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.

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

2021 ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
Reference Sequence ◽  
B Genome ◽  
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 oligos 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 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 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.

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

2020 ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
B Genome ◽  
A Genome ◽  
Genome Map ◽  
Reference Sequences ◽  
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. Thus, the identification of chromosomal variants in peanut remains a challenge, owing to a lack of efficient chromosomal markers. Results: A total 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 oligos were classified into 28 types, based on their positions, and overlapping signals in chromosomes. For each oligo types, a single and representative oligos was selected and modified with 6-carboxyfluorescein (FAM) and 6-carboxytetramethylrhodamine (TAMRA). Based on these 28 probes, a new multiplex #3 cocktail was developed with FAM-modified TIF-439, TIF-185-1, TIF-134-3, and TIF-165-3, and TAMRA-modified Ipa-1162, Ipa-1137, DP-1, and DP-5. This 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 peanut induced by radiation. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, and intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the other 15 were extensively mapped in the pericentric regions of chromosomes. Conclusions: The development of new oligo probes provides effective tools, which can be used to distinguish various chromosomes of peanut. Physical mapping reveals the genomic organization of repetitive oligos in peanut chromosomes by FISH. Following comparisons with their positions in the reference sequences, a genome map-based karyotype was established and used for the identification of chromosome variations in peanut.

scholarly journals Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut

2020 ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
5S Rdna ◽  
Repeated Sequence ◽  
Reference Sequence ◽  
Structural Variants ◽  
Genome Wide ◽  
Genome Map ◽  
Identification And Characterization

Abstract Background Chromosomal structural variants are important materials for crop breeding and genetic research. Oligo fluorescence in situ hybridization (oligo FISH) is a useful tool for the identification of chromosomal structural variants. Results We developed 114 new repetitive oligos based on genome-wide tandem repeats (TRs) using genomic reference sequences of the cultivar Tifrunner and the diploid species Arachis ipaensis by bioinformatics and FISH. These oligo probes were positioned and classified into 28 types. Signals produced by representative probes from eight types were in the secondary constriction, middle arm, and terminal regions; signals of four probe types were on the B subgenome; and one probe being able to produce signals on only one pair of chromosomes could be used to recognize a special genome or chromosomes of peanut. Based on new and previous oligo probes, we developed a cocktail Multiplex #3 including FAM modified TIF-439, TIF-185-1, TIF-134-3, TIF-165-3, and TAMRA modified Ipa-1162, Ipa-1137, DP-1, and DP-5, which combined with the total genomic DNA of A. duranensis and A. ipaensis probes, and 45S rDNA and 5S rDNA probes to establish a karyotype associated with the genome map of peanut and identify 14 chromosomal structural variants. Conclusions The new oligo probes are useful and convenient for distinguishing peanut chromosomes or specific segments of peanut chromosomes. Comparisons of oligo sites in the karyotype and chromosome plots of electronic location revealed the characteristics of repeated sequences, and showed that the assembly of repeated sequence in peanut genomic reference sequence was incomplete. We therefor demonstrated the great potentials of the new oligo probes in facilitating chromosome identification and characterization, and provided novel materials for further study and genetic improvement of peanut.

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.

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

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 665-672 ◽  
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.

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.

Molecular cytogenetics of Icelandic birch species: physical mapping by in situ hybridization and rDNA polymorphism

1995 ◽  
Vol 25 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Kesara Anamthawat-Jonsson ◽  
J.S. Heslop-Harrison
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Molecular Cytogenetics ◽  
Ribosomal Gene ◽  
Nucleolus Organizer ◽  
Environmental Conservation ◽  
Nucleolus Organizer Regions ◽  
A Genome ◽  
Breeding Programmes

The physical mapping of genes can reveal the organization of a genome and identify relationships of plant species, especially where they are involved in interspecific hybridization and polyploidy. Here we determine the chromosomal locations of the major ribosomal gene family (18S-5.8S-26S rDNA) by fluorescent in situ hybridization in two Icelandic birch species, Betulapubescens Ehrh. and Betulanana L. In the tetraploid birch (B. pubescens), the rDNA was localized on four major and two minor sites, while the diploid dwarf birch (B. nana) had four major sites. The major loci in both species were in nucleolus organizer regions, close to the centromeres of a pair of metacentric and a pair of sub-metacentric chromosomes. The dispersed interphase in situ hybridization pattern showed gene expression at all major sites. The two additional loci in B. pubescens, when detected, appeared to be sub-telomeric and inactive at interphase. Southern analysis of rDNA showed considerable restriction fragment length polymorphism in B. pubescens. Some polymorphism may reflect gene flow among populations and between the two co-existing birch species. The understanding of genome relationships, gene introgression, and evolution of birch species will be important to the breeding programmes steered towards environmental conservation and forestry.

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

Genome ◽  
2008 ◽  
Vol 51 (9) ◽  
pp. 714-720 ◽  
Author(s):  
Galina Pendinen ◽  
Tatjana Gavrilenko ◽  
Jiming Jiang ◽  
David M. Spooner
Keyword(s):  
In Situ Hybridization ◽  
Chromosome Pairing ◽  
Diploid Species ◽  
Genomic In Situ Hybridization ◽  
Tetraploid Species ◽  
Genome Donor ◽  
A Genome ◽  
Section Petota ◽  
Gish Analysis

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.

Sign in / Sign up

Export Citation Format

Share Document