Journal articles on the topic 'Chromosone mapping'
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1
Hausmann, Michael, C. Paul Popescu, Jeannine Boscher, Dominique Kerboœf, Jürgen Dölle, and Christoph Cremer. "Identification and Cytogenetic Analysis of an Abnormal Pig Chromosome for Flow Cytometry and Sorting." Zeitschrift für Naturforschung C 48, no. 7-8 (August 1, 1993): 645–53. http://dx.doi.org/10.1515/znc-1993-7-819.
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Abstract For cytogenetics of pig (Sus scrofa domestica) and the influence of chromosome aberrations on pig production, high interest exists in flow sorted chromosomes for gene mapping, to establish DNA-libraries, or to produce DNA-probes. Flow karyotyping and sorting as well as slit scan flow analysis of metaphase chromosomes of an abnormal cell type carrying a translocation marker chromosome 6/15 are described. Flow sorting of the largest chromosomes of these cells was performed. After sorting the chromosomes still had a well preserved morphology and were identified microscopically by G-banding. The quality of the band pattern of the sorted chromosomes was compatible to that of isolated chromosomes not subjected to flow cytometry. The sorted fraction showed an enrichment of chromosom e 6/15 and chromosome 1 which have quantitatively about the same integrated fluorescence intensity. Slit scan flow analysis was performed to discriminate these two chromosomes. Metacentric and submetacentric chromosom es were analyzed according to their bimodal slit scan profiles. Profiles of the largest chromosomes were distinguished by their different centromeric indices. Two groups were interpreted as the normal chromosome 1 and the translocation chromosom e 6/15.
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Matějíčková, J., M. Štípková, G. Sahana, T. Kott, J. Kyseľová, A. Matějíček, B. Kottová, J. Šefrová, M. Krejčová, and S. Melčová. "QTL mapping for production traits in Czech Fleckvieh cattle." Czech Journal of Animal Science 58, No. 9 (August 29, 2013): 396–403. http://dx.doi.org/10.17221/6939-cjas.
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The objective of this study was to find QTL for milk production traits in Czech Fleckvieh cattle on chromosomes 6, 7, 11, 14, and 23 where QTL were previously identified in other dairy cattle populations. Sixteen grandsire families were genotyped for 38 microsatellite markers on the selected chromosomes. A QTL mapping model based on variance component analysis was implemented via restricted maximum likelihood (REML) to estimate QTL positions and their effects. A significant QTL affecting fat percentage was found at the beginning of chromosome 14 (0 cM), near marker ILSTS039. Suggestive QTL associated with milk production traits appeared on other studied chromosomes (BTA6, BTA7, BTA11, and BTA23). This first QTL search on five chromosomes in Czech Fleckvieh population showed several suggestive QTL that can be promising for further studies and contribute to better understanding of genetics of milk production in the Czech Fleckvieh cattle.
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Sarma, R. N., L. Fish, B. S. Gill, and J. W. Snape. "Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes." Genome 43, no. 1 (February 1, 2000): 191–98. http://dx.doi.org/10.1139/g99-083.
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The wheat homoeologous Group 5 chromosomes were characterized physically in terms of rice linkage blocks using a deletion mapping approach. All three chromosomes, 5A, 5B, and 5D, were shown to have a similar structure, apart from the 4A-5A translocation on the distal end of chromosome arm 5AL. The physical mapping of rice markers on the deletion lines revealed that the whole of rice chromosome 9 is syntenous to a large block, proximal to the centromere, on the long arm. Likewise, a small segment of the distal end of the long arm showed conserved synteny with the distal one-third end of the long arm of rice chromosome 3. In between those conserved regions, there is a region on the long arm of the Group 5 chromosomes which shows broken synteny. The proximal part of the short arms of the Group 5 chromosomes showed conserved synteny with a segment of the short arm of rice chromosome 11 and the distal ends showed conserved synteny with a segment of rice chromosome 12. The physical locations of flowering time genes (Vrn and earliness per se) and the gene for grain hardness (Ha) on the Group 5 chromosomes were determined. These results indicate that comparative mapping using the deletion mapping approach is useful in the study of genome relationships, the physical location of genes, and can determine the appropriate gene cloning strategy. Key words: wheat, rice, comparative mapping, deletion lines.
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Kubaláková, M., M. Valárik, J. Barto, J. Vrána, J. Cíhalíková, M. Molnár-Láng, and J. Dolezel. "Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry." Genome 46, no. 5 (October 1, 2003): 893–905. http://dx.doi.org/10.1139/g03-054.
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Procedures for chromosome analysis and sorting using flow cytometry (flow cytogenetics) were developed for rye (Secale cereale L.). Suspensions of intact chromosomes were prepared by mechanical homogenization of synchronized root tips after mild fixation with formaldehyde. Histograms of relative fluorescence intensity obtained after the analysis of DAPI-stained chromosomes (flow karyotypes) were characterized and the chromosome content of the DNA peaks was determined. Chromosome 1R could be discriminated on a flow karyotype of S. cereale 'Imperial'. The remaining rye chromosomes (2R7R) could be discriminated and sorted from individual wheatrye addition lines. The analysis of lines with reconstructed karyotypes demonstrated a possibility of sorting translocation chromosomes. Supernumerary B chromosomes could be sorted from an experimental rye population and from S. cereale 'Adams'. Flow-sorted chromosomes were identified by fluorescence in situ hybridization (FISH) with probes for various DNA repeats. Large numbers of chromosomes of a single type sorted onto microscopic slides facilitated detection of rarely occurring chromosome variants by FISH with specific probes. PCR with chromosome-specific primers confirmed the identity of sorted fractions and indicated suitability of sorted chromosomes for physical mapping. The possibility to sort large numbers of chromosomes opens a way for the construction of large-insert chromosome-specific DNA libraries in rye.Key words: chromosome isolation, chromosome sorting, fluorescence in situ hybridization, repetitive DNA sequences, wheat-rye addition lines, B chromosomes, physical mapping.
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Allen, Sally Lyman, Dawn Zeilinger, and Eduardo Orias. "Mapping Three Classical Isozyme Loci in Tetrahymena: Meiotic Linkage of EstA to the ChxA Linkage Group." Genetics 144, no. 4 (December 1, 1996): 1489–96. http://dx.doi.org/10.1093/genetics/144.4.1489.
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We demonstrate a reliable method for mapping conventional loci and obtaining meiotic linkage data for the ciliated protozoan Tetrahymena thermophila. By coupling nullisomic deletion mapping with meiotic linkage mapping, loci known to be located on a particular chromosome or chromosome arm can be tested for recombination. This approach has been used to map three isozyme loci, EstA (Esterase A), EstB (Esterase B), and AcpA (Acid Phosphatase A), with respect to the ChxA locus (cycloheximide resistance) and 11 RAPDs (randomly amplified polymorphic DNAs). To assign isozyme loci to chromosomes, clones of inbred strains C3 or C2 were crossed to inbred strain B nullisomics. EstA, EstB and AcpA were mapped to chromosomes 1R, 3L and 3R, respectively. To test EstA and AcpA for linkage to known RAPD loci on their respective chromosomes, a panel of Round II (genomic exclusion) segregants from a B/C3 heterozygote was used. Using the MAPMAKER program, EstA was assigned to the ChxA linkage group on chromosome IR, and a detailed map was constructed that includes 10 RAPDs. AcpA (on 3R), while unlinked to all the RAPDs assigned to chromosome 3 by nullisomic mapping, does show linkage to a RAPD not yet assignable to chromosomes by nullisomic mapping.
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Bedo, D. G. "Polytene chromosome mapping in Ceratitis capitata (Diptera: Tephritidae)." Genome 29, no. 4 (August 1, 1987): 598–611. http://dx.doi.org/10.1139/g87-101.
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Polytene chromosome reference maps of the five autosomes of Ceratitis capitata from male pupal orbital bristle trichogen cells are presented and a correlation is established between two of them and the two largest of the five autosomes in the haploid mitotic complement. Characteristic features of each chromosome are described identifying areas that are difficult to analyze and noting the existence of common alternative band expression. A quantitative analysis of the mitotic karyotype of C. capitata indicates that the two smallest autosome pairs cannot be reliably distinguished. This may present problems with future attempts to establish homologies between the remaining mitotic and polytene chromosomes. A comparison of polytene chromosome banding patterns from salivary gland and trichogen cells failed to find any homologous regions, or even to identify homologous chromosomes. The banding differences are not explained by variation in puffing patterns, heterochromatin expression, or polyteny levels, but appear to reflect fundamental differences in banding patterns of the chromosomes in each tissue. Key words: Ceratitis capitata, polytene chromosome map, mitotic chromosome measurements.
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Ziolkowski, Piotr A., and Jan Sadowski. "FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas." Genome 45, no. 1 (February 1, 2002): 189–97. http://dx.doi.org/10.1139/g01-101.
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To improve resolution of physical mapping on Brassica chromosomes, we have chosen the pachytene stage of meiosis where incompletely condensed bivalents are much longer than their counterparts at mitotic metaphase. Mapping with 5S and 45S rDNA sequences demonstrated the advantage of pachytene chromosomes in efficient physical mapping and confirmed the presence of a novel 5S rDNA locus in Brassica oleracea, initially identified by genetic mapping using restriction fragment length polymorphism (RFLP). Fluorescence in situ hybridization (FISH) analysis visualized the presence of the third 5S rDNA locus on the long arm of chromosome C2 and confirmed the earlier reports of two 45S rDNA loci in the B. oleracea genome. FISH mapping of low-copy sequences from the Arabidopsis thaliana bacterial artificial chromosome (BAC) clones on the B. oleracea chromosomes confirmed the expectation of efficient and precise physical mapping of meiotic bivalents based on data available from A. thaliana and indicated conserved organization of these two BAC sequences on two B. oleracea chromosomes. Based on the heterologous in situ hybridization with BACs and their mapping applied to long pachytene bivalents, a new approach in comparative analysis of Brassica and A. thaliana genomes is discussed.Key words: Brassicaceae, pachytene chromosomes, FISH, rDNA, BACs.
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Cheng, Zhukuan, Gernot G. Presting, C. Robin Buell, Rod A. Wing, and Jiming Jiang. "High-Resolution Pachytene Chromosome Mapping of Bacterial Artificial Chromosomes Anchored by Genetic Markers Reveals the Centromere Location and the Distribution of Genetic Recombination Along Chromosome 10 of Rice." Genetics 157, no. 4 (April 1, 2001): 1749–57. http://dx.doi.org/10.1093/genetics/157.4.1749.
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AbstractLarge-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.
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Kang, Lin, Phillip George, Donald K. Price, Igor Sharakhov, and Pawel Michalak. "Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila." Cytogenetic and Genome Research 152, no. 4 (2017): 204–12. http://dx.doi.org/10.1159/000481790.
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Next-generation sequencing technologies have led to a decreased cost and an increased throughput in genome sequencing. Yet, many genome assemblies based on short sequencing reads have been assembled only to the scaffold level due to the lack of sufficient chromosome mapping information. Traditional ways of mapping scaffolds to chromosomes require a large amount of laboratory work and time to generate genetic and/or physical maps. To address this problem, we conducted a rapid technique which uses laser capture microdissection and enables mapping scaffolds of de novo genome assemblies directly to chromosomes in Hawaiian picture-winged Drosophila. We isolated and sequenced intact chromosome arms from larvae of D. differens. By mapping the reads of each chromosome to the recently assembled scaffolds from 3 Hawaiian picture-winged Drosophila species, at least 67% of the scaffolds were successfully assigned to chromosome arms. Even though the scaffolds are not ordered within a chromosome, the fast-generated chromosome information allows for chromosome-related analyses after genome assembling. We utilize this new information to test the faster-X evolution effect for the first time in these Hawaiian picture-winged Drosophila species.
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Lukaszewski, Adam J. "Genetic mapping in the 1R.1D wheat–rye translocated chromosomes." Genome 37, no. 6 (December 1, 1994): 945–49. http://dx.doi.org/10.1139/g94-134.
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Translocation chromosomes 1R.1D5+10−1 and 1R.1D5+10−2 were produced to improve bread-making quality in triticale and to manipulate the dosage of the Glu-D1 gene in wheat. They involve transfers of segments of the long arm of chromosome 1D of bread wheat to the long arm of rye chromosome 1R. The translocated long arms of the chromosomes were mapped genetically in wheat and triticale using polymorphism for C-banding patterns, allelic variation of the Glu-D1 gene, and a telocentric chromosome 1RL. The total frequency and the general distribution of recombination in the translocated arms was similar to that in normal long arms of group-1 chromosomes in wheat, rye, and triticale, except that the distal rye segments of the translocations showed a 15- to 20-fold increase in recombination frequency compared with normal 1R. Despite major differences in the physical structure of the translocated arms, both appeared very similar genetically, suggesting that genetic mapping is a poor indicator of the physical structure of translocations. Genetic length of the 1DL segment in chromosome 1R.1D5+10−1 was 31 cM, making the chromosome unsuitable for Glu-D1 dosage manipulation in wheat. The potential of chromosome 1R.1D5+10−2 for wheat breeding needs further testing. However, both chromosomes behave normally in hexaploid triticale.Key words: translocation, linkage, bread-making quality, wheat, triticale.
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Goodfellow, P. N. "Mapping the Y chromosome." Development 101, Supplement (March 1, 1987): 39. http://dx.doi.org/10.1242/dev.101.supplement.39.
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DNA probes isolated from the human Y chromosome have been used to resolve two fundamental problems concerning the biology of sex determination in man. Coincidentally, resolution of these problems has generated genetic maps of the short arm of the human Y chromosome and has allowed the regional localization of TDF. The first problem to be solved was the origin of XX males (de la Chapelle, this symposium): the majority of XX males are caused by a telomeric exchange between the X and Y chromosomes that results in TDF and a variable amount of Y-derived material being transferred to the X chromosome. The differing amounts of Y-derived material present in XX males has been used as the basis of a ‘deletion’ map of the Y chromosome (Müller; Ferguson-Smith & Affara; this symposium).
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Song, Junqi, Fenggao Dong, and Jiming Jiang. "Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research." Genome 43, no. 1 (February 1, 2000): 199–204. http://dx.doi.org/10.1139/g99-099.
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Lack of reliable techniques for chromosome identification is the major obstacle for cytogenetics research in plant species with large numbers of small chromosomes. To promote molecular cytogenetics research of potato (Solanum tuberosum, 2n = 4x = 48) we developed a bacterial artificial chromosome (BAC) library of a diploid potato species S. bulbocastanum. The library consists of 23 808 clones with an average insert size of 155 kb, and represents approximately 3.7 equivalents to the potato genome. The majority of the clones in the BAC library generated distinct signals on specific potato chromosomes using fluorescence in situ hybridization (FISH). The hybridization signals provide excellent cytological markers to tag individual potato chromosomes. We also demonstrated that the BAC clones can be mapped to specific positions on meiotic pachytene chromosomes. The excellent resolution of pachytene FISH can be used to construct a physical map of potato by mapping molecular marker-targeted BAC clones on pachytene chromosomes. Key words: potato, BAC library, chromosome identification, physical mapping, molecular cytogenetics.
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Castilho, A., and J. S. Heslop-Harrison. "Physical mapping of 5S and 18S–25S rDNA and repetitive DNA sequences in Aegilops umbellulata." Genome 38, no. 1 (February 1, 1995): 91–96. http://dx.doi.org/10.1139/g95-011.
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An accurate physical map of the location of the 5S and the 18S–5.8S–25S rRNA genes and a repetitive DNA sequence has been produced on Aegilops umbellulata Zhuk., (2n = 2x = 14) chromosomes by in situ hybridization. Chromosome morphology together with the hybridization pattern of pSc119.2, a DNA sequence from rye, allowed identification and discrimination of different chromosomes; pSc119.2 hybridizes with all Ae. umbellulata chromosomes at the telomeres, except for the short arm of chromosome 6U, and shows intercalary sites on the long arms of chromosomes 6U and 7U. The 5S and 18S–25S rDNA have been mapped physically only on the short arms of chromosomes 1U and 5U. On chromosome 1U the order of the genes is 5S rDNA subterminal and 18S–25S rDNA more proximal, while on chromosome 5U the position of the genes is reversed. The relative order of the genes, together with the hybridization pattern of the pSc119.2, is useful in identifying whole chromosomes or chromosome segments from Ae. umbellulata in recombinant or addition lines with wheat. The data help link the physical organization of chromosomes to the genetic map. Other members of the Triticeae vary in the presence and order of the 5S and 18S–25S rDNA sequences on groups 1 and 5, indicating multiple and complex evolutionary rearrangements of the chromosome arms.Key words: Triticum umbellulatum.
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Ito, Mikako, Nobuko Ohmido, Yukio Akiyama, Kiichi Fukui, and Takato Koba. "Characterization of Spinach Chromosomes by Condensation Patterns and Physical Mapping of 5S and 45S rDNAs by FISH." Journal of the American Society for Horticultural Science 125, no. 1 (January 2000): 59–62. http://dx.doi.org/10.21273/jashs.125.1.59.
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Molecular cytogenetic techniques and computer-aided karyotyping were applied to characterize the chromosomes of spinach (Spinacia oleracea L., 2n = 12). Chromosome lengths, arm ratios, and degrees of condensation at prometaphase chromosomes were analyzed using a software Chromosome Image Analyzing System III (CHIAS III). DNA probes prepared from rice (Oryza sativa L.) rDNA were applied to the spinach chromosomes by the fluorescence in situ hybridization (FISH) method. Three 45S rDNA loci were detected at the nucleolar organizing region (NOR) of Chromosome 5, and at terminal positions of short arms of Chromosomes 2 and 6. The loci of 5S rDNA were also found at three locations. One was at the subtelomeric region of the long arm of Chromosome 2 and the other two were at the proximal region of the long arm of Chromosome 5. All spinach chromosomes were identified which will provide valuable information for mapping genes on these chromosomes.
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Goodner, Brad W., Brian P. Markelz, M. Casey Flanagan, Chris B. Crowell, Jodi L. Racette, Brittany A. Schilling, Leah M. Halfon, J. Scott Mellors, and Gregory Grabowski. "Combined Genetic and Physical Map of the Complex Genome of Agrobacterium tumefaciens." Journal of Bacteriology 181, no. 17 (September 1, 1999): 5160–66. http://dx.doi.org/10.1128/jb.181.17.5160-5166.1999.
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ABSTRACT A combined genetic and physical map of the Agrobacterium tumefaciens A348 (derivative of C58) genome was constructed to address the discrepancy between initial single-chromosome genetic maps and more recent physical mapping data supporting the presence of two nonhomologous chromosomes. The combined map confirms the two-chromosome genomic structure and the correspondence of the initial genetic maps to the circular chromosome. The linear chromosome is almost devoid of auxotrophic markers, which probably explains why it was missed by genetic mapping studies.
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Favarato, Ramon M., Leila Braga Ribeiro, Rafaela P. Ota, Celeste M. Nakayama, and Eliana Feldberg. "Cytogenetic Characterization of Two Metynnis Species (Characiformes, Serrasalmidae) Reveals B Chromosomes Restricted to the Females." Cytogenetic and Genome Research 158, no. 1 (2019): 38–45. http://dx.doi.org/10.1159/000499954.
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Karyotypes and chromosomal characteristics with focus on B chromosomes of 2 species of the serrasalmid genus Metynnis, namely M. lippincottianus and M. maculatus, were examined using conventional (C-banding) and molecular (FISH mapping of minor and major rDNAs and Rex1, Rex3, and Rex6 retrotransposable elements) protocols. Both species possessed a diploid chromosome number of 2n = 62 and karyotypes composed of 32 metacentric + 28 submetacentric + 2 subtelocentric and 32 metacentric + 26 submetacentric + 4 subtelocentric, respectively; one small B element was found in the female genome of M. lippincottianus. C-banding revealed heterochromatin in the pericentromeric and terminal portions of all chromosomes of both species; the B chromosome was entirely heterochromatic. FISH showed 18S rDNA sites in 2 chromosome pairs in both species (pairs 19 and 22), and a large block in the B chromosome, while 5S rDNA signals were detected in the first pair of subtelocentric chromosomes in both species, moreover in M. maculatus an additional labeled pair 4 was observed. Mapping of the Rex1, Rex3, and Rex6 retrotransposable elements in the genomes of M. lippincottianus and M. maculatus indicated that they were dispersed throughout nearly all the chromosomes of the complement, except for the B chromosome of M. lippincottianus.
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Wakem, L. P., and F. Sherman. "Chromosomal assignment of mutations by specific chromosome loss in the yeast Saccharomyces cerevisiae." Genetics 125, no. 2 (June 1, 1990): 333–40. http://dx.doi.org/10.1093/genetics/125.2.333.
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Abstract Yeast 2-microns plasmids were integrated near the centromere of a different chromosome in each of 16 cir0 mapping strains of Saccharomyces cerevisiae. The specific chromosomes containing the integrated 2-microns plasmid DNA were lost at a high frequency after crossing the cir0 strains to cir+ strains. A recessive mutation in a cir+ strain can then be easily assigned to its chromosome using this set of mapping strains, since the phenotype of the recessive mutation will be manifested only in diploids having the integrated 2-microns plasmid and the unmapped mutation on homologous chromosomes.
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Leitch, I. J., and J. S. Heslop-Harrison. "Physical mapping of four sites of 5S rDNA sequences and one site of the α-amylase-2 gene in barley (Hordeum vulgare)." Genome 36, no. 3 (June 1, 1993): 517–23. http://dx.doi.org/10.1139/g93-071.
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The 5S rDNA sequences have been mapped on four pairs of barley (Hordeum vulgare L.) chromosomes using in situ hybridization and barley monotelotrisomic lines. The 5S rDNA sequences are located, genetically and physically, on the short arm of chromosome 1 (7I) and the long arms of chromosomes 2 (2I) and 3 (3I). The 5S rDNA sequence is also located on the physically long arm of chromosome 4 (4I). Only one site on chromosome 2(2I) has previously been reported. The characteristic locations of the 5S rDNA sequences make them useful as molecular markers to identify each barley chromosome. The physical position of the low-copy α-amylase-2 gene was determined using in situ hybridization; the location of this gene on the long arm of chromosome 1 (7I) was confirmed by reprobing the same preparation with the 5S rDNA probe. The results show that there is a discrepancy between the physical and genetic position of the α-amylase-2 gene.Key words: genetic mapping, physical mapping, barley, mapping, 5S DNA, α-amylase, in situ hybridization.
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Jiang, Jiming, and Bikram S. Gill. "Nonisotopic in situ hybridization and plant genome mapping: the first 10 years." Genome 37, no. 5 (October 1, 1994): 717–25. http://dx.doi.org/10.1139/g94-102.
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Nonisotopic in situ hybridization (ISH) was introduced in plants in 1985. Since then the technique has been widely used in various areas of plant genome mapping. ISH has become a routine method for physical mapping of repetitive DNA sequences and multicopy gene families. ISH patterns on somatic metaphase chromosomes using tandemly repeated sequences provide excellent physical markers for chromosome identification. Detection of low or single copy sequences were also reported. Genomic in situ hybridization (GISH) was successfully used to analyze the chromosome structure and evolution of allopolyploid species. GISH also provides a powerful technique for monitoring chromatin introgession during interspecific hybridization. A sequential chromosome banding and ISH technique was developed. The sequential technique is very useful for more precise and efficient mapping as well as cytogenetic determination of genomic affinities of individual chromosomes in allopolyploid species. A critical review is made on the present resolution of the ISH technique and the future outlook of ISH research is discussed.Key words: in situ hybridization, physical mapping, genome mapping, molecular cytogenetics.
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Ingles, Emory D., and Janine E. Deakin. "Comparative Cytogenetic Mapping and Telomere Analysis Provide Evolutionary Predictions for Devil Facial Tumour 2." Genes 11, no. 5 (April 28, 2020): 480. http://dx.doi.org/10.3390/genes11050480.
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The emergence of a second transmissible tumour in the Tasmanian devil population, devil facial tumour 2 (DFT2), has prompted questions on the origin and evolution of these transmissible tumours. We used a combination of cytogenetic mapping and telomere length measurements to predict the evolutionary trajectory of chromosome rearrangements in DFT2. Gene mapping by fluorescence in situ hybridization (FISH) provided insight into the chromosome rearrangements in DFT2 and identified the evolution of two distinct DFT2 lineages. A comparison of devil facial tumour 1 (DFT1) and DFT2 chromosome rearrangements indicated that both started with the fusion of a chromosome, with potentially critically short telomeres, to chromosome 1 to form dicentric chromosomes. In DFT1, the dicentric chromosome resulted in breakage–fusion–bridge cycles leading to highly rearranged chromosomes. In contrast, the silencing of a centromere on the dicentric chromosome in DFT2 stabilized the chromosome, resulting in a less rearranged karyotype than DFT1. DFT2 retains a bimodal distribution of telomere length dimorphism observed on Tasmanian devil chromosomes, a feature lost in DFT1. Using long term cell culture, we observed homogenization of telomere length over time. We predict a similar homogenization of telomere lengths occurred in DFT1, and that DFT2 is unlikely to undergo further substantial rearrangements due to maintained telomere length.
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Crane, Charles F., H. James Price, David M. Stelly, Don G. Czeschin Jr., and Thomas D. McKnight. "Identification of a homeologous chromosome pair by in situ DNA hybridization to ribosomal RNA loci in meiotic chromosomes of cotton (Gossypium hirsutum)." Genome 36, no. 6 (December 1, 1993): 1015–22. http://dx.doi.org/10.1139/g93-135.
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In situ DNA hybridization with 18S–28S and 5S ribosomal DNA probes was used to map 18S–28S nucleolar organizers and tandem 5S repeats to meiotic chromosomes of cotton (Gossypium hirsutum L.). Mapping was performed by correlating hybridization sites to particular positions in translocation quadrivalents. Arm assignment required translocation quadrivalents with at least one interstitial chiasma and sufficient distance between the hybridization site and the centromere. We had previously localized a major 18S–28S site to the short arm of chromosome 9; here we mapped two additional major 18S–28S sites to the short arm of chromosome 16 and the left arm of chromosome 23. We also identified and mapped a minor 18S–28S site to the short arm of chromosome 7. Two 5S sites of unequal size were identified, the larger one near the centromere of chromosome 9 and the smaller one near the centromere of chromosome 23. Synteny of 5S and 18S–28S sites indicated homeology of chromosomes 9 and 23, while positions of the other two 18S–28S sites supplement genetic evidence that chromosomes 7 and 16 are homeologous.Key words: in situ hybridization, physical mapping, ribosomal DNA loci, Gossypium hirsutum.
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Watanabe, N., N. Takesada, Y. Fujii, and P. Martinek. "Comparative Mapping of Genes for Brittle Rachis in Triticum." Czech Journal of Genetics and Plant Breeding 41, No. 2 (November 21, 2011): 39–44. http://dx.doi.org/10.17221/3671-cjgpb.
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The brittle rachis phenotype is of adaptive value in wild grass species because it causes spontaneous spike shattering. The genes on the homoeologous group 3 chromosomes determine the brittle rachis in Triticeae. A few genotypes with brittle rachis have also been found in the cultivated Triticum. Using microsatellite markers, the homoeologous genes for brittle rachis were mapped in hexaploid wheat (Triticum aestivum L.), durum wheat (Triticum turgidum L. conv. durum /Desf./) and Aegilops tauschii Coss. On chromosome 3AS, the gene for brittle rachis, Br<sub>2</sub>, was linked with the centromeric marker, Xgwm32, at the distance of 13.3 cM. Br<sub>3 </sub>was located on chromosome 3BS and linked with the centromeric marker,<br />Xgwm72 (14.2 cM). Br<sub>1 </sub>was located on chromosome 3DS. The distance from the centromeric marker Xgdm72 was 23.6 cM. The loci Br<sub>1</sub>, Br<sub>2</sub> and Br<sub>3</sub> determine disarticulation of rachides above the junction of the rachilla with the rachis so that a fragment of rachis is attached below each spikelet. The rachides of Ae. tauschii are brittle at every joint, so that the mature spike disarticulates into barrel type. The brittle rachis was determined by a dominant gene, Br<sup>t</sup>, which was linked to the centromeric marker, Xgdm72 (19.7 cM), on chromosome 3DS. A D-genome introgression line, R-61, was derived from the cross Bet Hashita/Ae. tauschii, whose rachis disarticulated as a wedge type. The gene for brittle rachis of R-61, tentatively designated as Br<sup>61</sup>, was distally located on chromosome 3DS, and was linked with the centromeric marker, Xgdm72 (27.5 cM). We discussed how the brittle rachis of R-61 originated genetically.
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Gómez, Martha I., M. Nurul Islam-Faridi, Sung-Sick Woo, Don Czeschin Jr., Michael S. Zwick, David M. Stelly, H. James Price, Keith F. Schertz, and Rod A. Wing. "FISH of a maize sh2-selected sorghum BAC to chromosomes of Sorghum bicolor." Genome 40, no. 4 (August 1, 1997): 475–78. http://dx.doi.org/10.1139/g97-063.
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Fluorescence in situ hybridization (FISH) of a 205 kb Sorghum bicolor bacterial artificial chromosome (BAC) containing a sequence complementary to maize sh2 cDNA produced a large pair of FISH signals at one end of a midsize metacentric chromosome of S. bicolor. Three pairs of signals were observed in metaphase spreads of chromosomes of a sorghum plant containing an extra copy of one arm of the sorghum chromosome arbitrarily designated with the letter D. Therefore, the sequence cloned in this BAC must reside in the arm of chromosome D represented by this monotelosome. This demonstrates a novel procedure for physically mapping cloned genes or other single-copy sequences by FISH, sh2 in this case, by using BACs containing their complementary sequences. The results reported herein suggest homology, at least in part, between one arm of chromosome D in sorghum and the long arm of chromosome 3 in maize.Key words: sorghum, maize, shrunken locus, physical mapping, fluorescence in situ hybridization, bacterial artificial chromosomes.
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Iannucci, Alessio, Marie Altmanová, Claudio Ciofi, Malcolm Ferguson-Smith, Jorge C. Pereira, Ivan Rehák, Roscoe Stanyon, et al. "Isolating Chromosomes of the Komodo Dragon: New Tools for Comparative Mapping and Sequence Assembly." Cytogenetic and Genome Research 157, no. 1-2 (2019): 123–31. http://dx.doi.org/10.1159/000496171.
Full textAbstract:
We developed new tools to build a high-quality chromosomal map of the Komodo dragon (Varanus komodoensis) available for cross-species phylogenomic analyses. First, we isolated chromosomes by flow sorting and determined the chromosome content of each flow karyotype peak by FISH. We then isolated additional Komodo dragon chromosomes by microdissection and amplified chromosome-specific DNA pools. The chromosome-specific DNA pools can be sequenced, assembled, and mapped by next-generation sequencing technology. The chromosome-specific paint probes can be used to investigate karyotype evolution through cross-species chromosome painting. Overall, the set of chromosome-specific DNA pools of V. komodoensis provides new tools for detailed phylogenomic analyses of Varanidae and squamates in general.
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Scacchetti, Priscilla C., Ricardo Utsunomia, José C. Pansonato-Alves, Marcelo R. Vicari, Roberto F. Artoni, Claudio Oliveira, and Fausto Foresti. "Chromosomal Mapping of Repetitive DNAs in Characidium (Teleostei, Characiformes): Genomic Organization and Diversification of ZW Sex Chromosomes." Cytogenetic and Genome Research 146, no. 2 (2015): 136–43. http://dx.doi.org/10.1159/000437165.
Full textAbstract:
The speciose neotropical genus Characidium has proven to be a good model for cytogenetic exploration. Representatives of this genus often have a conserved diploid chromosome number; some species exhibit a highly differentiated ZZ/ZW sex chromosome system, while others do not show any sex-related chromosome heteromorphism. In this study, chromosome painting using a W-specific probe and comparative chromosome mapping of repetitive sequences, including ribosomal clusters and 4 microsatellite motifs - (CA)15, (GA)15, (CG)15, and (TTA)10 -, were performed in 6 Characidium species, 5 of which possessed a heteromorphic ZW sex chromosome system. The W-specific probe showed hybridization signals on the W chromosome of all analyzed species, indicating homology among the W chromosomes. Remarkably, a single major rDNA-bearing chromosome pair was found in all species. The 18S rDNA localized to the sex chromosomes in C. lanei, C. timbuiense and C. pterostictum, while the major rDNA localized to one autosome pair in C. vidali and C. gomesi. In contrast, the number of 5S rDNA-bearing chromosomes varied. Notably, minor ribosomal clusters were identified in the W chromosome of C. vidali. Microsatellites were widely distributed across almost all chromosomes of the karyotypes, with a greater accumulation in the subtelomeric regions. However, clear differences in the abundance of each motif were detected in each species. In addition, the Z and W chromosomes showed the differential accumulation of distinct motifs. Our results revealed variability in the distribution of repetitive DNA sequences and their possible association with sex chromosome diversification in Characidium species.
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Uno, Yoshinobu, Chizuko Nishida, Chiyo Takagi, Takeshi Igawa, Naoto Ueno, Masayuki Sumida, and Yoichi Matsuda. "Extraordinary Diversity in the Origins of Sex Chromosomes in Anurans Inferred from Comparative Gene Mapping." Cytogenetic and Genome Research 145, no. 3-4 (2015): 218–29. http://dx.doi.org/10.1159/000431211.
Full textAbstract:
Sex determination in frogs (anurans) is genetic and includes both male and female heterogamety. However, the origins of the sex chromosomes and their differentiation processes are poorly known. To investigate diversity in the origins of anuran sex chromosomes, we compared the chromosomal locations of sex-linked genes in 4 species: the African clawed frog (Xenopus laevis), the Western clawed frog (Silurana/X. tropicalis), the Japanese bell-ring frog (Buergeria buergeri), and the Japanese wrinkled frog (Rana rugosa). Comparative mapping data revealed that the sex chromosomes of X. laevis, X. tropicalis and R. rugosa are different chromosome pairs; however, the sex chromosomes of X. tropicalis and B. buergeri are homologous, although this may represent distinct evolutionary origins. We also examined the status of sex chromosomal differentiation in B. buergeri, which possesses heteromorphic ZW sex chromosomes, using comparative genomic hybridization and chromosome painting with DNA probes from the microdissected W chromosome. At least 3 rearrangement events have occurred in the proto-W chromosome: deletion of the nucleolus organizer region and a paracentric inversion followed by amplification of non-W-specific repetitive sequences.
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Kubát, Z. "Chromosome walking with BAC clones as a method of genome mapping." Plant, Soil and Environment 53, No. 10 (January 7, 2008): 447–50. http://dx.doi.org/10.17221/2198-pse.
Full textAbstract:
Current sequencing projects are often based on random sequencing of genomic libraries followed by contig assembly by means of bioinformatics tools. This approach is convenient for whole genome sequencing projects. Chromosome walking described here is suitable for mapping and sequencing of short genomic regions in species where whole genome sequencing is not possible or for cloning gene from its closest known marker. This method is based on searching for overlapping BAC clones specific for the genomic region of interest.
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Crepaldi, Carolina, and Patricia P. Parise-Maltempi. "Heteromorphic Sex Chromosomes and Their DNA Content in Fish: An Insight through Satellite DNA Accumulation in Megaleporinus elongatus." Cytogenetic and Genome Research 160, no. 1 (2020): 38–46. http://dx.doi.org/10.1159/000506265.
Full textAbstract:
The repetitive DNA content of fish sex chromosomes provides valuable insights into specificities and patterns of their genetic sex determination systems. In this study, we revealed the genomic satellite DNA (satDNA) content of Megaleporinuselongatus, a Neotropical fish species with Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosomes, through high-throughput analysis and graph-based clustering, isolating 68 satDNA families. By physically mapping these sequences in female metaphases, we discovered 15 of the most abundant satDNAs clustered in its chromosomes, 9 of which were found exclusively in the highly heterochromatic W1. This heteromorphic sex chromosome showed the highest amount of satDNA accumulations in this species. The second most abundant family, MelSat02-26, shared FISH signals with the NOR-bearing pair in similar patterns and is linked to the multiple sex chromosome system. Our results demonstrate the diverse satDNA content in M. elongatus, especially in its heteromorphic sex chromosome. Additionally, we highlighted the different accumulation patterns and distribution of these sequences across species by physically mapping these satDNAs in other Anostomidae, Megaleporinusmacrocephalus and Leporinusfriderici (a species without differentiated sex chromosomes).
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Koo, Dal-Hoe, Vijay K. Tiwari, Eva Hřibová, Jaroslav Doležel, Bernd Friebe, and Bikram S. Gill. "Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat." Cytogenetic and Genome Research 148, no. 4 (2016): 314–21. http://dx.doi.org/10.1159/000447471.
Full textAbstract:
Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa.
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Jiang, Jiming, and Bikram S. Gill. "Sequential chromosome banding and in situ hybridization analysis." Genome 36, no. 4 (August 1, 1993): 792–95. http://dx.doi.org/10.1139/g93-104.
Full textAbstract:
Different combinations of chromosome N- or C-banding with in situ hybridization (ISH) or genomic in situ hybridization (GISH) were sequentially performed on metaphase chromosomes of wheat. A modified N-banding–ISH/GISH sequential procedure gave best results. Similarly, a modified C-banding – ISH/GISH procedure also gave satisfactory results. The variation of the hot acid treatment in the standard chromosome N- or C-banding procedures was the major factor affecting the resolution of the subsequent ISH and GISH. By the sequential chromosome banding – ISH/GISH analysis, multicopy DNA sequences and the breakpoints of wheat–alien translocations were directly allocated to specific chromosomes of wheat. The sequential chromosome banding– ISH/GISH technique should be widely applicable in genome mapping, especially in cytogenetic and molecular mapping of heterochromatic and euchromatic regions of plant and animal chromosomes.Key words: N-banding, C-banding, in situ hybridization, genomic in situ hybridization.
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CHAKRABORTY, Supriyo, Sheng-Chu WANG, and Zhao-Bang ZENG. "Mapping QTL for Grain Yield under Moisture Stress Environments in Rice (Oryza sativa L.)." Notulae Scientia Biologicae 3, no. 4 (November 17, 2011): 129–33. http://dx.doi.org/10.15835/nsb346344.
Full textAbstract:
Polygenes (QTLs) for grain yield were mapped on rice chromosomes under two moisture stress environments by multiple interval mapping (MIM) method in a double haploid (DH) population derived from a cross between a deep-rooted japonica and a shallow-rooted indica genotype. In environment 1 (E1), the MIM detected a total of six QTLs for grain yield on chromosomes-two QTLs on chromosome 1 and four QTLs on chromosome 5 along with one additive x additive epistasis. But in environment 2 (E2), the MIM detected five QTLs for grain yield on two chromosomes-three QTLs on chromosome 1 and two QTLs on chromosome 7. One common QTL on chromosome 1 flanked by the markers RG109-ME1014 was detected in both the environments, although the other detected QTLs differed between environments. The magnitude of QTL effect, percent genetic variance and percent phenotypic variance explained by each QTL was also estimated in both environments. The common QTL explained about 26.05 and 13.93% of genetic variance in E1 and E2, respectively. Estimated broad sense heritability for grain yield was 48.01 in E1 and 25.27% in E2.
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Liang, Jiangtao, Simon M. Bondarenko, Igor V. Sharakhov, and Maria V. Sharakhova. "Obtaining Polytene, Meiotic, and Mitotic Chromosomes from Mosquitoes for Cytogenetic Analysis." Cold Spring Harbor Protocols 2022, no. 12 (August 5, 2022): pdb.prot107872. http://dx.doi.org/10.1101/pdb.prot107872.
Full textAbstract:
Chromosome visualization is a key step for developing cytogenetic maps and idiograms, analyzing inversion polymorphisms, and identifying mosquito species. Three types of chromosomes—polytene, mitotic, and meiotic—are used in cytogenetic studies of mosquitoes. Here, we describe a detailed method for obtaining high-quality polytene chromosome preparations from the salivary glands of larvae and the ovaries of females forAnophelesmosquitoes. We also describe how to obtain mitotic chromosomes from imaginal discs of fourth-instar larvae and meiotic chromosomes from the testes of male pupae for all mosquitoes. These chromosomes can be used for fluorescence in situ hybridization (FISH), a fundamental technique in cytogenetic research that is used for physical genome mapping, detecting chromosomal rearrangements, and studying chromosome organization.
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Feng, Jiuhuan, Valerio Primomo, Zenglu Li, Yongping Zhang, Chao-Chien Jan, Lomas Tulsieram, and Steven S. Xu. "Physical localization and genetic mapping of the fertility restoration gene Rfo in canola (Brassica napus L.)." Genome 52, no. 4 (April 2009): 401–7. http://dx.doi.org/10.1139/g09-016.
Full textAbstract:
The Ogu cytoplasm for male sterility and its fertility restorer gene Rfo in canola ( Brassica napus L.) were originally introgressed from radish ( Raphanus sativus L.) and have been widely used for canola hybrid production and breeding. The objective of this study was to determine the physical location of the Rfo locus in the canola genome using fluorescence in situ hybridization and genetic mapping. For physical localization of the Rfo gene, two bacterial artificial chromosome (BAC) clones, G62 and B420, which were closely linked to the Rfo gene, were used as probes to hybridize with the somatic metaphase chromosomes of a canola hybrid variety, PHI-46 (46H02), containing the Rfo fragment. The results showed that both clones were physically located at the end of one large metacentric chromosome. By simultaneous use of two BAC clones and 45S rDNA repeated sequences as the probes, we demonstrated that the large metacentric chromosome probed with the two BAC clones did not carry 45S rDNA repeated sequences. The chromosome was 3.65 ± 0.74 µm in average length (20 cells) and ranked second in size among the chromosomes without 45S rDNAs. The centromere index of the chromosome (20 cells) was calculated as 43.74 ± 4.19. A comparison with previously reported putative karyotypes of B. napus (AACC) and its diploid ancestors Brassica rapa L. (AA) and Brassica oleracea L. (CC) suggests that the chromosome carrying the Rfo fragment might belong to one of three large metacentric chromosomes of the C genome. Genetic mapping has confirmed the localization of the Rfo fragment to the distal region of linkage group N19, which corresponds to the C genome in B. napus. This study has provided the evidence of the location of the Rfo gene on canola chromosomes and established a basic framework for further physical mapping and manipulation of the gene.
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Gadaleta, A., A. Giancaspro, S. L. Giove, S. Zacheo, O. Incerti, R. Simeone, P. Colasuonno, et al. "Development of a deletion and genetic linkage map for the 5A and 5B chromosomes of wheat (Triticum aestivum)." Genome 55, no. 6 (June 2012): 417–27. http://dx.doi.org/10.1139/g2012-028.
Full textAbstract:
The aims of the present study were to provide deletion maps for wheat ( Triticum aestivum L.) chromosomes 5A and 5B and a detailed genetic map of chromosome 5A enriched with popular microsatellite markers, which could be compared with other existing maps and useful for mapping major genes and quantitative traits loci (QTL). Physical mapping of 165 gSSR and EST–SSR markers was conducted by amplifying each primer pair on Chinese Spring, aneuploid lines, and deletion lines for the homoeologous group 5 chromosomes. A recombinant inbred line (RIL) mapping population that is recombinant for only chromosome 5A was obtained by crossing the wheat cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides and was used to develop a genetic linkage map of chromosome 5A. A total of 67 markers were found polymorphic between the parental lines and were mapped in the RIL population. Sixty-three loci and the Q gene were clustered in three linkage groups ordered at a minimum LOD score of 5, while four loci remained unlinked. The whole genetic 5A chromosome map covered 420.2 cM, distributed among three linkage groups of 189.3, 35.4, and 195.5 cM. The EST sequences located on chromosomes 5A and 5B were used for comparative analysis against Brachypodium distachyon (L.) P. Beauv. and rice ( Oryza sativa L.) genomes to resolve orthologous relationships among the genomes of wheat and the two model species.
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Emami, Mona Pishnamazzadeh, Nasser Mohebalipour, Ali Ebadi, Hassan Nourafcan, and Jalil Ajali. "Qtl mapping of some morphological traits of rice in a RILS population derived from Hashemi and modified Nemat varieties hybrid." Genetika 52, no. 3 (2020): 1087–106. http://dx.doi.org/10.2298/gensr2003087e.
Full textAbstract:
In this study, QTLs controlling traits related to crop and grain yield were mapped using 140 recombinant inbred lines (F9 and F10) along with 4 control genotypes in anaugment experiment based on a randomized complete block design in 2consecutive years. Population linkage map was consisted of 170 SSR3 / 2132 centimorgan (cM) markers of rice genome, and mean distance between adjacent markers was equal to 12.47 centimorgan (cM). Composite Interval Mapping analysis was done for studying number of days to flowering in the first year, a QTL was identified on chromosome 3 and in the second year, three QTLs were identified on chromosomes 2, 3, and 7, which were common on chromosome 3 in both years. Regarding plant height in the first and second years, a QTL was mapped on chromosome 1, which was similar in both years. In terms of number of tillers in the first year, four QTLs were identified on chromosomes 4 and 12 and in the second year two QTLs were identified on chromosomes 11 and 12, and regarding panicle length in the first year, one QTL was identified on chromosome 6 and in the second year two QTLs were identified on chromosomes 2 and 4, and in terms of flag leaf length in the first year, two QTLs were identified on chromosomes 6 and 7 and in the second year two QTLs were identified on chromosome 7.With respect to flag leaf width in the first year, two QTLs were identified on chromosomes 1and 3, and in the second year, one QTL was identified on chromosome 11, and in relation to Panicle exertion in the first year, three QTLs were identified on chromosomes 1, 2, and 8, and in the second year, two QTLs were identified on chromosomes 1 and 2.In regard to yield in the first year, one QTL was identified on chromosome 2 and in the second year, two QTLs were identified on chromosome 2. Also, clusters of genes were identified by Interval Mapping in the population with respect to different traits on chromosomes 1 (two cases) and 12 (one case).
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Speth, Benjamin, Joshua P. Rogers, Napatsakorn Boonyoo, A. J. VanMeter, Jordan Baumbach, Alina Ott, Jerott Moore, Tyler Cina, Reid Palmer, and Devinder Sandhu. "Molecular mapping of five soybean genes involved in male-sterility, female-sterility." Genome 58, no. 4 (April 2015): 143–49. http://dx.doi.org/10.1139/gen-2015-0044.
Full textAbstract:
In soybean, asynaptic and desynaptic mutants lead to abnormal meiosis and fertility reduction. Several male-sterile, female-sterile mutants have been identified and studied in soybean, however, some of these mutants have not been mapped to locations on soybean chromosomes. The objectives of this study were to molecularly map five male-sterile, female-sterile genes (st2, st4, st5, st6, and st7) in soybean and compare the map locations of these genes with already mapped sterility genes. Microsatellite markers were used in bulked segregant analyses to locate all five male-sterile, female-sterile genes to soybean chromosomes, and markers from the corresponding chromosomes were used on F2 populations to generate genetic linkage maps. The st2, st4, st5, st6, and st7 genes were located on molecular linkage group (MLG) B1 (chromosome 11), MLG D1a (chromosome 01), MLG F (chromosome 13), MLG B2 (chromosome 14), and D1b (chromosome 02), respectively. The st2, st4, st5, st6, and st7 genes were flanked to 10.3 (∼399 kb), 6.3 (∼164 kb), 3.9 (∼11.8 Mb), 11.0 (∼409 kb), and 5.3 cM (∼224 kb), and the flanked regions contained 57, 17, 362, 52, and 17 predicted genes, respectively. Future characterization of candidate genes should facilitate identification of the male- and female-fertility genes, which may provide vital insights on structure and function of genes involved in the reproductive pathway in soybean.
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Lohe, A. R., A. J. Hilliker, and P. A. Roberts. "Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster." Genetics 134, no. 4 (August 1, 1993): 1149–74. http://dx.doi.org/10.1093/genetics/134.4.1149.
Full textAbstract:
Abstract Heterochromatin in Drosophila has unusual genetic, cytological and molecular properties. Highly repeated DNA sequences (satellites) are the principal component of heterochromatin. Using probes from cloned satellites, we have constructed a chromosome map of 10 highly repeated, simple DNA sequences in heterochromatin of mitotic chromosomes of Drosophila melanogaster. Despite extensive sequence homology among some satellites, chromosomal locations could be distinguished by stringent in situ hybridizations for each satellite. Only two of the localizations previously determined using gradient-purified bulk satellite probes are correct. Eight new satellite localizations are presented, providing a megabase-level chromosome map of one-quarter of the genome. Five major satellites each exhibit a multi-chromosome distribution, and five minor satellites hybridize to single sites on the Y chromosome. Satellites closely related in sequence are often located near one another on the same chromosome. About 80% of Y chromosome DNA is composed of nine simple repeated sequences, in particular (AAGAC)n (8 Mb), (AAGAG)n (7 Mb) and (AATAT)n (6 Mb). Similarly, more than 70% of the DNA in chromosome 2 heterochromatin is composed of five simple repeated sequences. We have also generated a high resolution map of satellites in chromosome 2 heterochromatin, using a series of translocation chromosomes whose breakpoints in heterochromatin were ordered by N-banding. Finally, staining and banding patterns of heterochromatic regions are correlated with the locations of specific repeated DNA sequences. The basis for the cytochemical heterogeneity in banding appears to depend exclusively on the different satellite DNAs present in heterochromatin.
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Krawchuk, Michelle D., and Wayne P. Wahls. "Centromere Mapping Functions for Aneuploid Meiotic Products: Analysis of rec8, rec10 and rec11 Mutants of the Fission Yeast Schizosaccharomyces pombe." Genetics 153, no. 1 (September 1, 1999): 49–55. http://dx.doi.org/10.1093/genetics/153.1.49.
Full textAbstract:
AbstractRecent evidence suggests that the position of reciprocal recombination events (crossovers) is important for the segregation of homologous chromosomes during meiosis I and sister chromatids during meiosis II. We developed genetic mapping functions that permit the simultaneous analysis of centromere-proximal crossover recombination and the type of segregation error leading to aneuploidy. The mapping functions were tested in a study of the rec8, rec10, and rec11 mutants of fission yeast. In each mutant we monitored each of the three chromosome pairs. Between 38 and 100% of the chromosome segregation errors in the rec8 mutants were due to meiosis I nondisjunction of homologous chromosomes. The remaining segregation errors were likely the result of precocious separation of sister chromatids, a previously described defect in the rec8 mutants. Between 47 and 100% of segregation errors in the rec10 and rec11 mutants were due to nondisjunction of sister chromatids during meiosis II. In addition, centromere-proximal recombination was reduced as much as 14-fold or more on chromosomes that had experienced nondisjunction. These results demonstrate the utility of the new mapping functions and support models in which sister chromatid cohesion and crossover position are important determinants for proper chromosome segregation in each meiotic division.
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Bilgic, Hatice, Seungho Cho, David F. Garvin, and Gary J. Muehlbauer. "Mapping barley genes to chromosome arms by transcript profiling of wheat–barley ditelosomic chromosome addition lines." Genome 50, no. 10 (October 2007): 898–906. http://dx.doi.org/10.1139/g07-059.
Full textAbstract:
Wheat–barley disomic and ditelosomic chromosome addition lines have been used as genetic tools for a range of applications since their development in the 1980s. In the present study, we used the Affymetrix Barley1 GeneChip for comparative transcript analysis of the barley cultivar Betzes, the wheat cultivar Chinese Spring, and Chinese Spring – Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped 1257 barley genes to chromosome arms 1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL based on their transcript levels in the ditelosomic addition lines. The number of genes assigned to individual chromosome arms ranged from 24 to 197. We validated the physical locations of the genes through comparison with our previous chromosome-based physical mapping, comparative in silico mapping with rice and wheat, and single feature polymorphism (SFP) analysis. We found our physical mapping of barley genes to chromosome arms to be consistent with our previous physical mapping to whole chromosomes. In silico comparative mapping of barley genes assigned to chromosome arms revealed that the average genomic synteny to wheat and rice chromosome arms was 63.2% and 65.5%, respectively. In the 1257 mapped genes, we identified SFPs in 924 genes between the appropriate ditelosomic line and Chinese Spring that supported physical map placements. We also identified a single small rearrangement event between rice chromosome 9 and barley chromosome 4H that accounts for the loss of synteny for several genes.
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Haig, David. "A brief history of human autosomes." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1388 (August 29, 1999): 1447–70. http://dx.doi.org/10.1098/rstb.1999.0490.
Full textAbstract:
Comparative gene mapping and chromosome painting permit the tentative reconstruction of ancestral karyotypes. The modern human karyotype is proposed to differ from that of the most recent common ancestor of catarrhine primates by two major rearrangements. The first was the fission of an ancestral chromosome to produce the homologues of human chromosomes 14 and 15. This fission occurred before the divergence of gibbons from humans and other apes. The second was the fusion of two ancestral chromosomes to form human chromosome 2. This fusion occurred after the divergence of humans and chimpanzees. Moving further back in time, homologues of human chromosomes 3 and 21 were formed by the fission of an ancestral linkage group that combined loci of both human chromosomes, whereas homologues of human chromosomes 12 and 22 were formed by a reciprocal translocation between two ancestral chromosomes. Both events occurred at some time after our most recent common ancestor with lemurs. Less direct evidence suggests that the short and long arms of human chromosomes 8, 16 and 19 were unlinked in this ancestor. Finally, the most recent common ancestor of primates and artiodactyls is proposed to have possessed a chromosome that combined loci from human chromosomes 4 and 8p, a chromosome that combined loci from human chromosomes 16q and 19q, and a chromosome that combined loci from human chromosomes 2p and 20.
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Kurtz, T. W., and E. M. St Lezin. "Gene mapping in experimental hypertension." Journal of the American Society of Nephrology 3, no. 1 (July 1992): 28–34. http://dx.doi.org/10.1681/asn.v3128.
Full textAbstract:
In the rat, the results of genetic linkage studies by "candidate" gene or "positional mapping" approaches have suggested that DNA sequences that regulate blood pressure may be located in the vicinity of the kallikrein gene family on chromosome 1, the gene for angiotensin-converting enzyme on chromosome 10, the renin gene on chromosome 13, and the major histocompatibility complex on chromosome 20. Some studies have also suggested that blood pressure regulatory genes may be located on the sex chromosomes. Pending the results of confirmatory studies, these experiments should be interpreted with caution. However, with confirmation of these studies, it should be possible to create a variety of new animal models that will provide excellent opportunities for investigating the molecular, biochemical, and physiologic determinants of high blood pressure. In addition, in genetic studies in humans with essential hypertension, it may be worthwhile to target chromosome regions that are homologous to those implicated in linkage studies of hypertension in rodents. By narrowing the focus on selected areas of the genome, experimental linkage studies in the rat may also be used to guide the detailed molecular approaches ultimately required to identify the specific DNA sequence alterations that give rise to increased blood pressure.
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Voskuhl, Rhonda R., Amr H. Sawalha, and Yuichiro Itoh. "Sex chromosome contributions to sex differences in multiple sclerosis susceptibility and progression." Multiple Sclerosis Journal 24, no. 1 (January 2018): 22–31. http://dx.doi.org/10.1177/1352458517737394.
Full textAbstract:
Background: Why are women more susceptible to multiple sclerosis, but men have worse disability progression? Sex differences in disease may be due to sex hormones, sex chromosomes, or both. Objective: Determine whether differences in sex chromosomes can contribute to sex differences in multiple sclerosis using experimental autoimmune encephalomyelitis. Methods: Sex chromosome transgenic mice, which permit the study of sex chromosomes not confounded by differences in sex hormones, were used to examine an effect of sex chromosomes on autoimmunity and neurodegeneration, focusing on X chromosome genes. Results: T-lymphocyte DNA methylation studies of the X chromosome gene Foxp3 suggested that maternal versus paternal imprinting of X chromosome genes may underlie sex differences in autoimmunity. Bone marrow chimeras with the same immune system but different sex chromosomes in the central nervous system suggested that differential expression of the X chromosome gene Toll-like receptor 7 in neurons may contribute to sex differences in neurodegeneration. Conclusion: Mapping the transcriptome and methylome in T lymphocytes and neurons in females versus males could reveal mechanisms underlying sex differences in autoimmunity and neurodegeneration.
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Leitch, I. J., and J. S. Heslop-Harrison. "Physical mapping of the 18S–5.8S–26S rRNA genes in barley by in situ hybridization." Genome 35, no. 6 (December 1, 1992): 1013–18. http://dx.doi.org/10.1139/g92-155.
Full textAbstract:
The 18S–5.8S–26S rRNA genes have been located on five pairs of barley (Hordeum vulgare L., 2n = 2x = 14) chromosomes (in descending order of copy number, barley chromosome numbers 6, 7, 5, 1, and 2; homoeologous groups 6I, 5I, 1I, 7I, and 2I) by in situ hybridization followed by C-banding. All sites were at intercalary positions. The pairs of major sites on chromosomes 6 (6I)1 and 7 (5I) are well known. Silver staining of nuclei and meiotic analysis have previously indicated that additional rDNA sites may be present, but the presence of sites on a further three chromosome pairs was unexpected. Within the tribe Triticeae, few species have more than two pairs of rDNA sites, and they have not been reported on group 2 chromosomes. We propose calling the new sites Nor-I1 (on chromosome 5 (1I)), Nor-I4 (on chromosome 1 (7I)), and Nor-I5 (on chromosome 2 (2I)), and that any further rDNA sites on homoeologous group 2 chromosomes should be called Nor-5. As conventional, all designations are based on temporal order of discovery in the Triticeae and designating the H. vulgare genome as I. In situ hybridization is valuable for gene mapping, since it can detect the presence of genes with a very wide range of copy numbers at different sites.Key words: C-banding, nucleolus organizer regions, fluorescent in situ hybridization, Hordeum vulgare, gene mapping.
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Dias Silva, Yhanndra Karine, Mariela Analía Sader, Carla Munhoz, Maria Lucia Vieira, and Andrea Pedrosa-Harand. "Comparative cytogenetic mapping of chromosomes bearing rDNA sites in Passiflora subgenus Passiflora (Passifloracea)." Semina: Ciências Biológicas e da Saúde 38, no. 1supl (February 16, 2018): 139. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp139.
Full textAbstract:
The genus Passiflora L. comprises around 500 species with different haploid numbers (n = 6, 9, 10 e 12) and variability in the number of ribosomal DNA sites (rDNA). The subgenus Passiflora Juss. is one of the most diverse and includes several species of economic importance, such as Passiflora edulis and Passiflora alata Curtis, as well as Passiflora watsoniana Mast., which is endemic to Northeastern Brazil. These three species present 2n = 18 and two (P. edulis, P. alata) or three (P. watsoniana) pairs of 35S rDNA sites. In P. edulis, these sites are located in chromosomes 7 and 8, identified by fluorescent in situ hybridization (FISH) with chromosome-specific bacterial artificial chromosomes (BACs). With the aim of investigating the conservation of synteny between these species, we used FISH with BACs 173B16 and 164M13, markers for chromosome 7 and 8, respectively, followed by FISH with rDNA. As previously observed in P. edulis, 35S rDNA sites were observed in opposite arms to the BAC markers of chromosome 7 and 8 of both, P. alata and P. watsoniana. In P. alata, the 35S rDNA was observed in the short arm of chromosome 7 and in the long arm of chromosome 8, as in P. edulis. In P. watsoniana, however, the 35S rDNA was located in the long arm of three chromosome pairs, two of them confirmed as chromosomes 7 and 8. The change between short and long arms in the chromosome 8 of P. watsoniana, as well as the presence of an extra rDNA site, is compatible with its phylogenetic distance and indicates karyotypic changes even among species with n = 9 in the Passiflora subgenus.Financial support: CAPES, CNPq and FACEPE
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Han, F., A. Kleinhofs, S. E. Ullrich, A. Kilian, M. Yano, and T. Sasaki. "Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions." Genome 41, no. 3 (June 1, 1998): 373–80. http://dx.doi.org/10.1139/g98-027.
Full textAbstract:
The barley (Hordeum vulgare L.) chromosome 1 centromere region contains two adjacent overlapping quantitative trait loci (QTLs) for malting quality traits, and the chromosome 7L subtelomere region contains the stem rust (causal agent Puccinia graminis f.sp. tritici) resistance gene rpg4. To facilitate the saturation mapping of these two target regions, a synteny-based approach was employed. Syntenic relationships between the barley target regions and the rice (Oryza sativa) genome were established through comparative mapping. The barley chromosome 1 centromere region was found to be syntenic with rice chromosome 8 and parts of rice chromosomes 3 and 10. A 6- to 15-fold difference in genetic distance between barley and rice in the syntenic region was observed, owing to the apparent suppressed recombination in the barley chromosome 1 centromere region. Barley chromosome 7L was found to be syntenic with rice chromosome 3. The establishment of synteny with rice in the two target regions allows well-established and characterized rice resources to be utilized in fine mapping and map-based cloning studies.Key words: genome synteny, quantitative trait loci, QTL, disease resistance gene, Triticeae.
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Sahara, Ken, Atsuo Yoshido, František Marec, Iva Fuková, Hong-Bin Zhang, Cheng-Cang Wu, Marian R. Goldsmith, and Yuji Yasukochi. "Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH." Genome 50, no. 11 (November 2007): 1061–65. http://dx.doi.org/10.1139/g07-082.
Full textAbstract:
The successful assignment of the existing genetic linkage groups (LGs) to individual chromosomes and the second-generation linkage map obtained by mapping a large number of bacterial artificial chromosome (BAC) contigs in the silkworm, Bombyx mori , together with public nucleotide sequence databases, offer a powerful tool for the study of synteny between karyotypes of B. mori and other lepidopteran species. Conserved synteny of genes between particular chromosomes can be identified by comparatively mapping orthologous genes of the corresponding linkage groups with the help of BAC-FISH (fluorescent in situ hybridization). This technique was established in B. mori for 2 differently labeled BAC probes simultaneously hybridized to pachytene bivalents. To achieve higher-throughput comparative mapping using BAC-FISH in Lepidoptera, we developed a protocol for five-color BAC-FISH, which allowed us to map simultaneously 6 different BAC probes to chromosome 15 in B. mori. We identified orthologs of 6 B. mori LG15 genes (RpP0, RpS8, eIF3, RpL7A, RpS23, and Hsc70) for the tobacco hornworm, Manduca sexta , and selected the ortholog-containing BAC clones from an M. sexta BAC library. All 6 M. sexta BAC clones hybridized to a single M. sexta bivalent in pachytene spermatocytes. Thus, we have confirmed the conserved synteny between the B. mori chromosome 15 and the corresponding M. sexta chromosome (hence provisionally termed chromosome 15).
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Konerat, Jocicléia Thums, Vanessa Bueno, Lucas Baumgartner, Isabel Cristina Martins-Santos, and Vladimir Pavan Margarido. "B chromosome and NORs polymorphism in Callichthys callichthys (Linnaeus, 1758) (Siluriformes: Callichthyidae) from upper Paraná River, Brazil." Neotropical Ichthyology 12, no. 3 (June 23, 2014): 603–9. http://dx.doi.org/10.1590/1982-0224-20130189.
Full textAbstract:
B chromosomes are extra chromosomes from the normal chromosomal set, found in different organisms, highlighting their presence on the group of fishes. Callichthys callichthys from the upper Paraná River has a diploid number of 56 chromosomes (26 m-sm + 30 st-a) for both sexes, with the presence of a sporadically acrocentric B chromosome. Moreover, one individual presented a diploid number of 57 chromosomes, with the presence of a morphologically ill-defined acrocentric B chromosome in all analyzed cells. The physical mapping of 5S and 18S rDNA shows multiple 5S rDNA sites and only one pair of chromosomes with 18S sites in C. callichthys, except for two individuals. These two individuals presented a third chromosome bearing NORs (Ag-staining and 18S rDNA) where 5S and 18S rDNA genes are syntenic, differing only in position. The dispersion of the 18S rDNA genes from the main st-achromosome pair 25 to one of the chromosomes from the m-sm pair 4 would have originated two variant individuals, one of which with the ill-defined acrocentric B chromosome. Mechanisms to justify the suggested hypothesis about this B chromosome origin are discussed in the present study.
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Hohmann, Uwe, Winfried Busch, Katia Badaeva, Bernd Friebe, and Bikram S. Gill. "Molecular cytogenetic analysis of Agropyron chromatin specifying resistance to barley yellow dwarf virus in wheat." Genome 39, no. 2 (April 1, 1996): 336–47. http://dx.doi.org/10.1139/g96-044.
Full textAbstract:
Nine families of bread wheat (TC5, TC6, TC7, TC8, TC9, TC10, TC14, 5395-(243AA), and 5395) with resistance to barley yellow dwarf virus and containing putative translocations between wheat and a group 7 chromosome of Agropyron intermedium (L1 disomic addition line, 7Ai#1 chromosome) induced by homoeologous pairing or tissue culture were analyzed. C-banding, genomic in situ hybridization (GISH), and restriction fragment length polymorphism (RFLP) in combination with repetitive Agropyron-specific sequences and deletion mapping in wheat were used to determine the relative locations of the translocation breakpoints and the size of the transferred alien chromatin segments in hexaploid wheat–Agropyron translocation lines. All homoeologous compensating lines had complete 7Ai#1 or translocated 7Ai#1–7D chromosomes that substitute for chromosome 7D. Two complete 7Ai#1 (7D) substitution lines (5395-(243AA) and 5395), one T1BS–7Ai#1S∙7Ai#1L addition line (TC7), and two different translocation types, T7DS–7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and T7DS∙7DL–7Ai#1L (TC14), substituting for chromosome 7D were identified. The substitution line 5395-(243AA) had a reciprocal T1BS∙1BL–4BS/T1BL–4BS∙4BL translocation. TC14 has a 6G (6B) substitution. The RFLP data from deletion mapping studies in wheat using 37 group 7 clones provided 10 molecular tagged chromosome regions for homoeologous and syntenic group 7 wheat or Agropyron chromosomes. Together with GISH we identified three different sizes of the transferred Agropyron chromosome segments with approximate breakpoints at fraction length (FL) 0.33 in the short arm of chromosome T7DS–7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and another at FL 0.37 of the nonhomoeologous translocated chromosome T1BS–7Ai#1S∙7Ai#1L (TC7). One breakpoint was identified in the long arm of chromosome T7DS∙7DL–7Ai#1L (TC14) at FL 0.56. We detected some nonreciprocal translocations for the most proximal region of the chromosome arm of 7DL, which resulted in small duplications. Key words : C-banding, genomic in situ hybridization (GISH), physical mapping, translocation mapping, RFLP analysis.
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Hanic-Joyce, Pamela J. "MAPPING CDC MUTATIONS IN THE YEAST S. Cerevisiae BY RAD52-MEDIATED CHROMOSOME LOSS." Genetics 110, no. 4 (August 1, 1985): 591–607. http://dx.doi.org/10.1093/genetics/110.4.591.
Full textAbstract:
ABSTRACT Using the chromosome loss-mapping method of Schild and Mortimer, I have mapped several new temperature-sensitive mutations that define five CDC genes. Modified procedures were used to facilitate mapping temperature-sensitive mutations in general, and these modifications are discussed. The mutations were assigned to specific chromosomes by chromosome loss procedures, and linkage relationships were determined subsequently by standard tetrad analysis. Four of the mutations define new loci. The fifth mutation, cdc63-1, is shown to be allelic to previously known mutations in the PRT1 gene.
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Thongnetr, Weera, Surachest Aiumsumang, Rodjarin Kongkaew, Alonglod Tanomtong, Chatmongkon Suwannapoom, and Sumalee Phimphan. "Cytogenetic characterisation and chromosomal mapping of microsatellite and telomeric repeats in two gecko species (Reptilia, Gekkonidae) from Thailand." Comparative Cytogenetics 15, no. 1 (February 2, 2021): 41–52. http://dx.doi.org/10.3897/compcytogen.v15i1.58208.
Full textAbstract:
Studies of chromosomes of Cyrtodactylus jarujini Ulber, 1993 and C. doisuthep Kunya et al., 2014 to compare microsatellite and TTAGGG sequences by classical and molecular techniques were conducted in Thailand. Karyological typing from a conventional staining technique of C. jarujini and C. doisuthep showed diploid chromosome numbers of 40 and 34 while the Fundamental Numbers (NF) were 56 in both species. In addition, we created the chromosome formula of the chromosomes of C. jarujini showing that 2n (40) = Lsm1 + Lsm2 + Lt3 + Mm1 + Mt4 + Sm2 + Sa2 + St5 while that of C. doisuthep was 2n (34) = Lsm3 + Lm2 + Lt3 + Mm1 + Mt2 + Sm4 + Sa1 + St1. Ag-NOR staining revealed NOR-bearing chromosomes in chromosome pairs 13 and 14 in C. jarujini, and in chromosome pairs 9 and 13 in C. doisuthep. This molecular study used the FISH technique, as well as microsatellite probes including (A)20, (TA)15, (CGG)10, (CGG)10, (GAA)10, (TA)15 and TTAGGG repeats. The signals showed that the different patterns in each chromosome of the Gekkonids depended on probe types. TTAGGG repeats showed high distribution on centromere and telomere regions, while (A)20, (TA)15, (CGG)10, (CGG)10, (GAA)10 and (TA)15 bearing dispersed over the whole genomes including chromosomes and some had strong signals on only a pair of homologous chromosomes. These results suggest that the genetic linkages have been highly differentiated between the two species.