Direct FISH of 5S rDNA on tomato pachytene chromosomes places the gene at the heterochromatic knob immediately adjacent to the centromere of chromosome 1

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 216-221 ◽  
Author(s):  
Jie Xu ◽  
E. D. Earle
Keyword(s):  
Rare Event ◽  
5S Rdna ◽  
Heterochromatic Region ◽  
Conclusive Evidence ◽  
Chromosome 1 ◽  
Cytogenetic Map ◽  
Rdna Gene ◽  
Molecular Cytogenetic ◽  
Direct Fluorescence

We describe a molecular cytogenetic procedure for high resolution physical mapping of DNA markers, an essential step toward construction of an integrated molecular–classical–cytological map. Tomato was selected as material because its pachytene chromosomes are amenable for study and because detailed molecular, classical, and cytological maps are available. Karyotyping of acetocarmine-stained pachytene chromosomes showing detailed cytogenetic landmarks was combined with direct FISH of the 5S rDNA gene. This enabled us to pinpoint the 5S rDNA gene to the first heterochromatic knob immediately adjacent to the centromere in the short arm of chromosome 1. Thus the position of the 5S rDNA gene on the molecular map was related to the position of the 5S rDNA on the cytogenetic map. The results also provide conclusive evidence of the location of a functional gene in the pericentric heterochromatic region, a rare event to date in plants. We conclude that karyotyping of pachytene chromosomes can be combined with FISH to map a DNA sequence to a cytogenetically defined region and to determine the chromatin origin of an expressed gene. Key words : direct fluorescence in situ hybridization, 5S rDNA, pachytene chromosomes, heterochromatic gene.

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.

scholarly journals Molecular cytogenetic studies in rubber, Hevea brasiliensis Muell. Arg. (Euphorbiaceae)

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 464-467 ◽  
Author(s):  
Andrew R Leitch ◽  
K Yoong Lim ◽  
Ilia J Leitch ◽  
Michelle O'Neill ◽  
MeeLen Chye ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Ribosomal Dna ◽  
Hevea Brasiliensis ◽  
Consensus Sequence ◽  
Molecular Cytogenetics ◽  
5S Rdna ◽  
Single Pair ◽  
Interphase Nuclei ◽  
Molecular Cytogenetic

This paper reports the start of a molecular cytogenetics programme targeting the genome of the angiosperm tree species Hevea brasiliensis Muell. Arg. (rubber, 2n = 36), a major world crop about whose genetics very little is known. A metaphase karyotype of rubber is presented. In situ hybidization with the probe pTa71 for ribosomal DNA (rDNA) shows that there are four sites of probe hybidization occurring on two pairs of chromosomes called chromosomes 6 and 7 carrying sites NOR-1 and NOR-2, respectively. An examination of meristematic interphase nuclei shows that all four loci have the potential to be partially decondensed at interphase, although in many nuclei one or more loci appear fully condensed and apparently inactive. The probe pXVI revealed a single pair of chromosomes carrying 5S rDNA. The probes pTa71 and pXVI provide cytogenetic markers for three pairs of chromosomes that will be of use in genetic mapping programmes. The rubber chromosomes also have telomere sequences that hybridize with the Arabidopsis consensus sequence TTTAGGG. With the exception of the satellite region containing rDNA, which fluoresces brightly with chromomycin A3, fluorescence banding showed that there is no strong demarcation of the genome into GC- and AT-rich regions, as occurs in mammalian genomes.Key words: rubber, Hevea, genetic mapping, cytogenetics, ribosomal DNA, rDNA fluorescence banding.

Heterochromatin patterns and ribosomal DNA loci distribution in diploid and polyploid Crotalaria species (Leguminosae, Papilionoideae), and inferences on karyotype evolution

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 718-726 ◽  
Author(s):  
Mateus Mondin ◽  
Margarida L.R. Aguiar-Perecin
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Karyotype Evolution ◽  
5S Rdna ◽  
Rdna Locus ◽  
Variable Number ◽  
Chromosome 1 ◽  
Distamycin A ◽  
Rdna Sites

Most Crotalaria species display a symmetric karyotype with 2n = 16, but 2n = 14 is found in Chrysocalycinae subsection Incanae and 2n = 32 in American species of the section Calycinae. Seven species of the sections Chrysocalycinae, Calycinae, and Crotalaria were analyzed for the identification of heterochromatin types with GC- and AT-specific fluorochromes and chromosomal location of ribosomal DNA loci using fluorescent in situ hybridization (FISH). A major 45S rDNA locus was observed on chromosome 1 in all the species, and a variable number of minor ones were revealed. Only one 5S rDNA locus was observed in the species investigated. Chromomycin A3 (CMA) revealed CMA+ bands colocalized with most rDNA loci, small bands unrelated to ribosomal DNA on two chromosome pairs in Crotalaria incana, and CMA+ centromeric bands that were quenched by distamycin A were detected in species of Calycinae and Crotalaria sections. DAPI+ bands were detected in C. incana. The results support the species relationships based on flower specialization and were useful for providing insight into mechanisms of karyotype evolution. The heterochromatin types revealed by fluorochromes suggest the occurrence of rearrangements in repetitive DNA families in these heterochromatic blocks during species diversification. This DNA sequence turnover and the variability in number/position of rDNA sites could be interpreted as resulting from unequal crossing over and (or) transposition events. The occurrence of only one 5S rDNA locus and the smaller chromosome size in the polyploids suggest that DNA sequence losses took place following polyploidization events.

Physical organization of the major duplication on Brassica oleracea chromosome O6 revealed through fluorescence in situ hybridization with Arabidopsis and Brassica BAC probes

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1093-1103 ◽  
Author(s):  
E C Howell ◽  
S J Armstrong ◽  
G C Barker ◽  
G H Jones ◽  
G J King ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Brassica Oleracea ◽  
Artificial Chromosome ◽  
Genetic Distances ◽  
Chromosome 1 ◽  
Cytogenetic Map ◽  
Inverted Duplication ◽  
Close Relationship

The close relationship between Brassica oleracea and Arabidopsis thaliana has been used to explore the genetic and physical collinearity of the two species, focusing on an inverted segmental chromosome duplication within linkage group O6 of B. oleracea. Genetic evidence suggests that these segments share a common origin with a region of Arabidopsis chromosome 1. Brassica oleracea and Arabidopsis bacterial artificial chromosome probes have been used for fluorescence in situ hybridization analysis of B. oleracea pachytene chromosomes to further characterize the inverted duplication. This has been highly effective in increasing the local resolution of the cytogenetic map. We have shown that the physical order of corresponding genetic markers is highly conserved between the duplicated regions in B. oleracea and the physical lengths of the regions at pachytene are similar, while the genetic distances are considerably different. The physical marker order is also well conserved between Arabidopsis and B. oleracea, with only one short inversion identified. Furthermore, the relative physical distances between the markers in one segment of B. oleracea and Arabidopsis have stayed approximately the same. The efficacy of using fluorescence in situ hybridization, together with other forms of physical and genetic mapping, for elucidating such issues relating to synteny is discussed.Key words: collinearity, cytogenetic map, pachytene chromosomes, Brassica, Arabidopsis.

Physical mapping of four sites of 5S rDNA sequences and one site of the α-amylase-2 gene in barley (Hordeum vulgare)

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 517-523 ◽  
Author(s):  
I. J. Leitch ◽  
J. S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Hordeum Vulgare ◽  
Physical Mapping ◽  
5S Rdna ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Hordeum Vulgare L ◽  
Rdna Sequences ◽  
5S Rdna Sequence

The 5S rDNA sequences have been mapped on four pairs of barley (Hordeum vulgare L.) chromosomes using in situ hybridization and barley monotelotrisomic lines. The 5S rDNA sequences are located, genetically and physically, on the short arm of chromosome 1 (7I) and the long arms of chromosomes 2 (2I) and 3 (3I). The 5S rDNA sequence is also located on the physically long arm of chromosome 4 (4I). Only one site on chromosome 2(2I) has previously been reported. The characteristic locations of the 5S rDNA sequences make them useful as molecular markers to identify each barley chromosome. The physical position of the low-copy α-amylase-2 gene was determined using in situ hybridization; the location of this gene on the long arm of chromosome 1 (7I) was confirmed by reprobing the same preparation with the 5S rDNA probe. The results show that there is a discrepancy between the physical and genetic position of the α-amylase-2 gene.Key words: genetic mapping, physical mapping, barley, mapping, 5S DNA, α-amylase, in situ hybridization.

Physical mapping of the 5S rDNA gene complex in rice (Oryza sativa)

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 658-661 ◽  
Author(s):  
Y. C. Song ◽  
J. P. Gustafson
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Rice Chromosome ◽  
5S Rdna ◽  
Rice Cultivar ◽  
Chromosome 9 ◽  
Gene Complex ◽  
Rdna Gene ◽  
Biotin Labelling

This study was designed to use biotin labelling in situ hybridization to physically map the 5S rDNA genes to a chromosome arm location in rice. Chromosome preparations were made using an improved protoplast technique, which resulted in more mitotic cells with less overlying cytoplasmic and cellular debris. Cells in which both chromatids were labelled were observed. The hybridization detection level for the 5S rDNA gene complex was 17.22%. The results established that the 5S rDNA gene complex of rice is located at the end of the short arm of chromosome 9 in rice cultivar IR36. The similarities and differences of the 5S rDNA gene complex location between rice and other cereals and advantages of in situ hybridization for physical mapping are discussed.Key words: biotin labelling, in situ hybridization.

scholarly journals Characterization of Spinach Chromosomes by Condensation Patterns and Physical Mapping of 5S and 45S rDNAs by FISH

2000 ◽  
Vol 125 (1) ◽  
pp. 59-62 ◽  
Author(s):  
Mikako Ito ◽  
Nobuko Ohmido ◽  
Yukio Akiyama ◽  
Kiichi Fukui ◽  
Takato Koba
Keyword(s):  
Spinacia Oleracea ◽  
5S Rdna ◽  
Proximal Region ◽  
Chromosome 2 ◽  
Chromosome 5 ◽  
Molecular Cytogenetic ◽  
Nucleolar Organizing Region ◽  
Molecular Cytogenetic Techniques

Molecular cytogenetic techniques and computer-aided karyotyping were applied to characterize the chromosomes of spinach (Spinacia oleracea L., 2n = 12). Chromosome lengths, arm ratios, and degrees of condensation at prometaphase chromosomes were analyzed using a software Chromosome Image Analyzing System III (CHIAS III). DNA probes prepared from rice (Oryza sativa L.) rDNA were applied to the spinach chromosomes by the fluorescence in situ hybridization (FISH) method. Three 45S rDNA loci were detected at the nucleolar organizing region (NOR) of Chromosome 5, and at terminal positions of short arms of Chromosomes 2 and 6. The loci of 5S rDNA were also found at three locations. One was at the subtelomeric region of the long arm of Chromosome 2 and the other two were at the proximal region of the long arm of Chromosome 5. All spinach chromosomes were identified which will provide valuable information for mapping genes on these chromosomes.

scholarly journals Molecular cytogenetic study of Eranthis (Ranunculaceae)

2021 ◽  
Vol 20 (1) ◽  
pp. 305-308
Author(s):  
E. Yu. Mitrenina ◽  
A. S. Erst ◽  
E. D. Badaeva ◽  
S. S. Alekseeva ◽  
G. N. Artemov
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Ribosomal Dna ◽  
Cytogenetic Study ◽  
5S Rdna ◽  
45S Rdna ◽  
5.8S Rdna ◽  
Molecular Cytogenetic ◽  
Specific Hybridization

45S and 5S ribosomal DNA were originally localized on chromosomes of five species of winter aconits,namely, Eranthis cilicica, E. hyemalis (section Eranthis), E. pinnatifida, E. stellata и E. tanhoensis (section Shibateranthis).Fluorescence in situ hybridization was performed with oligonucleotide DNA probes Oligo-pTa71-2 and Oligo-5S rDNAof wheat that are complementary to 45S and 5S ribosomal DNA. In addition, oligonucleotide DNA probe (Oligo-5.8SrDNA-Ran, 50 b) for localization of 45S rDNA was designed and tested. This probe is based on the 5.8S rDNA sequencesof some species of fam. Ranunculaceae taken from GenBank. A specific hybridization of the Oligo-5S rDNA and Oligo5.8S rDNA-Ran probes with the chromosomes of Eranthis was shown. The use of the Oligo-pTa71-2 probe did not localizeclusters of 45S rDNA on chromosomes of studied species.

scholarly journals A Molecular Cytogenetic Map of Sorghum Chromosome1: Fluorescencein SituHybridization Analysis With Mapped Bacterial Artificial Chromosomes

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 345-353 ◽  
Author(s):  
M N Islam-Faridi ◽  
K L Childs ◽  
P E Klein ◽  
G Hodnett ◽  
M A Menz ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Linkage Map ◽  
Chromosome 1 ◽  
Fish Analysis ◽  
Cytogenetic Map ◽  
Structural Genomic ◽  
Artificial Chromosomes ◽  
Molecular Cytogenetic ◽  
Genomic Resources ◽  
Bac Fish

AbstractWe used structural genomic resources for Sorghum bicolor (L.) Moench to target and develop multiple molecular cytogenetic probes that would provide extensive coverage for a specific chromosome of sorghum. Bacterial artificial chromosome (BAC) clones containing molecular markers mapped across sorghum linkage group A were labeled as probes for fluorescence in situ hybridization (FISH). Signals from single-, dual-, and multiprobe BAC-FISH to spreads of mitotic chromosomes and pachytene bivalents were associated with the largest sorghum chromosome, which bears the nucleolus organizing region (NOR). The order of individual BAC-FISH loci along the chromosome was fully concordant to that of marker loci along the linkage map. In addition, the order of several tightly linked molecular markers was clarified by FISH analysis. The FISH results indicate that markers from the linkage map positions 0.0-81.8 cM reside in the short arm of chromosome 1 whereas markers from 81.8-242.9 cM are located in the long arm of chromosome 1. The centromere and NOR were located in a large heterochromatic region that spans ∼60% of chromosome 1. In contrast, this region represents only 0.7% of the total genetic map distance of this chromosome. Variation in recombination frequency among euchromatic chromosomal regions also was apparent. The integrated data underscore the value of cytological data, because minor errors and uncertainties in linkage maps can involve huge physical regions. The successful development of multiprobe FISH cocktails suggests that it is feasible to develop chromosome-specific “paints” from genomic resources rather than flow sorting or microdissection and that when applied to pachytene chromatin, such cocktails provide an especially powerful framework for mapping. Such a molecular cytogenetic infrastructure would be inherently cross-linked with other genomic tools and thereby establish a cytogenomics system with extensive utility in development and application of genomic resources, cloning, transgene localization, development of plant “chromonomics,” germplasm introgression, and marker-assisted breeding. In combination with previously reported work, the results indicate that a sorghum cytogenomics system would be partially applicable to other gramineous genera.

scholarly journals Cytogenetic markers using single-sequence probes reveal chromosomal locations of tandemly repetitive genes in scleractinian coral Acropora pruinosa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Joshua Vacarizas ◽  
Takahiro Taguchi ◽  
Takuma Mezaki ◽  
Masatoshi Okumura ◽  
Rei Kawakami ◽  
...  
Keyword(s):  
5S Rdna ◽  
Chromosome 8 ◽  
Chromosome 1 ◽  
Core Histone ◽  
Small Nuclear Rna ◽  
Banding Patterns ◽  
Rdna Probe ◽  
Rdna Sequences ◽  
Single Sequence

AbstractThe short and similar sized chromosomes of Acropora pose a challenge for karyotyping. Conventional methods, such as staining of heterochromatic regions, provide unclear banding patterns that hamper identification of such chromosomes. In this study, we used short single-sequence probes from tandemly repetitive 5S ribosomal RNA (rRNA) and core histone coding sequences to identify specific chromosomes of Acropora pruinosa. Both the probes produced intense signals in fluorescence in situ hybridization, which distinguished chromosome pairs. The locus of the 5S rDNA probe was on chromosome 5, whereas that of core histone probe was on chromosome 8. The sequence of the 5S rDNA probe was composed largely of U1 and U2 spliceosomal small nuclear RNA (snRNA) genes and their interspacers, flanked by short sequences of the 5S rDNA. This is the first report of a tandemly repetitive linkage of snRNA and 5S rDNA sequences in Cnidaria. Based on the constructed tentative karyogram and whole genome hybridization, the longest chromosome pair (chromosome 1) was heteromorphic. The probes also hybridized effectively with chromosomes of other Acropora species and population, revealing an additional core histone gene locus. We demonstrated the applicability of short-sequence probes as chromosomal markers with potential for use across populations and species of Acropora.

Sign in / Sign up

Export Citation Format

Share Document