Nejvíce citovaný článek - PubMed ID 24169776
A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.
- MeSH
- anotace sekvence MeSH
- Ascomycota fyziologie MeSH
- chléb MeSH
- chromozomy rostlin genetika MeSH
- genetická variace * MeSH
- genetické lokusy * MeSH
- klonování DNA MeSH
- mapování chromozomů MeSH
- nemoci rostlin genetika imunologie mikrobiologie MeSH
- odolnost vůči nemocem genetika MeSH
- pšenice genetika imunologie mikrobiologie MeSH
- rostlinné geny * MeSH
- Publikační typ
- časopisecké články MeSH
Fluorescence in situ hybridization with probes for 45 cDNAs and five tandem repeats revealed homoeologous relationships of Agropyron cristatum with wheat. The results will contribute to alien gene introgression in wheat improvement. Crested wheatgrass (Agropyron cristatum L. Gaertn.) is a wild relative of wheat and a promising source of novel genes for wheat improvement. To date, identification of A. cristatum chromosomes has not been possible, and its molecular karyotype has not been available. Furthermore, homoeologous relationship between the genomes of A. cristatum and wheat has not been determined. To develop chromosome-specific landmarks, A. cristatum genomic DNA was sequenced, and new tandem repeats were discovered. Their distribution on mitotic chromosomes was studied by fluorescence in situ hybridization (FISH), which revealed specific patterns for five repeats in addition to 5S and 45S ribosomal DNA and rye subtelomeric repeats pSc119.2 and pSc200. FISH with one tandem repeat together with 45S rDNA enabled identification of all A. cristatum chromosomes. To analyze the structure and cross-species homoeology of A. cristatum chromosomes with wheat, probes for 45 mapped wheat cDNAs covering all seven chromosome groups were localized by FISH. Thirty-four cDNAs hybridized to homoeologous chromosomes of A. cristatum, nine hybridized to homoeologous and non-homoeologous chromosomes, and two hybridized to unique positions on non-homoeologous chromosomes. FISH using single-gene probes revealed that the wheat-A. cristatum collinearity was distorted, and important structural rearrangements were observed for chromosomes 2P, 4P, 5P, 6P and 7P. Chromosomal inversions were found for pericentric region of 4P and whole chromosome arm 6PL. Furthermore, reciprocal translocations between 2PS and 4PL were detected. These results provide new insights into the genome evolution within Triticeae and will facilitate the use of crested wheatgrass in alien gene introgression into wheat.
BACKGROUND: Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. RESULTS: In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified. CONCLUSIONS: The sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome.
- Klíčová slova
- Chromosome arm 4VS, Flow sorting, Genome zipper, Haynaldia villosa, Scaffold,
- MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- genomika MeSH
- lipnicovité genetika MeSH
- mapování chromozomů MeSH
- pořadí genů genetika MeSH
- repetitivní sekvence nukleových kyselin genetika MeSH
- sekvenční analýza DNA * 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
Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.
- Klíčová slova
- Chromosome 4D survey sequence, Gene annotation, Gene content, Synteny, Triticum aestivum, Virtual gene order,
- MeSH
- chromozomy rostlin * MeSH
- exprimované sekvenční adresy chemie MeSH
- mapování chromozomů MeSH
- molekulární sekvence - údaje MeSH
- pořadí genů * MeSH
- pšenice genetika MeSH
- sekvenční analýza DNA MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Chromosomal rearrangements are a major driving force in shaping genome during evolution. Previous studies show that translocated genes could undergo elevated rates of evolution and recombination frequencies around these genes can be altered. Based on the recently released genome sequences of Triticum urartu, Aegilops tauschii, Brachypodium distachyon and bread wheat, an analysis of interchromosomal translocations in the hexaploid wheat genotype 'Chinese Spring' ('CS') was conducted based on chromosome shotgun sequences from individual chromosome arms of this genotype. RESULTS: A total of 720 genes representing putative interchromosomal rearrangements was identified. They were distributed across the 42 chromosome arms. About 59% of these translocated genes were those involved in the well-characterized translocations involving chromosomes 4A, 5A and 7B. The other 41% of the genes represent a large numbers of putative interchromosomal rearrangements which have not yet been described. The number of the putative translocation events in the D subgenome was about half of those presented in either the A or B subgenomes, which agreed well with that the times of interaction between the A and B subgenomes almost doubled that between either of them and the D subgenome. CONCLUSIONS: The possible existence of a large number of interchromosomal rearrangements detected in this study provide further evidence that caution should be taken when using synteny in ordering sequence contigs or in cloning genes in hexaploid wheat. The identification of these putative translocations in 'CS' also provide a base for a systematic evaluation of their presence or absence in the full spectrum of bread wheat and its close relatives, which could have significant implications in a wide array of fields ranging from studies of systematics and evolution to practical breeding.
The bread wheat (Triticum aestivum L.) genotype "Chinese Spring" ("CS") is the reference base in wheat genetics and genomics. Pericentric rearrangements in this genotype were systematically assessed by analyzing homoeoloci for a set of nonredundant genes from Brachypodium distachyon, Triticum urartu, and Aegilops tauschii in the CS chromosome shotgun sequence obtained from individual chromosome arms flow-sorted from CS aneuploid lines. Based on patterns of their homoeologous arm locations, 551 genes indicated the presence of pericentric inversions in at least 10 of the 21 chromosomes. Available data from deletion bin-mapped expressed sequence tags and genetic mapping in wheat indicated that all inversions had breakpoints in the low-recombinant gene-poor pericentromeric regions. The large number of putative intrachromosomal rearrangements suggests the presence of extensive structural differences among the three subgenomes, at least some of which likely occurred during the production of the aneuploid lines of this hexaploid wheat genotype. These differences could have significant implications in wheat genome research where comparative approaches are used such as in ordering and orientating sequence contigs and in gene cloning.
- Klíčová slova
- Chinese Spring, chromosomal rearrangement, comparative genomics, pericentric inversion, pericentromeric regions, translocation,
- MeSH
- body zlomu chromozomu MeSH
- centromera genetika MeSH
- chromozomální delece MeSH
- chromozomální inverze * MeSH
- chromozomy rostlin genetika MeSH
- genotyp MeSH
- pšenice genetika MeSH
- rekombinace genetická MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat. RESULTS: We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus. CONCLUSION: Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.
- MeSH
- Brachypodium genetika MeSH
- chromozomy rostlin genetika MeSH
- DNA rostlinná genetika MeSH
- duplikace genu MeSH
- fylogeneze MeSH
- genetické lokusy genetika MeSH
- genom rostlinný genetika MeSH
- inzerční mutageneze MeSH
- kontigové mapování MeSH
- molekulární evoluce * MeSH
- polyploidie MeSH
- pšenice genetika MeSH
- pseudogeny genetika MeSH
- rýže (rod) genetika MeSH
- sekvenční analýza DNA MeSH
- umělé bakteriální chromozomy MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- DNA rostlinná MeSH
Intergeneric hybrids of fescues (Festuca spp.) and ryegrasses (Lolium spp.) are unique for the ability of their chromosomes to pair essentially freely in meiotic metaphase I (MI). At the same time, their chromosomes can be readily recognized by genomic in-situ hybridization (GISH). Past genome-wide observations suggested that this homoeologous pairing was not completely random. In this study we extend the analysis to all seven individual chromosomes of F. pratensis introgressed into autotetraploid L. multiflorum and show that for any F. pratensis chromosome the choice of an MI pairing partner depends on the identity of the remaining chromosomes present in the quadruplet. In monosomic introgressions, the choice of a homologous or homoeologous partner was completely random; in disomics there was a slight preference for homologous pairing. Pairing preference was similar for each chromosome, suggesting that pairing affinity of all chromosomes is essentially the same and no structural rearrangements differentiate the two genera. Homoeologous crossover rates for individual chromosomes were similar and they were consistently lower than expected on the basis of the MI pairing. High homoeologous MI pairing in these hybrids may be due to a very permissive system of chromosome pairing control that overlooks differences between the parental chromosomes. Given the ease of genome discrimination by GISH in the Lolium-Festuca hybrids, the differences in repetitive DNA sequences must be substantial. On the other hand, it appears just as likely that while the DNA repeats diverged markedly during evolution, the sequences involved in chromosome pairing have been conserved enough to facilitate regular pairing partner recognition and crossing-over.
- MeSH
- chromozomy rostlin genetika MeSH
- Festuca genetika MeSH
- genom rostlinný genetika MeSH
- hybridizace genetická MeSH
- hybridizace in situ fluorescenční MeSH
- hybridizace in situ MeSH
- jílek genetika MeSH
- meióza * MeSH
- metafáze MeSH
- párování chromozomů genetika MeSH
- polyploidie MeSH
- rekombinace genetická * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
