The genomic composition of Tricepiro, a synthetic forage crop

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 154-159 ◽  
Author(s):  
María Rosa Ferrari ◽  
Eduardo J Greizerstein ◽  
Héctor A Paccapelo ◽  
Carlos A Naranjo ◽  
Angelines Cuadrado ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Chromosomal Location ◽  
Hexaploid Triticale ◽  
Genomic Constitution ◽  
Forage Crop ◽  
A Genome ◽  
Total Dna ◽  
Synthetic Hexaploid ◽  
Specific Sequences

Chromosome in situ hybridization (FISH and GISH) is a powerful tool for determining the chromosomal location of specific sequences and for analysing genome organization and evolution. Tricepiro (2n = 6x = 42) is a synthetic cereal obtained by G. Covas in Argentina (1972), which crosses hexaploid triticale (2n = 6x = 42) and octoploid Trigopiro (2n = 8x = 56). Several years of breeding produced a forage crop with valuable characteristics from Secale, Triticum, and Thinopyrum. The aim of this work is to analyse the real genomic constitution of this important synthetic crop. In situ hybridization using total DNA of Secale, Triticum, and Thinopyrum as a probe (GISH) labelled with biotin and (or) digoxigenin showed that tricepiro is composed of 14 rye chromosomes and 28 wheat chromosomes. Small zones of introgression of Thinopyrum on wheat chromosomes were detected. The FISH using the rye repetitive DNA probe pSc 119.2 labelled with biotin let us characterize the seven pairs of rye chromosomes. Moreover, several wheat chromosomes belonging to A and B genomes were distinguished. Therefore, tricepiro is a synthetic hexaploid (2n = 6x = 42) being AABBRR in its genomic composition, with zones of introgression of Thinopyrum in the A genome of wheat.Key words: tricepiro, trihybrid, Triticum, Secale, Thinopyrum, in situ hybridization, FISH, GISH, genomic composition, synthetic forage crop.

Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 706-713 ◽  
Author(s):  
Concha Linares ◽  
Antonio Serna ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Diploid Species ◽  
D Genome ◽  
Specific Sequence ◽  
Chromosomal Organization ◽  
Intergenomic Translocations ◽  
A Genome ◽  
Slot Blot Analysis ◽  
Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

scholarly journals Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
Reference Sequence ◽  
A Genome ◽  
Genome Map ◽  
Chromosomal Variants

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.

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 ◽  
1996 ◽  
Vol 39 (3) ◽  
pp. 535-542 ◽  
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.

Chromosomal localization and characterization of rDNA loci in the Brassica A and C genomes

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 582-587 ◽  
Author(s):  
R. J. Snowdon ◽  
W. Köhler ◽  
A. Köhler
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Ribosomal Dna ◽  
Diploid Species ◽  
Rdna Locus ◽  
Chromosome Morphology ◽  
Rdna Site ◽  
A Genome ◽  
Rdna Loci

Using fluorescence in situ hybridization, we located ribosomal DNA loci on prometaphase chromosomes of the diploid species Brassica rapa and Brassica oleracea and their amphidiploid Brassica napus. Based on comparisons of chromosome morphology and hybridization patterns, we characterized the individual B. napus rDNA loci according to their presumed origins in the Brassica A and C genomes. As reported in other studies, the sum of rDNA loci observed on B. rapa (AA genome) and B. oleracea (CC genome) chromosomes was one greater than the total number of loci seen in their amphidiploid B. napus (AACC). Evidence is presented that this reduction in B. napus rDNA locus number results from the loss of the smallest A genome rDNA site in the amphidiploid.Key words: Brassica, fluorescence in situ hybridization, ribosomal DNA, rDNA.

The genome composition of hexaploid Psammopyrum athericum and octoploid Psammopyrum pungens (Poaceae: Triticeae)

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 164-169 ◽  
Author(s):  
Pernilla Ellneskog-Staam ◽  
Björn Salomon ◽  
Roland von Bothmer ◽  
Kesara Anamthawat-Jónsson
Keyword(s):  
In Situ Hybridization ◽  
Genome Analysis ◽  
Genomic In Situ Hybridization ◽  
Agropyron Cristatum ◽  
Genome Composition ◽  
Genomic Constitution ◽  
Hybridization Pattern ◽  
Genomic Probe

The genomic constitution of two species in the genus Psammopyrum, i.e., Ps. athericum (2n = 6x = 42) and Ps. pungens (2n = 8x = 56), was studied by genomic in situ hybridization (GISH). In Ps. athericum, one diploid chromosome set hybridized to a genomic probe from Pseudoroegneria ferganensis (St genome), one diploid set to a probe from Agropyron cristatum (P genome), and one diploid set to a probe from Thinopyrum junceiforme (EbEe genomes) or Th. bessarabicum (Eb genome). Substituting the St-genome probe with an L-genome probe from Festucopsis serpentinii resulted in exactly the same hybridization pattern, suggesting a genomic constitution of EStP or ELP for Ps. athericum. The same probes used on Ps. pungens showed two diploid sets of chromosomes hybridizing to the St-genome probe, one diploid set hybridizing to the P-genome probe, and one diploid set hybridizing to the EbEe-genome probe. The L-genome probe hybridized to approximately 14 of the chromosomes that were labeled by the St-genome probe. Hence the genomic constitution for Ps. pungens is proposed to be EStStP or EStLP.Key Words: Psammopyrum athericum, Psammopyrum pungens, in situ hybridization, Elytrigia pycnantha, Elytrigia pungens, genome analysis.

scholarly journals Use of Genomic in Situ Hybridization (GISH) to Track Genetic Introgression in Onion

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 513B-513
Author(s):  
Anfu Hou ◽  
Ellen B. Peffley
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Genomic In Situ Hybridization ◽  
Genetic Introgression ◽  
A Genome

Introgression of genes in species crosses can be observed morphologically in backcrossed or selfed progenies, but the phenotype does not give information about the movement of DNAs. Cytogenetic markers allow for visualization of specific DNAs in a genome. Few cytogenetic markers are available in onion to monitor the introgression of DNA in species crosses. Genomic in situ hybridization (GISH) provides a way to locate unique DNA sequences contributed by parents. We are using GISH to monitor the movement of DNAs from A. fistulosum into A. cepa. Results of experiments using A. fistulosum as probe DNA, and A. cepa as blocking DNA will be reported. Also presented are hybridization sites observed in F1BC3 progeny of the GISH.

Molecular Cytogenetic Analysis and Meiotic Pairing Behavior of Progenies Originating from a Hexaploid Triticale (×Triticosecale, Wittmack) and Bread Wheat (Triticum aestivum, L.) Cross

2020 ◽  
Vol 160 (1) ◽  
pp. 47-56
Author(s):  
Aybeniz J. Aliyeva ◽  
András Farkas ◽  
Naib Kh. Aminov ◽  
Klaudia Kruppa ◽  
Márta Molnár-Láng ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Chromosome Pairing ◽  
Addition Line ◽  
Meiotic Pairing ◽  
Hexaploid Triticale ◽  
Substitution Lines ◽  
Molecular Cytogenetic ◽  
Triticale Line ◽  
Pairing Behavior

The chromosomal constitution of 9 dwarf (D) and 8 semidwarf (SD) lines derived by crossing hexaploid Triticale line NA-75 (AABBRR, 2n = 6x = 42) with Triticumaestivum (AABBDD, 2n = 6x = 42) cv. Chinese Spring was investigated using molecular cytogenetic techniques: fluorescence in situ hybridization and genomic in situ hybridization. A wheat-rye translocation (T4DS.7RL), 8 substitution lines, and a ditelosomic addition line (7RSdt) were identified. In the substitution lines, 1, 2, or 4 pairs of wheat chromosomes, belonging to the A, B, or D genome, were replaced by rye chromosomes. Substitutions between chromosomes belonging to different wheat genomes [5B(5A), 1D(1B)] also occurred. The lines were genetically stable, each carrying 42 chromosomes, except the wheat-rye ditelosomic addition line, which carried 21 pairs of wheat chromosomes and 1 pair of rye telocentric chromosomes (7RS). The chromosome pairing behavior of the lines was studied during metaphase I of meiosis. The chromosome pairing level and the number of ring bivalents were different for each line. Besides rod bivalents, univalent and multivalent associations (tri- and quadrivalents) were also detected. The main goal of the experiment was to develop genetically stable wheat/Triticale recombinant lines carrying chromosomes/chromatin fragments originating from the R genome of Triticale line NA-75. Introgression of rye genes into hexaploid wheat can broaden its genetic diversity, and the newly developed lines can be used in wheat breeding programs.

Genomic in situ hybridization (GISH) reveals high chromosome pairing affinity between Lolium perenne and Festuca mairei

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 398-403 ◽  
Author(s):  
Mingshu Cao ◽  
David A Sleper ◽  
Fenggao Dong ◽  
Jiming Jiang
Keyword(s):  
In Situ Hybridization ◽  
Lolium Perenne ◽  
Chromosome Pairing ◽  
Cytogenetic Analysis ◽  
Direct Evidence ◽  
Genomic In Situ Hybridization ◽  
Genomic Constitution ◽  
Conventional Cytogenetic Analysis ◽  
Festuca Mairei

Intergeneric hybridizations have been made between species of Lolium and Festuca. It has been demonstrated, largely through conventional cytogenetic analysis, that the genomes of the two genera are related, however, much information is lacking on exactly how closely related the genomes are between the two species. We applied genomic in situ hybridization (GISH) techniques to the F1 hybrids of tetraploid Festuca mairei with a genomic constitution of M1M1M2M2 and diploid Lolium perenne with a genomic constitution of LL. It was shown in the triploid hybrids (LM1M2) that the chromosomes of M1 and M2 from F. mairei could pair with each other, and it was further discovered that L chromosomes of L. perenne paired with M1 and M2 chromosomes. Our results showed that meiocytes of Lolium-Festuca are amenable to GISH analysis, and provided direct evidence for the hypothesis that the chromosomes of Lolium and Festuca may be genetically equivalent and that reciprocal mixing of the genomes may be possible. Key words: Lolium, Festuca, in situ hybridization, meiosis.

Chromosomal distribution of a repeated DNA sequence from C-genome heterochromatin and the identification of a new ribosomal DNA locus in the Avena genus

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 548-557 ◽  
Author(s):  
Araceli Fominaya ◽  
Gregorio Hueros ◽  
Yolanda Loarce ◽  
Esther Ferrer
Keyword(s):  
In Situ Hybridization ◽  
Satellite Dna ◽  
Repeated Dna ◽  
Chromosomal Distribution ◽  
Genome Chromosome ◽  
26S Rdna ◽  
A Genome ◽  
C Genome ◽  
Repeated Dna Sequence

Satellite DNA specific to the oat C genome was sequenced and located on chromosomes of diploid, tetraploid, and hexaploid Avena ssp. using in situ hybridization. The sequence was present on all seven C genome chromosome pairs and hybridized to the entire length of each chromosome, with the exception of the terminal segments of some chromosome pairs. Three chromosome pairs belonging to the A genome showed hybridization signals near the telomeres of their long arms. The existence of intergenomic chromosome rearrangements and the deletions of the repeated units are deduced from these observations. The number of rDNA loci (18S–5.8S–26S rDNA) was determined for the tetraploid and hexaploid oat species. Simultaneous in situ hybridization with the satellite and rDNA probes was used to assign the SAT chromosomes of these species to their correct genomes.Key words: oats, satellite DNA, rDNA, in situ hybridization, genome evolution.

Intergenomic recombination in F1 lily hybrids (Lilium) and its significance for genetic variation in the BC1 progenies as revealed by GISH and FISH

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 884-894 ◽  
Author(s):  
R Barba-Gonzalez ◽  
M S Ramanna ◽  
R G.F Visser ◽  
J M Van Tuyl
Keyword(s):  
In Situ Hybridization ◽  
Phenotypic Expression ◽  
2N Gametes ◽  
Backcross Progeny ◽  
Unreduced Gametes ◽  
Normal Chromosome ◽  
Recombinant Chromosome ◽  
Intergenomic Recombination ◽  
A Genome

Intergenomic recombination was assessed in a BC1 population of Oriental (O) × Asiatic (A) lilies (Lilium) backcrossed to Asiatic parents. This population consisted of 38 plants generated from the 2n gametes from 2 genotypes (951502-1 and 952400-1) of the diploid F1, Oriental × Asiatic lilies (2n = 2x = 24) as parents. In the majority of BC1 plants, there was evidence that first division restitution, with and without crossovers, resulted in functional gametes. However, there were 5 BC1 plants in which 2n gametes originated from indeterminate meiotic restitution (IMR). Based on the number of recombinant chromosomes for a particular homoeologous pair, 3 types of plants were identified: (i) those with both the reciprocal product of a crossover (O/A, A/O, where O represents the centromere of the O genome and A the recombinant segment of Asiatic chromosome, and vice versa); (ii) those with 1 normal chromosome of the O genome and a recombinant chromosome (O, A/O); and (iii) those with 1 normal chromosome of the A genome and a recombinant chromosome (A, O/A). An important feature of A × OA backcross progeny is the occurrence of substitutions for the segment distal in the crossover wherever the recombinant chromosome O/A was present. In the case of IMR, the substitution occurred for both proximal and distal recombinant segments. The significance of these substitutions is that they offer the potential for the phenotypic expression of recessive genes in polyploids (i.e., nulliplex genotype).Key words: genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), unreduced gametes, allopolyploid.

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