Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes

5S rDNA loci have been mapped on barley chromosomes by in situ hybridization using five reciprocal translocation lines. Two kinds of DNA probes covering either the 5S rDNA coding region or the 5S rDNA coding and flanking noncoding regions were used. They were prepared by direct cloning from interphase nuclei and simultaneous direct labeling in PCR. Four 5S rDNA loci were detected in a haploid genome by the 5S rDNA coding region, whereas in addition, the four or six 5S rDNA related sites, depending on the variety used, were revealed by the probe covering the flanking region. The four 5S rDNA loci revealed and mapped on the barley chromosomes: 2 (2I), 3 (3I), 1 (7I), and 4 (4I) were designated 5SRrn-I1, 5SRrn-I2, 5SRrn-I3 and 5SRrn-I4, respectively, in descending order of copy number of 5S rRNA genes.Key words: Hordeum vulgare, 5S rDNA, in situ hybridization, direct cloning, direct labeling.

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The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽

10.1139/g96-068 ◽

1996 ◽

Vol 39 (3) ◽

pp. 535-542 ◽

Cited By ~ 63

Author(s):

Concha Linares ◽

Juan González ◽

Esther Ferrer ◽

Araceli Fominaya

Keyword(s):

In Situ Hybridization ◽

Dna Sequence ◽

Diploid Species ◽

5S Rdna ◽

Rdna Genes ◽

26S Rdna ◽

A Genome ◽

Rdna Loci ◽

C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

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Detection of a variable number of 18S-5.8S-26S and 5S ribosomal DNA loci by fluorescent in situ hybridization in diploid and tetraploid Arachis species

Genome ◽

10.1139/g98-092 ◽

1999 ◽

Vol 42 (1) ◽

pp. 52-59 ◽

Cited By ~ 27

Author(s):

S N Raina ◽

Y Mukai

Keyword(s):

In Situ Hybridization ◽

5S Rdna ◽

Gene Families ◽

Ribosomal Gene ◽

Rrna Genes ◽

Tetraploid Species ◽

Arachis Species ◽

26S Rdna ◽

Rdna Loci

In order to obtain new information on the genome organization of Arachis ribosomal DNA, more particularly among A. hypogaea and its close relatives, the distribution of the 18S-5.8S-26S and 5S ribosomal RNA gene families on the chromosomes of 21 diploid and tetraploid Arachis species, selected from six of nine taxonomic sections, was analyzed by in situ hybridization with pTa71 (18S-5.8S-26S rDNA) and pTa794 (5S rDNA) clones. Two major 18S-5.8S-26S rDNA loci with intense signals were found in the nucleolus organizer regions (NOR) of each of the diploid and tetraploid species. In addition to extended signals at major NORs, two to six medium and (or) minute-sized signals were also observed. Variability in the number, size, and location of 18S-5.8S-26S sites could generally distinguish species within the same genome as well as between species with different genomes. The use of double fluorescence in situ hybridization enabled us to locate the positions of 5S rRNA genes in relation to the chromosomal location of 18S-5.8S-26S rRNA genes in Arachis chromosomes which were difficult to karyotype. Two or four 5S rDNA loci and 18S-5.8S-26S rDNA loci were generally located on different chromosomes. The tandemly repeated 5S rDNA sites were diagnostic for T and C genomes. In one species, each of B and Am genomes, the two ribosomal gene families were observed to occur at the same locus. Barring A. ipaensis and A. valida, all the diploid species had characteristic centromeric bands in all the 20 chromosomes. In tetraploid species A. hypogaea and A. monticola only 20 out of 40 chromosomes showed centromeric bands. Comparative studies of distribution of the two ribosomal gene families, and occurrence of centromeric bands in only 20 chromosomes of the tetraploid species suggests that A. villosa and A. ipaensis are the diploid progenitors of A. hypogaea and A. monticola. This study excludes A. batizocoi as the B genome donor species for A. hypogaea and A. monticola.Key words: Arachis species, 5S rRNA, 18S-5.8S-26S rRNA, in situ hybridization, evolution.

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Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽

10.1139/g11-035 ◽

2011 ◽

Vol 54 (9) ◽

pp. 710-717 ◽

Cited By ~ 26

Author(s):

B. Kolano ◽

B.W. Gardunia ◽

M. Michalska ◽

A. Bonifacio ◽

D. Fairbanks ◽

...

Keyword(s):

In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Repetitive Sequences ◽

Chenopodium Quinoa ◽

5S Rdna ◽

Rrna Gene ◽

Fish Analysis ◽

Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

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Genome differentiation in Aegilops. 2. Physical mapping of 5S and 18S–26S ribosomal RNA gene families in diploid species

Genome ◽

10.1139/g96-145 ◽

1996 ◽

Vol 39 (6) ◽

pp. 1150-1158 ◽

Cited By ~ 77

Author(s):

Ekatherina D. Badaeva ◽

Bernd Friebe ◽

Bikram S. Gill

Keyword(s):

In Situ Hybridization ◽

Ribosomal Rna ◽

5S Rdna ◽

Gene Families ◽

Aegilops Species ◽

Ribosomal Rna Gene ◽

26S Rdna ◽

Genome Differentiation ◽

Rdna Loci

The distribution of the 5S and 18S–5.8S–26S (18S–26S) ribosomal RNA (rRNA) gene families on chromosomes of all diploid Aegilops species was studied by in situ hybridization with pTa71 (18S–26S rDNA) and pTa794 (5S rDNA) DNA clones. One major 18S–26S rDNA locus was found in the nucleolus organizer region (NOR) of each of the species Aegilops tauschii and Aegilops uniaristata and two loci were detected in the remaining species. In addition to major NORs, from one to nine minor loci were observed; their numbers and chromosomal locations were species-specific. Some minor loci were polymorphic, whereas others were conserved. One or two 5S rDNA loci were observed in the short arms of the chromosomes of groups 1 and 5 of all diploid Aegilops species except Ae. uniaristata, where one 5S rDNA site was located in the distal part of the long arm of chromosome 1N. The 5S rDNA loci were not associated with NORs; however, the relative positions of two ribosomal RNA gene families were diagnostic for chromosomes of homoeologous groups 1, 5, and 6. Implications of these results for establishing phylogenetic relationships of diploid Aegilops species and mechanisms of genome differentiation are discussed. Key words : wheat, Triticum, Aegilops, 5S rRNA, 18S–26S rRNA, in situ hybridization, evolution.

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FISH analysis of Zanthoxylum armatum based on oligonucleotides for 5S rDNA and (GAA)6

Genome ◽

10.1139/gen-2018-0009 ◽

2018 ◽

Vol 61 (9) ◽

pp. 699-702 ◽

Cited By ~ 3

Author(s):

Xiaomei Luo ◽

Juncheng Liu ◽

Jingyan Wang ◽

Wei Gong ◽

Liang Chen ◽

...

Keyword(s):

In Situ Hybridization ◽

5S Rdna ◽

Fish Analysis ◽

Oligonucleotide Probes ◽

Mitotic Metaphase ◽

Metaphase Chromosomes ◽

Zanthoxylum Armatum ◽

Rdna Loci ◽

Cytogenetic Studies

Fluorescence in situ hybridization (FISH) using oligonucleotide probes for (GAA)6 (18 bp) and ribosomal DNA (rDNA) (5S rDNA, 41 bp) was applied to analyse Zanthoxylum armatum. (GAA)6 loci were detected on the pericentromeric regions of five chromosome pairs, and 5S rDNA loci were also detected on the pericentromeric regions of another two chromosome pairs. The densities and locations of (GAA)6 and 5S rDNA signals varied between individual chromosomes. High-intensity (GAA)6 signals were detected at the centromeres of two large and two smaller metacentric chromosomes. Relatively strong (GAA)6 signals were detected at the centromeres of two relatively small metacentric chromosomes, although strong 5S rDNA signals were detected at the centromeres of two additional smaller metacentric chromosomes. Weak (GAA)6 signals were detected at the centromeres of four large metacentric chromosomes, whereas weak 5S rDNA signals were detected at the centromeres of two smaller metacentric chromosomes. The remaining chromosomes exhibited no signals. Zanthoxylum armatum had 2n = ∼128. The lengths of the mitotic metaphase chromosomes ranged from 1.22 to 2.34 μm. Our results provide information that may be beneficial for future cytogenetic studies and could contribute to the physical assembly of the Zanthoxylum genome.

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Molecular cytogenetic analysis ofAegilops cylindrica Host

Genome ◽

10.1139/g98-151 ◽

1999 ◽

Vol 42 (3) ◽

pp. 497-503 ◽

Cited By ~ 32

Author(s):

Gabriella Linc ◽

Bernd R Friebe ◽

Ralf G Kynast ◽

Marta Molnar-Lang ◽

Bela Köszegi ◽

...

Keyword(s):

In Situ Hybridization ◽

5S Rdna ◽

Rdna Locus ◽

Fish Analysis ◽

Aegilops Cylindrica ◽

Fish Genome ◽

C Banding ◽

Rdna Loci ◽

25S Rdna

The genomic constitution of Aegilops cylindrica Host (2n = 4x = 28, DcDcCcCc) was analyzed by C-banding, genomic in situ hybridization (GISH), and fluorescence in situ hybridization (FISH) using the DNA clones pSc119, pAs1, pTa71, and pTA794. The C-banding patterns of the Dc- and Cc-genome chromosomes of Ae. cylindrica are similar to those of D-and C-genome chromosomes of the diploid progenitor species Ae. tauschii Coss. and Ae. caudata L., respectively. These similarities permitted the genome allocation and identification of the homoeologous relationships of the Ae. cylindrica chromosomes. FISH analysis detected one major 18S-5.8S-25S rDNA locus in the short arm of chromosome 1Cc. Minor 18S-5.8S-25S rDNA loci were mapped in the short arms of 5Dc and 5Cc. 5S rDNA loci were identified in the short arm of chromosomes 1Cc, 5Dc, 5Cc, and 1Dc. GISH analysis detected intergenomic translocation in three of the five Ae. cylindrica accessions. The breakpoints in all translocations were non-centromeric with similar-sized segment exchanges.Key words: Aegilops cylindrica, C-banding, GISH, FISH, genome evolution.

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