Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 860-867 ◽  
Author(s):  
E A Salina ◽  
O M Numerova ◽  
H Ozkan ◽  
M Feldman
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
First Generation ◽  
Tandem Repeats ◽  
Southern Hybridization ◽  
Homoeologous Pairing ◽  
Genomic Changes ◽  
Intergenomic Recombination ◽  
Copy Numbers

The genomic content of the subtelomeric repeated sequences Spelt1 and Spelt52 was studied by dot, Southern, and in situ hybridization in 11 newly synthesized amphiploids of Aegilops and Triticum, and data were compared with the parental plants. Spelt1 had reduced copy numbers in the first generation of three synthetic amphiploids, but two others did not change; Spelt52 was amplified in nine amphiploids and did not change in two. In the second allopolyploid generation, Spelt1 copy number did not change, whereas there was amplification of Spelt52 in some allopolyploids and decreases in others. Neither allopolyploidy level nor the direction of the cross affected the patterns of change in the newly synthesized amphiploids. Changes did not result from intergenomic recombination because similar alterations were noticed in allopolyploids with and without Ph1, a gene that suppresses homoeologous pairing. No differences in Spelt1 and Spelt52 tandem organization were found by Southern hybridization. The significance of these data are discussed in relation to the establishment of newly formed allopolyploids.Key words: Aegilops, genomic changes, polyploidy, subtelomeric tandem repeats, Triticum, wheat.

Outcome prediction to cetuximab in advanced colorectal cancer: Analysis of EGFR and HER2 gene copy number by fluorescence in situ hybridization

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 10569-10569
Author(s):  
N. Personeni ◽  
G. De Hertogh ◽  
S. Störkel ◽  
M. Debiec-Rychter ◽  
K. Geboes ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Tumor Cells ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Her2 Gene ◽  
Egfr Amplification ◽  
Paired Samples ◽  
Copy Numbers

10569 Background: Recent studies suggest that increased epidermal growth factor receptor (EGFR) gene copy number assessed by in situ hybridization predicts response to cetuximab in patients (pts) with advanced colorectal cancer (mCRC). Additionally, preclinical data indicate that HER2, a member of the EGFR family, can modulate the efficacy of anti-EGFR monoclonal antibodies. Methods: We assessed EGFR and HER2 gene copies by fluorescent in situ hybridization (FISH) on paraffin-embedded samples from 70 pts with mCRC treated with cetuximab alone or with irinotecan. FISH was assessed either on primary tumors (55 pts) or on metastases (15 pts) according to two parameters: the absolute copy number of genes and chromosome (chr) centromeres, and their frequencies in 100 tumor cells. A sensitivity analysis was performed and fitted to outcome data in an attempt to define relevant cutoffs. EGFR protein expression by immunohistochemistry was deemed positive with =10% tumor cells being stained. Multiple paired samples originating from different tumor sources were analyzed whenever available (27 pts). Results: The overall response rate was 25%. Prevalent FISH patterns were disomy (8%) and balanced polysomy (90%) for EGFR gene and chr 7. EGFR amplification was seen in two pts (2%), of which only one responded. HER2 amplification was seen in two of 54 pts (3%), both experiencing stable disease. Average EGFR copies and frequency of tumor cells with >2 copies respectively ranged from 1.6 to 4.0 and from 10% to 90%, thus reflecting a substantial tumor heterogeneity. Despite assessing multiple centile cutoffs of gene copy numbers and their frequencies in tumor cells, we found no association between EGFR and HER2 copy numbers and objective response, time to progression, and overall survival. Analysis of paired samples did not improve the predictive value of EGFR copies by FISH. Excluding EGFR amplification, associated to a strong (3+) EGFR staining, we found no correlation between EGFR copy number and protein expression. Conclusions: Neither EGFR nor HER2 copies by FISH, nor EGFR expression, are predictors of outcome in mCRC pts treated with cetuximab. FISH might still play a role in screening EGFR and HER2 amplification, but cost-effectiveness is debatable. [Table: see text]

Molecular cytogenetic analysis of supernumerary heterochromatic segments in Rumex acetosa

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 391-397 ◽  
Author(s):  
Fukashi Shibata ◽  
Masahiro Hizume ◽  
Yuzo Kuroki
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
Tandem Repeats ◽  
Mitotic Chromosomes ◽  
Dioecious Plant ◽  
Rumex Acetosa ◽  
Interphase Nuclei ◽  
Heterochromatic Segment ◽  
Molecular Cytogenetic

The dioecious plant Rumex acetosa shows intraspecific karyotype variation, caused by supernumerary heterochromatic segments or DAPI (4',6-diamidino-2 phenylindole)-bands at the ends of the short arms of three pairs of autosomes. A DNA sequence (RAE730) specific to the supernumerary heterochromatic segments was cloned and sequenced. RAE730 was about 730 bp and AT-rich (71% AT-content). Using fluorescence in situ hybridization (FISH), RAE730 was localized in the supernumerary DAPI-positive heterochromatic segments on several mitotic chromosomes and chromocenters in interphase nuclei, but not in the DAPI-bands of Y or B chromosomes. RAE730 was tandemly arranged in the genome, and the copy number varied between plants from 40 000 to 304 000 copies per 2C, corresponding to the relative amount of supernumerary heterochromatic segments per genome. These results indicate that the karyotype variation caused by the supernumerary heterochromatic segment was generated by amplification or reduction of the tandem repeats of RAE730. Key words: Rumex acetosa, repetitive sequence, supernumerary heterochromatic segment, intraspecific karyotype variation, DAPI-band.

scholarly journals Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
Reference Sequence ◽  
A Genome ◽  
Genome Map ◽  
Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

Synthesis and cytological characterization of trigeneric hybrids of durum wheat with and without Ph1

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1173-1181 ◽  
Author(s):  
Prem P Jauhar ◽  
M Doğramaci ◽  
T S Peterson
Keyword(s):  
In Situ Hybridization ◽  
Chromosome Pairing ◽  
Genetic Recombination ◽  
Genomic In Situ Hybridization ◽  
Homoeologous Pairing ◽  
Alien Gene Transfer ◽  
Chromosome 5B ◽  
Alien Gene ◽  
Trigeneric Hybrids

Wild grasses in the tribe Triticeae, some in the primary or secondary gene pool of wheat, are excellent reservoirs of genes for superior agronomic traits, including resistance to various diseases. Thus, the diploid wheatgrasses Thinopyrum bessarabicum (Savul. and Rayss) Á. Löve (2n = 2x = 14; JJ genome) and Lophopyrum elongatum (Host) Á. Löve (2n = 2x = 14; EE genome) are important sources of genes for disease resistance, e.g., Fusarium head blight resistance that may be transferred to wheat. By crossing fertile amphidiploids (2n = 4x = 28; JJEE) developed from F1 hybrids of the 2 diploid species with appropriate genetic stocks of durum wheat, we synthesized trigeneric hybrids (2n = 4x = 28; ABJE) incorporating both the J and E genomes of the grass species with the durum genomes A and B. Trigeneric hybrids with and without the homoeologous-pairing suppressor gene, Ph1, were produced. In the absence of Ph1, the chances of genetic recombination between chromosomes of the 2 useful grass genomes (JE) and those of the durum genomes (AB) would be enhanced. Meiotic chromosome pairing was studied using both conventional staining and fluorescent genomic in situ hybridization (fl-GISH). As expected, the Ph1-intergeneric hybrids showed low chromosome pairing (23.86% of the complement), whereas the trigenerics with ph1b (49.49%) and those with their chromosome 5B replaced by 5D (49.09%) showed much higher pairing. The absence of Ph1 allowed pairing and, hence, genetic recombination between homoeologous chromosomes. Fl-GISH analysis afforded an excellent tool for studying the specificity of chromosome pairing: wheat with grass, wheat with wheat, or grass with grass. In the trigeneric hybrids that lacked chromosome 5B, and hence lacked the Ph1 gene, the wheat–grass pairing was elevated, i.e., 2.6 chiasmata per cell, a welcome feature from the breeding standpoint. Using Langdon 5D(5B) disomic substitution for making trigeneric hybrids should promote homoeologous pairing between durum and grass chromosomes and hence accelerate alien gene transfer into the durum genomes.Key words: alien gene transfer, chiasma (xma) frequency, chromosome pairing, fluorescent genomic in situ hybridization (fl-GISH), homoeologous-pairing regulator, specificity of chromosome pairing, wheatgrass.

A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 665-672 ◽  
Author(s):  
Zhi-Jun Cheng ◽  
Minoru Murata
Keyword(s):  
In Situ Hybridization ◽  
Tandem Repeats ◽  
Diploid Species ◽  
Upstream Region ◽  
Aegilops Speltoides ◽  
Repeat Family ◽  
B Genome ◽  
Intervening Sequences ◽  
Wild Diploid Species

AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

Abstract LB190: DNAscopeTM: A novel chromogenic in-situ hybridization technology for high-resolution detection of DNA copy number and structural variations

2021 ◽  
Author(s):  
Li-Chong Wang ◽  
Farzaneh Tondnevis ◽  
Courtney Todorov ◽  
Jayson Gaspar ◽  
Aparna Sahajan ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Copy Number ◽  
Structural Variations ◽  
Dna Copy Number ◽  
Chromogenic In Situ Hybridization

Identification and characterization of normal length nonfluorescent Y chromosomes: cytogenetic analysis, Southern hybridization and non-isotopic in situ hybridization

1990 ◽  
Vol 85 (6) ◽  
pp. 569-575 ◽  
Author(s):  
Frank Speleman ◽  
Bart Van der Auwera ◽  
Kathelijne Mangelschots ◽  
Miet Vercruyssen ◽  
Ton Raap ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Cytogenetic Analysis ◽  
Southern Hybridization ◽  
Normal Length ◽  
Y Chromosomes ◽  
Identification And Characterization

scholarly journals In situ analysis of FGFR2 mRNA and comparison with FGFR2 gene copy number by dual-color in situ hybridization in a large cohort of gastric cancer patients

2017 ◽  
Vol 21 (3) ◽  
pp. 401-412 ◽  
Author(s):  
Yasutoshi Kuboki ◽  
Christoph A. Schatz ◽  
Karl Koechert ◽  
Sabine Schubert ◽  
Janine Feng ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
In Situ Hybridization ◽  
Cancer Patients ◽  
Copy Number ◽  
Gene Copy Number ◽  
In Situ Analysis ◽  
Gene Copy ◽  
Fgfr2 Gene ◽  
Gastric Cancer Patients

Use of Chromogenic In Situ Hybridization to Identify MYCN Gene Copy Number in Neuroblastoma Using Routine Tissue Sections

2006 ◽  
Vol 30 (5) ◽  
pp. 635-642 ◽  
Author(s):  
Paul S. Thorner ◽  
Michael Ho ◽  
Susan Chilton-MacNeill ◽  
Maria Zielenska
Keyword(s):  
In Situ Hybridization ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Tissue Sections ◽  
Mycn Gene ◽  
Chromogenic In Situ Hybridization

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.

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