Alien introgressions introduce beneficial alleles into existing crops and hence, are widely used in plant breeding. Generally, introgressed alien chromosomes show reduced meiotic pairing relative to the host genome, and may be eliminated over generations. Reduced pairing appears to result from a failure of some telomeres of alien chromosomes to incorporate into the leptotene bouquet at the onset of meiosis, thereby preventing chiasmate pairing. In this study, we analysed somatic nuclei of rye introgressions in wheat using 3D-FISH and found that while introgressed rye chromosomes or chromosome arms occupied discrete positions in the Rabl's orientation similar to chromosomes of the wheat host, their telomeres frequently occupied positions away from the nuclear periphery. The frequencies of such abnormal telomere positioning were similar to the frequencies of out-of-bouquet telomere positioning at leptotene, and of pairing failure at metaphase I. This study indicates that improper positioning of alien chromosomes that leads to reduced pairing is not a strictly meiotic event but rather a consequence of a more systemic problem. Improper positioning in the nuclei probably impacts the ability of introgressed chromosomes to migrate into the telomere bouquet at the onset of meiosis, preventing synapsis and chiasma establishment, and leading to their gradual elimination over generations.

• Klíčová slova
• 3D-FISH, chromatin, genome stability, hybrid, introgression, nucleus, rye, wheat,
• MeSH
• buněčné jadérko MeSH
• centromera MeSH
• chromozomální nestabilita * MeSH
• chromozomy rostlin * MeSH
• hybridizace in situ fluorescenční MeSH
• mitóza MeSH
• pšenice genetika   MeSH
• telomery MeSH
• Publikační typ
• časopisecké články MeSH

This study highlights the agronomic potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeologue recombination in wheat. Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat (Triticum aestivum) is known to contain numerous such "alien" introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 24,981 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timopheevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbour a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeologue recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.

• MeSH
• chromozomy rostlin * genetika   MeSH
• genová introgrese MeSH
• lokus kvantitativního znaku * MeSH
• mapování chromozomů MeSH
• nemoci rostlin genetika   mikrobiologie   MeSH
• odolnost vůči nemocem * genetika   MeSH
• pšenice * genetika   mikrobiologie   MeSH
• rekombinace genetická MeSH
• šlechtění rostlin MeSH
• Publikační typ
• časopisecké články MeSH

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.

• Klíčová slova
• GenomeZipper, alien introgression, chromosome rearrangement, chromosome translocation, comparative analysis, linkage drag,
• MeSH
• Ascomycota patogenita   MeSH
• chléb MeSH
• chromozomy rostlin genetika   metabolismus   MeSH
• DNA rostlinná genetika   MeSH
• genetické markery MeSH
• mapování chromozomů MeSH
• mikrosatelitní repetice MeSH
• nemoci rostlin genetika   mikrobiologie   MeSH
• odolnost vůči nemocem MeSH
• počítačová simulace MeSH
• pšenice genetika   mikrobiologie   MeSH
• rostlinné geny MeSH
• sekvence nukleotidů MeSH
• translokace genetická MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• genetické markery MeSH

Visualization of chromosome territories is a challenging task in plant genomes due to the lack of chromosome-specific probes, especially in species with large genomes. On the other hand, combination of flow sorting, genomic in situ hybridization (GISH), confocal microscopy, and employment of software for 3D modeling enables to visualize and characterize chromosome territories (CT) in interspecific hybrids. Here, we describe the protocol for the analysis of CTs in wheat-rye and wheat-barley hybrids, including amphiploids and introgression forms, where a pair of chromosomes or chromosome arms from one species is introgressed into the genome of another species. In this way, the architecture and dynamics of CTs in various tissues and different stages of cell cycle can be analyzed.

• Klíčová slova
• 3D FISH, Chromosome territory, Confocal microscopy, Imaris, Interphase nucleus, Plant hybrid,
• MeSH
• buněčné jádro genetika   MeSH
• chromozomy rostlin * genetika   MeSH
• genom rostlinný MeSH
• hybridizace in situ MeSH
• zavlečené druhy * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

During interphase, the chromosomes of eukaryotes decondense and they occupy distinct regions of the nucleus, called chromosome domains or chromosome territories (CTs). In plants, the Rabl's configuration, with telomeres at one pole of nucleus and centromeres at the other, appears to be common, at least in plants with large genomes. It is unclear whether individual chromosomes of plants adopt defined, genetically determined addresses within the nucleus, as is the case in mammals. In this study, the nuclear disposition of alien rye and barley chromosomes and chromosome arm introgressions into wheat while using 3D-FISH in various somatic tissues was analyzed. All of the introgressed chromosomes showed Rabl's orientation, but their relative positions in the nuclei were less clear. While in most cases pairs of introgressed chromosomes occupied discrete positions, their association (proximity) along their entire lengths was rare, and partial association only marginally more frequent. This arrangement is relatively stable in various tissues and during various stages of the cell cycle. On the other hand, the length of a chromosome arm appears to play a role in its positioning in a nucleus: shorter chromosomes or chromosome arms tend to be located closer to the centre of the nucleus, while longer arms are more often positioned at the nuclear periphery.

• Klíčová slova
• 3D-FISH, barley, chromatin, hybrid, introgression, nucleus, rye, wheat,
• MeSH
• buněčné jádro MeSH
• chromatin genetika   MeSH
• chromozomy rostlin * MeSH
• hybridizace in situ fluorescenční * metody   MeSH
• interfáze * genetika   MeSH
• ječmen (rod) genetika   MeSH
• počítačové zpracování obrazu MeSH
• průtoková cytometrie MeSH
• pšenice genetika   MeSH
• žito genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chromatin MeSH

Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D. Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47 Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.

• MeSH
• Aegilops genetika   MeSH
• Basidiomycota růst a vývoj   patogenita   MeSH
• chromozomy rostlin MeSH
• fenotyp MeSH
• genetické markery MeSH
• genová introgrese MeSH
• jednonukleotidový polymorfismus MeSH
• listy rostlin genetika   mikrobiologie   MeSH
• mapování chromozomů MeSH
• nemoci rostlin genetika   mikrobiologie   MeSH
• odolnost vůči nemocem genetika   MeSH
• pšenice genetika   mikrobiologie   MeSH
• rekombinace genetická MeSH
• rostlinné geny MeSH
• šlechtění rostlin MeSH
• telomery genetika   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• genetické markery MeSH

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% of BC382 and 22.7% of BC642 lines, while 88.5% of BC382 and 84% of BC642 lines contained Mb-genome chromatin, predominantly the chromosomes 4Mb and 5Mb. The presence of alien chromatin was confirmed by microscopic analysis of mitotic metaphase cells using GISH and FISH, which allowed precise determination of the size and position of the introgression events. New Mv9kr1-Ae. biuncialis MvGB382 4Mb and 5Mb disomic addition lines together with a 5DS.5DL-5MbL recombination were identified. A possible effect of the 5MbL distal region on seed length has also been observed. Moreover, previously developed Mv9kr1-MvGB642 introgression lines were more precisely characterized. The newly developed cytogenetic stocks represent valuable genetic resources for wheat improvement, highlighting the importance of utilizing diverse genetic materials to enhance wheat breeding strategies.

• Klíčová slova
• Aegilops biuncialis, Chromosome addition lines, DArTseq analysis, Thousand-grain weight, Wheat-Aegilops introgressions,
• MeSH
• Aegilops * genetika   MeSH
• chromatin * genetika   metabolismus   MeSH
• chromozomy rostlin * genetika   MeSH
• genetické markery MeSH
• genom rostlinný * MeSH
• genotyp MeSH
• genotypizační techniky MeSH
• genová introgrese MeSH
• mapování chromozomů MeSH
• pšenice * genetika   MeSH
• šlechtění rostlin metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chromatin * MeSH
• genetické markery MeSH

Despite a long history, the production of useful alien introgression lines in wheat remains difficult mainly due to linkage drag and incomplete genetic compensation. In addition, little is known about the molecular mechanisms underlying the impact of foreign chromatin on plant phenotype. Here, a comparison of the transcriptomes of barley, wheat and a wheat-barley 7HL addition line allowed the transcriptional impact both on 7HL genes of a non-native genetic background and on the wheat gene complement as a result of the presence of 7HL to be assessed. Some 42% (389/923) of the 7HL genes assayed were differentially transcribed, which was the case for only 3% (960/35 301) of the wheat gene complement. The absence of any transcript in the addition line of a suite of chromosome 7A genes implied the presence of a 36 Mbp deletion at the distal end of the 7AL arm; this deletion was found to be in common across the full set of Chinese Spring/Betzes barley addition lines. The remaining differentially transcribed wheat genes were distributed across the whole genome. The up-regulated barley genes were mostly located in the proximal part of the 7HL arm, while the down-regulated ones were concentrated in the distal part; as a result, genes encoding basal cellular functions tended to be transcribed, while those encoding specific functions were suppressed. An insight has been gained into gene transcription in an alien introgression line, thereby providing a basis for understanding the interactions between wheat and exotic genes in introgression materials.

• Klíčová slova
• RNA-seq, alien introgression, chromosomal rearrangement, deletion, gene transcription, transcriptome modification,
• MeSH
• genom rostlinný * MeSH
• ječmen (rod) genetika   metabolismus   MeSH
• pšenice genetika   metabolismus   MeSH
• sekvenční delece MeSH
• transkriptom * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

The cultivated Brassica species include numerous vegetable and oil crops of global importance. Three genomes (designated A, B and C) share mesohexapolyploid ancestry and occur both singly and in each pairwise combination to define the Brassica species. With organizational errors (such as misplaced genome segments) corrected, we showed that the fundamental structure of each of the genomes is the same, irrespective of the species in which it occurs. This enabled us to clarify genome evolutionary pathways, including updating the Ancestral Crucifer Karyotype (ACK) block organization and providing support for the Brassica mesohexaploidy having occurred via a two-step process. We then constructed genus-wide pan-genomes, drawing from genes present in any species in which the respective genome occurs, which enabled us to provide a global gene nomenclature system for the cultivated Brassica species and develop a methodology to cost-effectively elucidate the genomic impacts of alien introgressions. Our advances not only underpin knowledge-based approaches to the more efficient breeding of Brassica crops but also provide an exemplar for the study of other polyploids.

• MeSH
• biologická evoluce MeSH
• Brassica genetika   MeSH
• genom rostlinný * MeSH
• genová introgrese MeSH
• polyploidie MeSH
• rostlinné geny MeSH
• zemědělské plodiny genetika   MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseases with a significant impact on wheat production. Towards understanding the contribution of Th. elongatum 7EL to improvement of disease resistance in wheat, the genomic sequence of the 7EL fragment present in the wheat Chinese Spring (CS) telosomic addition line CS-7EL was determined and the contribution and impact of 7EL on the rachis transcriptome during FHB infection was compared between CS and CS-7EL. RESULTS: We assembled the Th. elongatum 7EL chromosome arm using a reference-guided approach. Combining this assembly with the available reference sequence for CS hexaploid wheat provided a reliable reference for interrogating the transcriptomic differences in response to infection conferred by the 7EL fragment. Comparison of the transcriptomes of rachis tissues from CS and CS-7EL showed expression of Th. elongatum transcripts as well as modulation of wheat transcript expression profiles in the CS-7EL line. Expression profiles at 4 days after infection with Fusarium graminearum, the causal agent of FHB, showed an increased in expression of genes associated with an effective defense response, in particular glucan endo-1,3-beta-glucosidases and chitinases, in the FHB-resistant line CS-7EL while there was a larger increase in differential expression for genes associated with the level of fungal infection in the FHB-susceptible line CS. One hundred and seven 7EL transcripts were expressed in the smallest 7EL region defined to carry FHB resistance. CONCLUSION: 7EL contributed to CS-7EL transcriptome by direct expression and through alteration of wheat transcript profiles. FHB resistance in CS-7EL was associated with transcriptome changes suggesting a more effective defense response. A list of candidate genes for the FHB resistance locus on 7EL has been established.

• Klíčová slova
• Alien introgression, Disease resistance, Fusarium graminearum, Non-coding RNA, RNA-seq, Thinopyrum elongatum, Transcriptome, Triticum aestivum,
• MeSH
• chromozomy rostlin * genetika   MeSH
• Fusarium * MeSH
• genomika MeSH
• lipnicovité * genetika   mikrobiologie   MeSH
• nemoci rostlin * genetika   mikrobiologie   MeSH
• odolnost vůči nemocem * genetika   MeSH
• transkriptom MeSH
• Publikační typ
• časopisecké články MeSH