Allopolyploid speciation of the Mexican tetraploid potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization

Thirty-six percent of the wild potato ( Solanum L. section Petota Dumort.) species are polyploid, and about half of the polyploids are tetraploid species (2n = 4x = 48). Determination of the type of polyploidy and development of the genome concept for members of section Petota traditionally has been based on the analysis of chromosome pairing in species and their hybrids and, most recently, DNA sequence phylogenetics. Based on these data, the genome designation AABB was proposed for Mexican tetraploid species of series Longipedicellata Buk. We investigated this hypothesis with genomic in situ hybridization (GISH) for both representatives of the series, S. stoloniferum Schltdl. and S. hjertingii Hawkes. GISH analysis supports an AABB genome constitution for these species, with S. verrucosum Schltdl. (or its progenitor) supported as the A genome donor and another North or Central American diploid species (S. cardiophyllum Lindl., S. ehrenbergii (Bitter) Rydb., or S. jamesii Torrey) as the B genome donor. GISH analysis of chromosome pairing of S. stoloniferum also confirms the strict allopolyploid nature of this species. In addition, fluorescence in situ hybridization data suggest that 45S rDNA regions of the two genomes of S. stoloniferum were changed during coevolution of A and B genomes of this allotetraploid species.

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

Genome ◽

10.1139/g99-007 ◽

1999 ◽

Vol 42 (4) ◽

pp. 706-713 ◽

Cited By ~ 10

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.

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

BMC Plant Biology ◽

10.1186/s12870-021-02875-0 ◽

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.

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Synthesis and cytological characterization of trigeneric hybrids of durum wheat with and without Ph1

Genome ◽

10.1139/g04-082 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1173-1181 ◽

Cited By ~ 28

Author(s):

Prem P Jauhar ◽

M Doğramaci ◽

T S Peterson

Keyword(s):

In Situ Hybridization ◽

Chromosome Pairing ◽

Genetic Recombination ◽

Genomic In Situ Hybridization ◽

Homoeologous Pairing ◽

Alien Gene Transfer ◽

Chromosome 5B ◽

Alien Gene ◽

Trigeneric Hybrids

Wild grasses in the tribe Triticeae, some in the primary or secondary gene pool of wheat, are excellent reservoirs of genes for superior agronomic traits, including resistance to various diseases. Thus, the diploid wheatgrasses Thinopyrum bessarabicum (Savul. and Rayss) Á. Löve (2n = 2x = 14; JJ genome) and Lophopyrum elongatum (Host) Á. Löve (2n = 2x = 14; EE genome) are important sources of genes for disease resistance, e.g., Fusarium head blight resistance that may be transferred to wheat. By crossing fertile amphidiploids (2n = 4x = 28; JJEE) developed from F1 hybrids of the 2 diploid species with appropriate genetic stocks of durum wheat, we synthesized trigeneric hybrids (2n = 4x = 28; ABJE) incorporating both the J and E genomes of the grass species with the durum genomes A and B. Trigeneric hybrids with and without the homoeologous-pairing suppressor gene, Ph1, were produced. In the absence of Ph1, the chances of genetic recombination between chromosomes of the 2 useful grass genomes (JE) and those of the durum genomes (AB) would be enhanced. Meiotic chromosome pairing was studied using both conventional staining and fluorescent genomic in situ hybridization (fl-GISH). As expected, the Ph1-intergeneric hybrids showed low chromosome pairing (23.86% of the complement), whereas the trigenerics with ph1b (49.49%) and those with their chromosome 5B replaced by 5D (49.09%) showed much higher pairing. The absence of Ph1 allowed pairing and, hence, genetic recombination between homoeologous chromosomes. Fl-GISH analysis afforded an excellent tool for studying the specificity of chromosome pairing: wheat with grass, wheat with wheat, or grass with grass. In the trigeneric hybrids that lacked chromosome 5B, and hence lacked the Ph1 gene, the wheat–grass pairing was elevated, i.e., 2.6 chiasmata per cell, a welcome feature from the breeding standpoint. Using Langdon 5D(5B) disomic substitution for making trigeneric hybrids should promote homoeologous pairing between durum and grass chromosomes and hence accelerate alien gene transfer into the durum genomes.Key words: alien gene transfer, chiasma (xma) frequency, chromosome pairing, fluorescent genomic in situ hybridization (fl-GISH), homoeologous-pairing regulator, specificity of chromosome pairing, wheatgrass.

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

Genome ◽

10.1139/g97-076 ◽

1997 ◽

Vol 40 (4) ◽

pp. 582-587 ◽

Cited By ~ 50

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.

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The genomic identification of some monosomics of Avena sativa L. cv. Sun II using genomic in situ hybridization

Genome ◽

10.1139/g95-094 ◽

1995 ◽

Vol 38 (4) ◽

pp. 747-751 ◽

Cited By ~ 30

Author(s):

J. M. Leggett ◽

G. S. Markhand

Keyword(s):

In Situ Hybridization ◽

Avena Sativa ◽

Genomic Dna ◽

Diploid Species ◽

Genomic In Situ Hybridization ◽

Chromosome Translocations ◽

C Genome

Genomic in situ hybridization using total genomic DNA extracted from the C genome diploid species Avena eriantha (2n = 2x = 14, genome CpCp) was used to identify monosomics (2n = 6x − 1 = 41) of the constituent genomes of the hexaploid cultivated oat A. sativa L. cv. Sun II (2n = 6x = 42, genomes AACCDD). The results demonstrate 3 AD/C and 6 C/AD chromosome translocations, indicate that five of the missing monosomics are derived from the C genome, and show that there are duplicates within the partial monosomic series. Chromosome polymorphisms between some monosomic lines are also demonstrated.Key words: Avena, monosomics, genomic in situ hybridization, genomic identification.

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Meiotic chromosome pairing in intergeneric hybrids of colchicaceous ornamentals revealed by genomic in situ hybridization (GISH)

Euphytica ◽

10.1007/s10681-014-1152-y ◽

2014 ◽

Vol 200 (2) ◽

pp. 251-257 ◽

Cited By ~ 2

Author(s):

Tomonari Kishimoto ◽

Miki Yamakawa ◽

Daisuke Nakazawa ◽

Junji Amano ◽

Sachiko Kuwayama ◽

...

Keyword(s):

In Situ Hybridization ◽

Chromosome Pairing ◽

Meiotic Chromosome ◽

Intergeneric Hybrids ◽

Genomic In Situ Hybridization ◽

Meiotic Chromosome Pairing

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

HortScience ◽

10.21273/hortsci.32.3.513b ◽

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.

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

Genome ◽

10.1139/g99-129 ◽

2000 ◽

Vol 43 (2) ◽

pp. 398-403 ◽

Cited By ~ 9

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.

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