hybrids with wheat and their disproportionate contribution to aneuploidy, but appears responsible for initiating chiasmate pairing of distantly positioned segments of homology in an inversion heterozygote.