Application of fiber-FISH in physical mapping of Arabidopsis thaliana

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 566-572 ◽  
Author(s):  
Scott A Jackson ◽  
Ming Li Wang ◽  
Howard M Goodman ◽  
Jiming Jiang
Keyword(s):  
Arabidopsis Thaliana ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Physical Mapping ◽  
Molecular Techniques ◽  
Fish Analysis ◽  
Contig Assembly ◽  
Fish Technique ◽  
Bac Clones

Arabidopsis thaliana has become a model plant species for genetic studies because of its small genome and short juvenility period. However, the small chromosomes of this species are not suitable for classical cytogenetic studies. Here we demonstrate that the fluorescence in situ hybridization (FISH) technique using extended DNA fibers can be a powerful tool in the physical mapping of the A. thaliana genome. Using a refined fiber-FISH technique we were able to measure DNA clusters as long as 1.71 Mb, more than 1% of the A. thaliana genome. Several small DNA loci, including the telomeres and a dispersed repetitive DNA sequence, mi167, were also analyzed with this technique. The results show that without known adjacent DNA markers such small DNA loci cannot be mapped precisely using fiber-FISH. One of the most difficult obstacles in physical mapping by contig assembly is closing the gaps that are present between adjacent contigs. Currently available molecular techniques are not sufficient to accurately estimate the physical sizes of these gaps. We isolated bacterial artificial chromosome (BAC) clones bordering gaps 2 and 3 on the physical contig map of A. thaliana chromosome II. The BAC clones were used in fiber-FISH analysis and the physical sizes of the two gaps were estimated as 31 kb and more than 500 kb, respectively. Thus, we have demonstrated that fiber-FISH is an efficient technique for determining the physical size of gaps on molecular contig maps. Key words: fluorescence in situ hybridization, DNA fibers, physical mapping, genome analysis.

scholarly journals High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres

1996 ◽  
Vol 9 (3) ◽  
pp. 421-430 ◽  
Author(s):  
Paul F. Fransz ◽  
Carlos Alonso-Blanco ◽  
Tsvetana B. Liharska ◽  
Anton J.M. Peeters ◽  
Pim Zabel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
In Situ Hybridization ◽  
High Resolution ◽  
Fluorescence In Situ Hybridization ◽  
Physical Mapping ◽  
Extended Dna Fibres

scholarly journals Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 833-838 ◽  
Author(s):  
Scott A Jackson ◽  
Zhukuan Cheng ◽  
Ming Li Wang ◽  
Howard M Goodman ◽  
Jiming Jiang
Keyword(s):  
Arabidopsis Thaliana ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Brassica Rapa ◽  
Physical Mapping ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Comparative Genome ◽  
Artificial Chromosomes

Abstract Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

scholarly journals Application of the FISH Technique to Visualize Sex Chromosomes in Domestic Cat Spermatozoa

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2106
Author(s):  
Barbara Kij-Mitka ◽  
Halina Cernohorska ◽  
Svatava Kubickova ◽  
Sylwia Prochowska ◽  
Wojciech Niżański ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Sex Chromosomes ◽  
Chromosomal Abnormalities ◽  
Molecular Cytogenetics ◽  
Molecular Probes ◽  
Domestic Cat ◽  
Fish Technique ◽  
Y Chromosomes

Fluorescence in situ hybridization is a molecular cytogenetics technique that enables the visualization of chromosomes in cells via fluorescently labeled molecular probes specific to selected chromosomes. Despite difficulties in carrying out the FISH technique on sperm, related to the need for proper nuclear chromatin decondensation, this technique has already been used to visualize chromosomes in human, mouse, cattle, swine, horse, and dog spermatozoa. Until now, FISH has not been performed on domestic cat sperm; therefore, the aim of this study was to visualize sex chromosomes in domestic cat sperm. The results showed the presence of X and Y chromosomes in feline spermatozoa. The procedure used for sperm decondensation and fluorescence in situ hybridization was adequate to visualize chromosomes in domestic cat spermatozoa and, in the future, it may be used to determine the degree of chromosomal abnormalities in these gametes.

Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 179-189 ◽  
Author(s):  
J L Stephens ◽  
S E Brown ◽  
N L.V Lapitan ◽  
D L Knudson
Keyword(s):  
In Situ Hybridization ◽  
Hordeum Vulgare ◽  
Fluorescence In Situ Hybridization ◽  
Linkage Map ◽  
Physical Mapping ◽  
Physical Map ◽  
Primary Objective ◽  
Hybridization Technique ◽  
Hordeum Vulgare L

The primary objective of this study was to elucidate gene organization and to integrate the genetic linkage map for barley (Hordeum vulgare L.) with a physical map using ultrasensitive fluorescence in situ hybridization (FISH) techniques for detecting signals from restriction fragment length polymorphism (RFLP) clones. In the process, a single landmark plasmid, p18S5Shor, was constructed that identified and oriented all seven of the chromosome pairs. Plasmid p18S5Shor was used in all hybridizations. Fourteen cDNA probes selected from the linkage map for barley H. vulgare 'Steptoe' × H. vulgare 'Morex' (Kleinhofs et al. 1993) were mapped using an indirect tyramide signal amplification technique and assigned to a physical location on one or more chromosomes. The haploid barley genome is large and a complete physical map of the genome is not yet available; however, it was possible to integrate the linkage map and the physical locations of these cDNAs. An estimate of the ratio of base pairs to centimorgans was an average of 1.5 Mb/cM in the distal portions of the chromosome arms and 89 Mb/cM near the centromere. Furthermore, while it appears that the current linkage maps are well covered with markers along the length of each arm, the physical map showed that there are large areas of the genome that have yet to be mapped.Key words: Hordeum vulgare, barley, physical mapping, FISH, cDNA, genetics, linkage, chromosome, BACs.

scholarly journals Characterizing Atypical BCL6 Signal Patterns Detected by Digital Fluorescence In Situ Hybridization (FISH) Analysis

2018 ◽  
Vol 38 (6) ◽  
pp. 619-622
Author(s):  
Michael Liew ◽  
Leslie R. Rowe ◽  
Phillipe Szankasi ◽  
Christian N. Paxton ◽  
Todd Kelley ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Fish Analysis

scholarly journals Fluorescence In Situ Hybridization (FISH) Analysis of the Locations of the Oligonucleotides 5S rDNA, (AGGGTTT)3, and (TTG)6 in Three Genera of Oleaceae and Their Phylogenetic Framework

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 375 ◽  
Author(s):  
Xiaomei Luo ◽  
Juncheng Liu
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
5S Rdna ◽  
Fish Analysis ◽  
Cytogenetic Map ◽  
Ligustrum Lucidum ◽  
Starting Point ◽  
Central Regions ◽  
Almost All

We report the cytogenetic map for a collection of species in the Oleaceae, and test similarities among the karyotypes relative to their known species phylogeny. The oligonucleotides 5S ribosomal DNA (rDNA), (AGGGTTT)3, and (TTG)6 were used as fluorescence in situ hybridization (FISH) probes to locate the corresponding chromosomes in three Oleaceae genera: Fraxinus pennsylvanica, Syringa oblata, Ligustrum lucidum, and Ligustrum × vicaryi. Forty-six small chromosomes were identified in four species. (AGGGTTT)3 signals were observed on almost all chromosome ends of four species, but (AGGGTTT)3 played no role in distinguishing the chromosomes but displayed intact chromosomes and could thus be used as a guide for finding chromosome counts. (TTG)6 and 5S rDNA signals discerned several chromosomes located at subterminal or central regions. Based on the similarity of the signal pattern (mainly in number and location and less in intensity) of the four species, the variations in the 5S rDNA and (TTG)6 distribution can be ordered as L. lucidum < L. × vicaryi < F. pennsylvanica < S. oblata. Variations have observed in the three genera. The molecular cytogenetic data presented here might serve as a starting point for further larger-scale elucidation of the structure of the Oleaceae genome, and comparison with the known phylogeny of Oleaceae family.

Physical mapping of connexin 32 (GJB1) and 43 (GJA1) genes to bovine Chromosomes Xq22 and 9q15/16 by fluorescence in situ hybridization

1996 ◽  
Vol 7 (8) ◽  
pp. 634-635 ◽  
Author(s):  
B. Castiglioni ◽  
L. Ferretti ◽  
M. L. Tenchini ◽  
A. Mezzelani ◽  
T. Simonic ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Physical Mapping ◽  
Connexin 32

scholarly journals Comparative Performance of Breast Cancer Human Epidermal Growth Factor Receptor 2 Fluorescence In Situ Hybridization and Brightfield In Situ Hybridization on College of American Pathologists Proficiency Tests

2018 ◽  
Vol 142 (10) ◽  
pp. 1254-1259 ◽  
Author(s):  
Katherine B. Geiersbach ◽  
Julia A. Bridge ◽  
Michelle Dolan ◽  
Lawrence J. Jennings ◽  
Diane L. Persons ◽  
...  
Keyword(s):  
Breast Cancer ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Proficiency Testing ◽  
Copy Number ◽  
Fish Analysis ◽  
Proficiency Tests ◽  
Comparative Performance ◽  
Significant Difference

Context.— Fluorescence in situ hybridization (FISH) and brightfield in situ hybridization (ISH) are 2 clinically approved laboratory methods for detecting ERBB2 (HER2) amplification in breast cancer. Objective.— To compare the performance of FISH and brightfield ISH on proficiency testing administered by the College of American Pathologists Laboratory Accreditation Program. Design.— Retrospective review was performed on 70 tissue core samples in 7 separate proficiency testing surveys conducted between 2009 and 2013. Results.— The samples included 13 consensus-amplified tissue cores, 53 consensus-nonamplified cores, and 4 cores that did not reach consensus for FISH and/or brightfield ISH. There were 2552 individual responses for FISH and 1871 individual responses for brightfield ISH. Consensus response rates were comparable for FISH (2474 of 2524; 98.0%) and brightfield ISH (2135 of 2189; 97.5%). The FISH analysis yielded an average HER2 copy number per cell that was significantly higher (by 2.86; P = .02) compared with brightfield ISH for amplified cores. For nonamplified cores, FISH yielded slightly, but not significantly, higher (by 0.17; P = .10) HER2 copy numbers per cell. There was no significant difference in the average HER2 to control ratio for either consensus-amplified or consensus-nonamplified cores. Participants reported “unable to analyze” more frequently for brightfield ISH (244 of 2453; 9.9%) than they did for FISH (160 of 2684; 6.0%). Conclusions.— Our study indicates a high concordance rate in proficiency testing surveys, with some significant differences noted in the technical performance of these assays. In borderline cases, updated American Society of Clinical Oncology/College of American Pathologists cutoff thresholds that place greater emphasis on HER2 copy number per cell could accentuate those differences between FISH and brightfield ISH.

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