Development and Application of Transposable Element-Based Chromosomal Markers for the St Genome in Triticeae

2019 ◽  
Vol 159 (4) ◽  
pp. 215-224
Author(s):  
Ruijuan Liu ◽  
Feng Yu ◽  
Linna Wei ◽  
Bo Liu ◽  
Demei Liu ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Dna Analysis ◽  
Repetitive Sequences ◽  
Distribution Patterns ◽  
Signal Distribution ◽  
Sequence Composition ◽  
Plasmid Library ◽  
Chromosomal Markers

The St genome, originating from Pseudoroegneria (Nevski) Á. Löve, plays an important role in Triticeae. In this study, the Pseudoroegneria stipifolia genome (2n = 2x = 14, StSt) was screened to identify sequences that could be used for FISH. A total of 163 effective clones were obtained from the genomic plasmid library which was constructed by DNase I digestion of P. stipifolia nuclear genomic DNA. Analysis of these clones identified 112 with characteristics of transposable elements (TEs), 13 with characteristics of tandem repetitive sequences, 8 with characteristics of mRNA sequences, and 30 unknown sequences. Fluorescent signals were detected for 11 of 41 TE sequences on P. stipifolia chromosomes after in situ hybridization and were divided into 4 types according to signal distribution patterns: over the whole St genome chromosomes, telomere to pericentromeric regions, centromere to pericentromeric regions, and terminal regions. The affinity between St and Y genomes was studied using the 11 TE probes in 3 StStYY species. Five TE probes showed no obvious difference between subgenomes, 2 probes displayed divergence only in 2 StStYY species, and 4 probes exhibited significant differences among 3 StStYY species. These results provide a preliminary understanding of the sequence composition of the St genome and enabled 11 novel TE probes to be developed and applied.

Physical organization of repetitive sequences and chromosome diversity of barley revealed by fluorescence in situ hybridization (FISH)

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 329-339 ◽  
Author(s):  
Siyu Zhang ◽  
Minqiu Zhu ◽  
Yi Shang ◽  
Jiaqi Wang ◽  
Dawadundup ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Polymorphic Information Content ◽  
Repetitive Sequences ◽  
Chromosome Research ◽  
Sequence Composition ◽  
Induced Mutants ◽  
Chromosome 4H ◽  
Chromosomal Polymorphisms

Fluorescence in situ hybridization (FISH) using oligonucleotides is a simple and convenient method for chromosome research. In this study, 34 of 46 previously developed oligonucleotides produced signals in barley. Together with two plasmid clones and one PCR-amplified cereal centromere repeat (CCS1) probe, 37 repetitive sequences were chromosomally located produced three types of signals covering different positions on the chromosomes. The centromeric and pericentric regions had a more complex genomic organization and sequence composition probably indicative of higher contents of heterochromatin. An efficient multi-plex probe containing eight oligonucleotides and a plasmid clone of 45S rDNA was developed. Thirty-three barley karyotypes were developed and compared. Among them, 11 irradiation-induced mutants of cultivar 08-49 showed no chromosomal variation, whereas 22 cultivar and landrace accessions contained 28 chromosomal polymorphisms. Chromosome 4H was the most variable and 6H was the least variable based on chromosome polymorphic information content (CPIC). Five polymorphic chromosomes (1H-2, 2H-1, 3H-3, 5H-2, and 6H-2) were dominant types, each occurring in more than 50% of accessions. The multi-plex probe should facilitate identification of further chromosomal polymorphisms in barley.

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 431-441 ◽  
Author(s):  
Evgueni V Ananiev ◽  
M Isabel Vales ◽  
Ronald L Phillips ◽  
Howard W Rines
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Genomic Dna ◽  
Repetitive Sequences ◽  
Repeated Sequences ◽  
C Genome ◽  
Copy Dna

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.Key words: oat, cosmid library, in situ hybridization.

C-banding and fluorescence in situ hybridization studies of the wheat–alien hybrid 'Agrotana'

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 477-481 ◽  
Author(s):  
Jie Xu ◽  
R. L. Conner ◽  
A. Laroche
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Chromosome Engineering ◽  
C Banding ◽  
Chinese Spring Wheat ◽  
Mother Cells ◽  
Alien Chromatin ◽  
Chromosome Segments

'Agrotana', a wheat-alien hybrid (2n = 56), is a potential source of resistance to common root rot, stem rust, wheat streak mosaic virus, and the wheat curl mite. However, the origin of 'Agrotana', reported to be durum wheat × Agropyron trichophorum (pubescent wheatgrass), is uncertain. The objective of this investigation was to determine the chromosome constitution of 'Agrotana' using C-banding and fluorescence in situ hybridization techniques. The F1 hybrid of 'Agrotana' × 'Chinese Spring' wheat showed 7 I + 21 II in 14.9% of the pollen mother cells, evidence of the presence of the A, B, and D genomes in 'Agrotana'. The hybrid had 16 heavily C-banded chromosomes, namely 4A, and 1-7B of wheat, and a translocation that probably involved wheat chromosomes 2A and 2D. In situ hybridization using biotinylated genomic DNA of Ag. trichophorum cv. Greenleaf blocked with CS DNA failed to identify the alien chromosomes in 'Agrotana', indicating that the alien chromosomes were not likely derived from pubescent wheatgrass. In situ hybridization using labelled wheat genomic DNA blocked with 'Agrotana' DNA revealed that 'Agrotana' had 40 wheat, 14 alien, and 2 (a pair) wheat–alien translocated chromosomes. There was no homology between wheat and the alien chromosomes or chromosome segments involved in the wheat–alien recombinant. Two of the seven pairs of alien chromosomes were homoeologous to each other. The ability to identify alien chromatin in wheat using labelled wheat DNA instead of labelled alien DNA will be particularly useful in chromosome engineering of wheat germplasms having alien chromatin of unknown origin.Key words: wheat–alien hybrid, C-banding, fluorescence in situ hybridization, labelled wheat DNA as probe.

A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 138-142 ◽  
Author(s):  
Michael S. Zwick ◽  
Robert E. Hanson ◽  
M. Nurul Islam-Faridi ◽  
David M. Stelly ◽  
Rod A. Wing ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Copy Number ◽  
Genomic Dna ◽  
Mammalian Species ◽  
Repetitive Dnas ◽  
Rapid Procedure ◽  
Dna Elements ◽  
Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

Genomic in situ hybridization to sectioned nuclei shows chromosome domains in grass hybrids

1990 ◽  
Vol 95 (3) ◽  
pp. 335-341
Author(s):  
A.R. Leitch ◽  
W. Mosgoller ◽  
T. Schwarzacher ◽  
M.D. Bennett ◽  
J.S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Microscope Level ◽  
Hordeum Chilense ◽  
Root Tip ◽  
Interphase Nuclei ◽  
Light Microscope Level ◽  
Thin Sections ◽  
Electron Microscopes

In situ hybridization using biotinylated total genomic DNA and avidin detection systems was adapted for examination of thin-sectioned plant material in the light and electron microscopes. Root tip material was preserved prior to sectioning, so that the in vivo disposition of the chromatin was maintained. Use of total genomic DNA from Secale africanum as a probe enabled the chromatin from the two parental genomes in the grass hybrid Hordeum chilense × S. africanum to be distinguished. The biotinylated probe preferentially labelled the chromosomes of S. africanum origin. DNA-DNA hybrids were visualized at the light-microscope level by Texas Red fluorescence and at the electron-microscope level by the enzymic precipitation of DAB (diaminobenzidine) or by colloidal gold particles. The use of thin sections allowed the location of probe hybridization to be established unequivocally in both metaphase and interphase nuclei. Analysis of interphase nuclei showed that chromatin originating from the two parental genomes did not intermix but occupied distinct domains.

scholarly journals Ph-negative chronic myeloid leukemia: molecular analysis of ABL insertion into M-BCR on chromosome 22

Blood ◽  
1990 ◽  
Vol 76 (9) ◽  
pp. 1812-1818 ◽  
Author(s):  
CM Morris ◽  
N Heisterkamp ◽  
MA Kennedy ◽  
PH Fitzgerald ◽  
J Groffen
Keyword(s):  
In Situ Hybridization ◽  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Fusion Gene ◽  
Repetitive Sequences ◽  
Chromosome 9 ◽  
Leukemic Cells ◽  
Chromosome 22 ◽  
Chromosome 9Q34

Abstract Leukemic cells from a patient with Ph-negative chronic myeloid leukemia (CML) had a normal karyotype. M-BCR was rearranged and chromosome in situ hybridization showed an ABL insertion between 5′ and 3′ M-BCR on an apparently normal chromosome 22. The association of 5′ BCR and 3′ ABL at the 5′ junction of the chromosome 9 insert was typical of that found for the BCR-ABL fusion gene in other patients with the standard t(9;22) and CML. With an M-bcr-3′ probe, we cloned and characterized a 3′ junction fragment. Field inversion gel electrophoresis and chromosome in situ hybridization studies using a probe isolated from genomic DNA 5′ of the junction showed that 3′ M-BCR was joined to a region of chromosome 9q34 rich in repetitive sequences and lying some distance 3′ of ABL. The chromosome 9 insert was at least 329 kilobases long and included 3′ ABL and a larger portion of chromosome 9q34. Our results allowed us to exclude transposon- or retroviral-mediated insertion of ABL into chromosome 22. Instead, we favored a two- translocation model in which a second translocation reconstituted a standard t(9;22)(q34;q11) but left the chromosome 9 insert, including 3′ ABL, in chromosome 22.

The interspecific genome structure of cultivated banana, Musa spp. revealed by genomic DNA in situ hybridization

2000 ◽  
Vol 100 (2) ◽  
pp. 177-183 ◽  
Author(s):  
A. D’Hont ◽  
A. Paget-Goy ◽  
J. Escoute ◽  
F. Carreel
Keyword(s):  
In Situ Hybridization ◽  
Genomic Dna ◽  
Genome Structure ◽  
Musa Spp

scholarly journals Comparison Between Integrated Genomic DNA/RNA Profiling and Fluorescence In Situ Hybridization in the Detection of MYC, BCL-2, and BCL-6 Gene Rearrangements in Large B-Cell Lymphomas

2019 ◽  
Vol 153 (3) ◽  
pp. 353-359 ◽  
Author(s):  
Daniel P Cassidy ◽  
Jennifer R Chapman ◽  
Rafael Lopez ◽  
Kyle White ◽  
Yao-Shan Fan ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
B Cell ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Standard Of Care ◽  
Gene Rearrangements ◽  
B Cell Lymphomas ◽  
Rna Profiling ◽  
Large B Cell

Abstract Objectives To compare fluorescence in situ hybridization (FISH) and a commercially available sequencing assay for comprehensive genomic profiling (CGP) to determine the best approach to identify gene rearrangements (GRs) in large B-cell lymphomas (LBCLs). Methods Comparison of standard-of-care FISH assays (including a two-probe approach for MYC; break-apart and fusion probes) and an integrated genomic DNA/RNA sequencing CGP approach on a set of 69 consecutive LBCL cases. Results CGP detected GRs, including those involving MYC (1), BCL-2 (3), and BCL-6 (3), not detected by FISH. FISH detected non–IgH-MYC (4) and BCL-6 (2) GRs that were not detected by CGP. In four instances, standalone CGP or FISH testing would have missed a double-hit lymphoma. Conclusions CGP was superior to FISH in the detection of IgH-MYC rearrangements but was inferior for the detection of non–IgH-MYC rearrangements. Our study demonstrates the rationale for development of a customized approach to identify GRs in LBCLs.

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