Intraspecific divergence in wheats of the Timopheevi group as revealed by in situ hybridization with tandem repeats of the Spelt1 and Spelt52 families

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.

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

Genetics ◽

10.1093/genetics/164.2.665 ◽

2003 ◽

Vol 164 (2) ◽

pp. 665-672 ◽

Cited By ~ 4

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.

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

Genome ◽

10.1139/g04-044 ◽

2004 ◽

Vol 47 (5) ◽

pp. 860-867 ◽

Cited By ~ 46

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.

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The pericentromeric heterochromatin of the grass Zingeria biebersteiniana (2n = 4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences

Genome ◽

10.1139/g01-092 ◽

2001 ◽

Vol 44 (6) ◽

pp. 955-961 ◽

Cited By ~ 19

Author(s):

Verity A Saunders ◽

Andreas Houben

Keyword(s):

In Situ Hybridization ◽

Tandem Repeat ◽

Tandem Repeats ◽

Repetitive Sequences ◽

Pericentromeric Region ◽

Pericentromeric Heterochromatin ◽

Repeat Family ◽

Dna Reassociation ◽

Copy Dna

DNA reassociation and hydroxyapatite chromatography were used to isolate high-copy DNA of the grass Zingeria biebersteiniana (2n = 4). In situ hybridization demonstrated that the DNA isolated was enriched for pericentromere-specific repetitive sequences. One abundant pericentromere-specific component is the differentially methylated tandem-repeat family Zbcen1. Other sequences isolated, Zb46 and Zb47A, are dispersed and display similarity to parts of the gypsy- and copia-like retrotransposable elements of other grasses. In situ hybridization with the copia-like sequence Zb47A resulted in dispersed labelling along the chromosome arms, with a significant signal accumulation in the pericentromeric region of all chromosomes. It is concluded that the pericentromeric heterochromatin of Z. biebersteiniana is composed of members of the Zbcen1 tandem repeat family and that these tandem arrays are intermingled with accumulated putative copia-like retrotransposon sequences. An observed Rabl interphase orientation suggests that the length of the chromosomes rather than the genome size is the determining factor of the Rabl phenomenon.Key Words: centromere, heterochromatin, tandemly repeated DNA, retrotransposon-like, DNA reassociation.

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Organization and distribution of a Sau3A tandem repeated DNA sequence in Picea (Pinaceae) species

Genome ◽

10.1139/g98-054 ◽

1998 ◽

Vol 41 (4) ◽

pp. 560-565 ◽

Cited By ~ 12

Author(s):

Garth R Brown ◽

Craig H Newton ◽

John E Carlson

Keyword(s):

In Situ Hybridization ◽

Dna Sequence ◽

Picea Glauca ◽

Tandem Repeats ◽

Picea Sitchensis ◽

Repeated Dna ◽

Metaphase Chromosomes ◽

Genes Encoding ◽

Repeated Dna Sequence

Repeated DNA families contribute to the large genomes of coniferous trees but are poorly characterized. We report the analysis of a 142 bp tandem repeated DNA sequence identified by the restriction enzyme Sau3A and found in approximately 20 000 copies in Picea glauca. Southern hybridization indicated that the repeated DNA family is specific to the genus, was amplified early in its evolution, and has undergone little structural alteration over evolutionary time. Fluorescence in situ hybridization localized arrays of the Sau3A repeating element to the centromeric regions of different subsets of the metaphase chromosomes of P. glauca and the closely related Picea sitchensis, suggesting that mechanisms leading to the intragenomic movement of arrays may be more active than those leading to mutation of the repeating elements themselves. Unambiguous identification of P. glauca and P. sitchensis chromosomes was made possible by co-localizing the Sau3A tandem repeats and the genes encoding the 5S and 18S-5.8S-26S ribosomal RNAs.Key words: Picea, repeated DNA, in situ hybridization, centromere.

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Molecular cytogenetic analysis of durum wheat × tritordeum hybrids

Genome ◽

10.1139/g97-049 ◽

1997 ◽

Vol 40 (3) ◽

pp. 362-369 ◽

Cited By ~ 11

Author(s):

J. Lima-Brito ◽

H. Guedes-Pinto ◽

G. E. Harrison ◽

J. S. Heslop-Harrison

Keyword(s):

In Situ Hybridization ◽

Plant Breeding ◽

Durum Wheat ◽

Dna Sequences ◽

Genomic Dna ◽

Tandem Repeats ◽

Nuclear Architecture ◽

Molecular Cytogenetics ◽

Hordeum Chilense

Southern and in situ hybridization were used to examine the chromosome constitution, genomic relationships, repetitive DNA sequences, and nuclear architecture in durum wheat × tritordeum hybrids (2n = 5x = 35), where tritordeum is the fertile amphiploid (2n = 6x = 42) between Hordeum chilense and durum wheat. Using in situ hybridization, H. chilense total genomic DNA hybridized strongly to the H. chilense chromosomes and weakly to the wheat chromosomes, which showed some strongly labelled bands. pHcKB6, a cloned repetitive sequence isolated from H. chilense, enabled the unequivocal identification of each H. chilense chromosome at metaphase. Analysis of chromosome disposition in prophase nuclei, using the same probes, showed that the chromosomes of H. chilense origin were in individual domains with only limited intermixing with chromosomes of wheat origin. Six major sites of 18S–26S rDNA genes were detected on the chromosomes of the hybrids. Hybridization to Southern transfers of restriction enzyme digests using genomic DNA showed some variants of tandem repeats, perhaps owing to methylation. Both techniques gave complementary information, extending that available from phenotypic, chromosome morphology, or isozyme analysis, and perhaps are useful for following chromosomes or chromosome segments during further crossing of the lines in plant breeding programs.Key words: In situ hybridization, molecular cytogenetics, plant breeding, Hordeum chilense, Southern hybridization, durum wheat, hybrids.

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Chromosomal mapping of tandem repeats in the Yesso Scallop, Patinopecten yessoensis (Jay, 1857), utilizing fluorescence in situ hybridization

Comparative Cytogenetics ◽

10.3897/compcytogen.v10i1.7391 ◽

2016 ◽

Vol 10 (1) ◽

pp. 157-169 ◽

Cited By ~ 6

Author(s):

Xiaoting Huang ◽

Xuan Li ◽

Zujing Yang ◽

Huan Liao ◽

Zhengrui Zhang ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Tandem Repeats ◽

Chromosomal Mapping ◽

Patinopecten Yessoensis ◽

Yesso Scallop

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Characterization of a tandemly repeated subtelomeric sequence with inverted telomere repeats in maize

Genome ◽

10.1139/g09-005 ◽

2009 ◽

Vol 52 (3) ◽

pp. 286-293 ◽

Cited By ~ 11

Author(s):

Jun Li ◽

Fei Yang ◽

Jia Zhu ◽

Shibin He ◽

Lijia Li

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Tandem Repeats ◽

Repeated Sequence ◽

Metaphase Chromosomes ◽

Single Chromosome ◽

Amplification Band ◽

Subtelomeric Sequence ◽

Subtelomeric Regions

In this study, two complementary telomere primers were applied to a single-primer PCR. A clear amplification band was obtained with one primer, while a smear pattern was seen with the other primer. Sequence analysis of the isolated clones from this specific amplification band revealed that a 412 bp clone designated as MTAS1 shared high homology with a reported subtelomeric sequence (382 bp) from maize ( Zea mays L.), which indicated that this clone was possibly present at subtelomeric regions. The clone MTAS1 displayed a novel structural feature flanked by the forward and inverted telomere repeats. Southern hybridization revealed a ladder of hybridization bands, suggesting that MTAS1 was a tandemly repeated sequence. Fluorescence in situ hybridization results showed that the strong MTAS1 signals were present at the ends of short arms of several long chromosomes, confirming that MTAS1 was a subtelomeric sequence and the high brightness of signals further indicated this cloned sequence was a highly and tandemly repetitive sequence in maize. Fluorescence in situ hybridization with telomeric DNA and MTAS1 as probes on metaphase chromosomes and extended genomic DNA fibers showed that hybridization signals of this clone located adjacent to or overlapped with signals of telomere tandem repeats distributed heterogeneously in subtelomeric regions of several chromosomes and even exhibited differences in two subtelomeres of a single chromosome.

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Insight into the Chromosome Structure of the Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) by a Combined Use of GISH and FISH Techniques

Plants ◽

10.3390/plants9040542 ◽

2020 ◽

Vol 9 (4) ◽

pp. 542

Author(s):

Egizia Falistocco

Keyword(s):

In Situ Hybridization ◽

Medicago Sativa ◽

Tandem Repeats ◽

Chromosome Structure ◽

Substantial Part ◽

Telomeric Repeats ◽

Evolutionary Pathway ◽

Suitable Material ◽

Interstitial Telomeric Repeats

Cytogenetic research in Medicago sativa subsp. sativa L., the cultivated tetraploid alfalfa (2n = 4x = 32), has lagged behind other crops mostly due to the small size and the uniform morphology of its chromosomes. However, in the last decades, the development of molecular cytogenetic techniques based on in situ hybridization has largely contributed to overcoming these limitations. The purpose of this study was to extend our knowledge about the chromosome structure of alfalfa by using a combination of genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) techniques. The results of self-GISH (sGISH) suggested that a substantial part of the repetitive fraction of the genome of subsp. sativa is constituted by tandem repeats typical of satellite DNA. The coincidence of sGISH and C-banding patterns supported this assumption. The FISH mapping of the Arabidopsis-type TTTAGGG telomeric repeats demonstrated, for the first time, that the alfalfa telomeres consist of this type of sequence and revealed a massive presence of interstitial telomeric repeats (ITRs). In the light of this finding M. sativa appears to be a suitable material for studying the origin and function of such extra telomeric repeats. To further exploit this result, investigation will be extended to the diploid subspp. coerulea and falcata in order to explore possible connections between the distribution of ITRs, the ploidy level, and the evolutionary pathway of the taxa.

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