A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era

Abstract Background The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species. Results Tandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa. Conclusions This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.

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A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era

10.21203/rs.3.rs-231781/v1 ◽

2021 ◽

Author(s):

Wenxi Jiang ◽

Chengzhi Jiang ◽

Weiguang Yuan ◽

Meijun Zhang ◽

Zijie Fang ◽

...

Keyword(s):

Chromosomal Rearrangements ◽

Repetitive Sequences ◽

Identification System ◽

Chromosome Identification ◽

Nomenclature System ◽

Chromosome Translocations ◽

C Banding ◽

Group Assignment ◽

Standard Karyotype

Abstract Background The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species. Results Tandem repetitive sequences were predicted and physically located on chromosomal regions of the Avena sativa genomes. Thirteen new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of eleven hexaploid and diploid Avena accessions. We established a high resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations. Conclusion This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.

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Karyotyping Dasypyrum breviaristatum chromosomes with multiple oligonucleotide probes reveals the genomic divergence in Dasypyrum

Genome ◽

10.1139/gen-2020-0147 ◽

2021 ◽

Author(s):

Zhihui Yu ◽

Hongjin Wang ◽

Wenxi Jiang ◽

Chengzhi Jiang ◽

Weiguang Yuan ◽

...

Keyword(s):

Repetitive Sequences ◽

Wheat Breeding ◽

Evolutionary Divergence ◽

Oligonucleotide Probes ◽

Addition Lines ◽

Partial Amphiploid ◽

Standard Karyotype ◽

Molecular Marker Analysis ◽

Dasypyrum Breviaristatum

The perennial species Dasypyrum breviaristatum (genome Vb) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of D. breviaristatum chromosomes will be useful for the detection of Dasypyrum chromatin in wheat background. We established the standard karyotype of 1Vb-7Vb chromosomes through non-denaturing fluorescence in situ hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat-D. breviaristatum partial amphiploid TDH-2 (AABBVbVb) and newly identified wheat-D. breviaristatum disomic translocation and addition lines D2138 (6VbS.2VbL), D2547 (4Vb) and D2532 (3VbS.6VbL) by comparative molecular marker analysis. The ND-FISH with multiple oligo probes were conducted on the durum wheat-D. villosum amphiploid TDV-1 and large karyotype differences between D. breviaristatum and D. villosum was revealed. These ND-FISH probes will be valuable for screening the wheat-Dasypyrum derivative lines for chromosome identification, and newly developed wheat-D. breviaristatum addition lines may broaden the gene pool of wheat breeding. The differences between D. villosum and D. breviaristatum chromosomes revealed by ND-FISH will help us understand evolutionary divergence of repetitive sequences within the genus Dasypyrum.

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Chromosome Identification in Potato Trisomics(2n=2x+1=25) by Conventional Staining, Giemsa C-banding and Non-radioactive in situ Hybridization.

CYTOLOGIA ◽

10.1508/cytologia.59.405 ◽

1994 ◽

Vol 59 (4) ◽

pp. 405-417 ◽

Cited By ~ 4

Author(s):

M. Wagenvoort ◽

G. J. A. Rouwendal ◽

G. Kuiper-Groenwold ◽

H. P. J. de Vries van Hulten

Keyword(s):

In Situ Hybridization ◽

Chromosome Identification ◽

C Banding

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Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum)

Genome ◽

10.1139/g91-128 ◽

1991 ◽

Vol 34 (5) ◽

pp. 830-839 ◽

Cited By ~ 340

Author(s):

B. S. Gill ◽

B. Friebe ◽

T. R. Endo

Keyword(s):

Triticum Aestivum ◽

Wheat Chromosome ◽

Chromosome Analysis ◽

Triticum Aestivum L ◽

Nomenclature System ◽

C Banding ◽

Structural Aberrations ◽

Individual Bands ◽

Standard Karyotype ◽

Band Number

A standard karyotype based on N-banding, C-banding, and modified C-banding has been constructed for Triticum aestivum L. 'Chinese Spring'. An idiogram and a nomenclature system have been developed for the description of individual bands. Nomenclatural rules have been proposed for the description of chromosomal structural aberrations and polymorphic bands in other wheat cultivars. As a rule each short arm (S) and a long arm (L) consists of a series of dark bands (C-bands) and light bands (mainly euchromatic) and by definition there are no interbands. In some cases, each arm has been subdivided into two or more regions. The description of a band requires designation of a chromosome number, arm (S or L), region, and band. The region number is separated from the band number by a decimal point. Except for arms 1AS, 3AL, 4AS, and 6AS, all wheat chromosome arms have one or more intercalary C-bands and are divisible into three or more bands. It is hoped that the proposed karyotype and nomenclature system will be widely adopted and lay the foundation of definitive chromosome analysis in wheat.Key words: C-banding, N-banding, common wheat, heterochromatin, idiogram.

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The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family

Annals of Animal Science ◽

10.2478/v10220-012-0001-y ◽

2012 ◽

Vol 12 (1) ◽

pp. 5-13 ◽

Cited By ~ 1

Author(s):

Klaudia Pawlina ◽

Monika Bugno-Poniewierska

Keyword(s):

Chromosomal Rearrangements ◽

Repetitive Sequences ◽

Molecular Cytogenetics ◽

Ideal Object ◽

Fish Technique ◽

Additional Information ◽

Object Of Study ◽

Cross Species Chromosome Painting ◽

Painting Probes

The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae FamilyGenome analysis is necessary to trace evolutionary rearrangements and relationships between species. Initially, to this end, the tools of classical cytogenetics were used but along with the development of molecular cytogenetics methods it became possible to analyse the genome more thoroughly. One of the widely used methods is fluorescence in situ hybridization (FISH) and its different types. Zoo-FISH, or cross-species chromosome painting, which uses painting probes specific for whole chromosomes, enables detecting homologous synteny blocks, the occurrence of which is evidence that species share a common ancestry and are related. Zoo-FISH technique is complemented by FISH with probes specific to chromosome arms or repetitive sequences (telomeres, centromeres), which provide additional information about karyotype organization, as well as karyotype polymorphism and conservation. Another method used is FISH with gene-specific probes, which enable the localization of single loci, thus making it possible to determine linkages between genes and verify data obtained after using painting probes in Zoo-FISH technique. Because of its diverse karyotype and rapid karyotypic evolution, the Equidae family is an ideal object of study using a number of methods based on in situ hybridization, which, in turn, enables information to be obtained at many levels of DNA organization.

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Standard karyotype of Triticum longissimum and its cytogenetic relationship with T. aestivum

Genome ◽

10.1139/g93-098 ◽

1993 ◽

Vol 36 (4) ◽

pp. 731-742 ◽

Cited By ~ 59

Author(s):

Bernd Friebe ◽

Neal Tuleen ◽

Jiming Jiang ◽

Bikram S. Gill

Keyword(s):

In Situ Hybridization ◽

Addition Line ◽

Addition Lines ◽

Substitution Lines ◽

Chromosome Addition ◽

C Banding ◽

Chromosome Addition Lines ◽

Standard Karyotype ◽

Fertility Genes

C-banding polymorphism was analyzed in 17 accessions of Triticum longissimum from Israel and Jordan, and a generalized idiogram of this species was established. C-banding analysis was further used to identify two sets of disomic T. aestivum – T. longissimum chromosome addition lines and 13 ditelosomic addition lines and one monotelosomic (6S1L) addition line. C-banding was also used to identify T. aestivum – T. longissimum chromosome substitution and translocation lines. Two major nucleolus organizing regions (NORs) on 5S1 and 6S1 and one minor NOR on 1S1 were detected by in situ hybridization using a 18S–26S rDNA probe. Sporophytic and gametophytic compensation tests were used to determine the homoeologous relationships of T. longissimum chromosomes. The T. longissimum chromosomes compensate rather well and fertility was restored even in substitution lines involving wheat chromosomes 2A, 4B, and 6B that contain major fertility genes. Except for the deleterious gametocidal genes, T. longissimum can be considered as a suitable donor of useful genes for wheat improvement.Key words: Triticum aestivum, Triticum longissimum, homoeology, C-banding, in situ hybridization.

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Distribution of highly repeated DNA sequences in species of the genus Lens Miller

Genome ◽

10.1139/g03-077 ◽

2003 ◽

Vol 46 (6) ◽

pp. 1118-1124 ◽

Cited By ~ 16

Author(s):

Incoronata Galasso

Keyword(s):

Dna Sequences ◽

Lens Culinaris ◽

Repetitive Sequences ◽

5S Rdna ◽

Chromosome Identification ◽

Mitotic Chromosomes ◽

Genomic Relationships ◽

Lens Nigricans ◽

25S Rdna

Multiple-target fluorescence in situ hybridization (FISH) was applied on mitotic chromosomes of seven Lens taxa using two highly repetitive sequences (pLc30 and pLc7) isolated from the cultivated lentil and the multigene families for the 18S–5.8S–25S (pTa71) and 5S rRNA (pTa794) from wheat simultaneously as probes. The number and location of pLc30 and pLc7 sites on chromosomes varied markedly among the species, whereas the hybridization pattern of 5S rDNA and 18S–5.8S–25S rDNA was less variable. In general, each species showed a typical FISH karyotype and few differences were observed among accessions belonging to the same species, except for the accessions of Lens odemensis. The most similar FISH karyotype to the cultivated lentil is that of Lens culinaris subsp. orientalis, whereas Lens nigricans and Lens tomentosus are the two species that showed the most divergent FISH patterns compared with all taxa for number and location of pLc30 and 18S–5.8S–25S rDNA sites.Key words: chromosome identification, comparative FISH karyotype, wild Lens species, genomic relationships.

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A universal chromosome identification system for maize and wild Zea species

10.1101/2020.01.22.915942 ◽

2020 ◽

Author(s):

Guilherme T. Braz ◽

Lívia do Vale Martins ◽

Tao Zhang ◽

Patrice S. Albert ◽

James A. Birchler ◽

...

Keyword(s):

Distribution Patterns ◽

Identification System ◽

Chromosome 4 ◽

Chromosome Identification ◽

Closely Related Species ◽

Eukaryotic Species ◽

A New Technique ◽

Fish Signal ◽

Distinct Distribution

AbstractMaize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared to other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species.

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Fluorescence in situ hybridization of bovine Alu-like sequences to bovine and ovine chromosomes

Genome ◽

10.1139/g93-129 ◽

1993 ◽

Vol 36 (5) ◽

pp. 984-986 ◽

Cited By ~ 3

Author(s):

E. Rajcan-Separovic ◽

M. P. Sabour

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Repetitive Sequences ◽

Chromosome Identification ◽

Banding Patterns ◽

Alu Sequences ◽

Diffuse Distribution

Fluorescence in situ hybridization procedures have been applied to study the distribution of Alu-like sequences on bovine and ovine chromosomes. Unlike in man and mouse, where the Alu sequences produced discrete R-like bands, a more diffuse distribution of Alu-like sequences was observed on both bovine and ovine chromosomes. Under the conditions used, banding patterns useful for chromosome identification were not detected.Key words: bovine Alu-like repetitive sequences, bovine and ovine chromosomes, fluorescence in situ hybridization.

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The trihybrid genome constitution of Bacillus lynceorum (Insecta Phasmatodea) and its karyotypic variations

Genome ◽

10.1139/g93-044 ◽

1993 ◽

Vol 36 (2) ◽

pp. 317-326 ◽

Cited By ~ 16

Author(s):

S. Manaresi ◽

O. Marescalchi ◽

V. Scali

Keyword(s):

Silver Staining ◽

Chromosomal Rearrangements ◽

Centromeric Heterochromatin ◽

Genome Constitution ◽

C Banding ◽

Centromeric Function ◽

Stick Insects ◽

Standard Karyotype ◽

Staining Techniques

The standard karyotype and a wide array of repatterned cytotypes from 21 demes of the double-allotriploid thelytokous Bacillus lynceorum have been analyzed by means of Giemsa, C-banding, and silver-staining techniques. The present study substantially amends the first karyotype description and also analyzes in detail the chromosomal rearrangements to trace their most likely derivation. Bacillus lynceorum cytotypes also provide a well-documented instance of an intraspecific gain of centromeric function. The contribution of three different specific haplosets is particularly evidenced from centromeric heterochromatin pattern and satellite/Ag-NOR locations. In stick insects, both hybridogenetic and parthenogenetic Bacillus hybrids, including B. lynceorum, can utilize the rDNA of all available parental haplosets, although a hierarchical role of the B. rossius genome seems to emerge. Satellite/Ag-NOR patterns, besides clearly allowing the recognition of ancestral parental genomes, also suggest a polyphyletic origin for B. lynceorum, which, to our knowledge, represents the only described karyotype of a trihybrid invertebrate.Key words: Bacillus lynceorum, C-banding cytotypes, NOR hierarchy, centric fissions, thelytoky.

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