Artykuły w czasopismach na temat „Chromosome mapping”
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Iannucci, Alessio, Marie Altmanová, Claudio Ciofi, Malcolm Ferguson-Smith, Jorge C. Pereira, Ivan Rehák, Roscoe Stanyon i in. "Isolating Chromosomes of the Komodo Dragon: New Tools for Comparative Mapping and Sequence Assembly". Cytogenetic and Genome Research 157, nr 1-2 (2019): 123–31. http://dx.doi.org/10.1159/000496171.
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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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Uno, Yoshinobu, Chizuko Nishida, Chiyo Takagi, Takeshi Igawa, Naoto Ueno, Masayuki Sumida i Yoichi Matsuda. "Extraordinary Diversity in the Origins of Sex Chromosomes in Anurans Inferred from Comparative Gene Mapping". Cytogenetic and Genome Research 145, nr 3-4 (2015): 218–29. http://dx.doi.org/10.1159/000431211.
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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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González-Siso, M. Isabel, M. Angeles Freire-Picos, M. Esperanza Cerdán, M. Wésolowski-Louvel i H. Fukuhara. "Chromosomal mapping of the KlCYC1 gene from Kluyveromyces lactis". Genome 37, nr 3 (1.06.1994): 515–17. http://dx.doi.org/10.1139/g94-073.
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Chromosomal assignment of the KlCYC1 gene from Kluyveromyces lactis has been performed by hybridization of the labelled probe to a DNA blot of isolated chromosomes. A clear hybridization signal to chromosome VI is reported.Key words: Kluyveromyces lactis, cytochrome c gene, chromosomal mapping.
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Schild, David, i Robert K. Mortimer. "A MAPPING METHOD FOR SACCHAROMYCES CEREVISIAE USING rad52-INDUCED CHROMOSOME LOSS". Genetics 110, nr 4 (1.08.1985): 569–89. http://dx.doi.org/10.1093/genetics/110.4.569.
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ABSTRACT Saccharomyces cerevisiae diploids homozygous for the rad52-1 mutation have previously been shown to lose chromosomes mitotically. Spontaneous events and events following low levels of X-ray or methyl methanesulfonate treatment result in monosomic diploids, whereas higher levels of treatment result in near haploidization. This rad52-1-dependent chromosome loss has been used to develop a new mapping method which can be used to assign a previously unmapped gene to a chromosome. Chromosome loss mapping can be done in either of two ways: (1) if a diploid, homozygous for rad52-1 but heterozygous for a variety of other recessive markers, is constructed with an unmapped recessive mutation in coupling with known chromosomal markers, chromosome loss will result in the coordinate expression of the mutation and other recessive markers on the same chromosome; (2) if, however, the diploid is constructed with the unmapped mutation in repulsion to chromosomal markers, then even haploidization will never result in the coordinate expression of the unmapped mutation and other markers on the same homologous chromosome pair—This mapping method and subsequent tetrad analyses have been used to locate hom6 on chromosome X, ade4 on chromosome XIII and cdc31 on chromosome XV and to demonstrate that met5, previously assigned to chromosome V, actually maps to chromosome X; the met- marker on chromosome V has been shown to be met6. GAL80 and SUP5, previously assigned to an unmapped fragment, have now been mapped to the right arm of chromosome XIII.
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Hausmann, Michael, C. Paul Popescu, Jeannine Boscher, Dominique Kerboœf, Jürgen Dölle i Christoph Cremer. "Identification and Cytogenetic Analysis of an Abnormal Pig Chromosome for Flow Cytometry and Sorting". Zeitschrift für Naturforschung C 48, nr 7-8 (1.08.1993): 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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Favarato, Ramon M., Leila Braga Ribeiro, Rafaela P. Ota, Celeste M. Nakayama i Eliana Feldberg. "Cytogenetic Characterization of Two Metynnis Species (Characiformes, Serrasalmidae) Reveals B Chromosomes Restricted to the Females". Cytogenetic and Genome Research 158, nr 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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Goodfellow, P. N. "Mapping the Y chromosome". Development 101, Supplement (1.03.1987): 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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Lohe, A. R., A. J. Hilliker i P. A. Roberts. "Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster." Genetics 134, nr 4 (1.08.1993): 1149–74. http://dx.doi.org/10.1093/genetics/134.4.1149.
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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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Yuan, Xiuyun, Siqi Yuan, Ya Liu, Yun Xia i Xiaomao Zeng. "Microsatellites mapping for non-model species with chromosomal rearrangement: a case study in the frog Quasipaa boulengeri (Anura: Dicroglossidae)". Genome 60, nr 8 (sierpień 2017): 707–11. http://dx.doi.org/10.1139/gen-2016-0200.
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Gene mapping is an important resource for understanding the evolution of genes and cytogenetics. Model species with a known genetic map or genome sequence allow for the selection of genetic markers on a desired chromosome, while it is hard to locate these markers on chromosomes of non-model species without such references. A frog species, Quasipaa boulengeri, shows chromosomal rearrangement polymorphisms, making itself a fascinating model for chromosomal speciation mediated by suppressed recombination. However, no markers have been located on its rearranged chromosomes. We present a complete protocol to map microsatellites based on mechanical microdissection and chromosome amplification techniques. Following this protocol, we mapped 71 microsatellites of Q. boulengeri at the chromosome level. In total, eight loci were assigned to rearranged chromosomes, and the other 63 loci might attach to other chromosomes. These microsatellites could be used to compare the gene flow and verify the chromosomal suppressed recombination hypothesis in Q. boulengeri. This integrated protocol could be effectively used to map genes to chromosomes for non-model species.
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Liang, Jiangtao, Simon M. Bondarenko, Igor V. Sharakhov i Maria V. Sharakhova. "Obtaining Polytene, Meiotic, and Mitotic Chromosomes from Mosquitoes for Cytogenetic Analysis". Cold Spring Harbor Protocols 2022, nr 12 (5.08.2022): pdb.prot107872. http://dx.doi.org/10.1101/pdb.prot107872.
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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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Cadle, M. M., L. M. Rayfuse, M. K. Walker-Simmons i S. S. Jones. "Mapping of abscisic acid responsive genes and vp1 to chromosomes in wheat and Lophopyrum elongatum". Genome 37, nr 1 (1.02.1994): 129–32. http://dx.doi.org/10.1139/g94-016.
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The plant hormone abscisic acid (ABA) affects developmental and physiological processes that can impact crop production. These processes include germination, environmental stress responses in vegetative tissue, embryo maturation, and dormancy. Identification and molecular tagging of ABA-responsive genes, as well as the vp1 gene, required for ABA sensitivity, may be valuable in developing breeding strategies designed for manipulating ABA-regulated traits. Using aneuploid genetic stocks and alien substitution lines the chromosomal location of vp1 and seven abscisic acid (ABA) responsive genes was determined in wheat and Lophopyrum elongatum (Host) Löve. Clones (gene homology, if known, in parentheses) isolated from wheat hybridized to wheat and L. elongatum homoeologous chromosome groups as follows: pMA80 (dhn), chromosome 4; pMA1949 (group 3 LEA (1I)), chromosome 3S; pMA1951, chromosome 5S; pMA1959 (Em), chromosome 1L; pMA2005 (group 3 LEA), chromosome 1S; and PKABA1, chromosome 2L. Clone pBS128, corresponding to an ABA-responsive gene from Bromus secalinus, hybridized to wheat chromosome 2S. The cDNA clone pcvp23 that is homologous to vp1, a gene required for ABA responsiveness and the prevention of precocious germination in maize embryos, did not hybridize well with wheat but hybridized to chromosomes 3L and 7β in L. elongatum. Three of the clones mapped previously in barley by other researchers, pMA1949, pMA1951, pMA1959, were found here to be on the corresponding homoeologous chromosomes in wheat.Key words: abscisic acid, Triticum aestivum, Lophopyrum elongatum, homeology, mapping.
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Weber, D., i T. Helentjaris. "Mapping RFLP loci in maize using B-A translocations." Genetics 121, nr 3 (1.03.1989): 583–90. http://dx.doi.org/10.1093/genetics/121.3.583.
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Abstract Plants hypoploid for specific segments of each of the maize (Zea mays L.) chromosomes were generated using 24 different B-A translocations. Plants carrying each of the B-A translocations were crossed as male parents to inbreds, and sibling progeny hypoploid or not hypoploid for specific chromosomal segments were recovered. Genomic DNAs from the parents, hypoploid progeny, and nonhypoploid (euploid or hyperploid) progeny for each of these B-A translocations were digested with restriction enzymes, electrophoresed in agarose gels, blotted onto reusable nylon membranes, and probed with nick-translated, cloned DNA fragments which had been mapped previously by restriction fragment length polymorphism (RFLP) analysis to the chromosome involved in the B-A translocation. The chromosomal segment on our RFLP map which was uncovered by each of the B-A translocations was determined. This work unequivocally identified the short and long arms of each chromosome on this map, and it also identified the region on each chromosome which contains the centromere. Because the breakpoints of the B-a translocations were previously known on the cytological and the conventional genetic maps, this study also allowed this RFLP map to be more highly correlated with these maps.
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Ruiz, Alfredo, José María Ranz, Mario Cáceres i Carmen Segarra. "Chromosomal evolution and comparative gene mapping in the Drosophila repleta species group". Brazilian Journal of Genetics 20, nr 4 (grudzień 1997): 553–65. http://dx.doi.org/10.1590/s0100-84551997000400003.
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A review of our recent work on the cromosomal evolution of the Drosophila repleta species group is presented. Most studies have focused on the buzzatii species complex, a monophyletic set of 12 species which inhabit the deserts of South America and the West Indies. A statistical analysis of the length and breakpoint distribution of the 86 paracentric inversions observed in this complex has shown that inversion length is a selected trait. Rare inversions are usually small while evolutionary successful inversions, fixed and polymorphic, are predominantly of medium size. There is also a negative correlation between length and number of inversions per species. Finally, the distribution of inversion breakpoints along chromosome 2 is non-random, with chromosomal regions which accumulate up to 8 breakpoints (putative "hot spots"). Comparative gene mapping has also been used to investigate the molecular organization and evolution of chromosomes. Using in situ hybridization, 26 genes have been precisely located on the salivary gland chromosomes of D. repleta and D. buzzatii; another nine have been tentatively identified. The results are fully consistent with the currently accepted chromosomal homologies between D. repleta and D. melanogaster, and no evidence for reciprocal translocations or pericentric inversions has been found. The comparison of the gene map of D. repleta chromosome 2 with that of the homologous chromosome 3R of D. melanogaster shows an extensive reorganization via paracentric inversions and allows to estimate an evolution rate of ~1 inversion fixed per million years for this chromosome
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Riera-Lizarazu, O., M. I. Vales, E. V. Ananiev, H. W. Rines i R. L. Phillips. "Production and Characterization of Maize Chromosome 9 Radiation Hybrids Derived From an Oat-Maize Addition Line". Genetics 156, nr 1 (1.09.2000): 327–39. http://dx.doi.org/10.1093/genetics/156.1.327.
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Abstract In maize (Zea mays L., 2n = 2x = 20), map-based cloning and genome organization studies are often complicated because of the complexity of the genome. Maize chromosome addition lines of hexaploid cultivated oat (Avena sativa L., 2n = 6x = 42), where maize chromosomes can be individually manipulated, represent unique materials for maize genome analysis. Maize chromosome addition lines are particularly suitable for the dissection of a single maize chromosome using radiation because cultivated oat is an allohexaploid in which multiple copies of the oat basic genome provide buffering to chromosomal aberrations and other mutations. Irradiation (gamma rays at 30, 40, and 50 krad) of a monosomic maize chromosome 9 addition line produced maize chromosome 9 radiation hybrids (M9RHs)—oat lines possessing different fragments of maize chromosome 9 including intergenomic translocations and modified maize addition chromosomes with internal and terminal deletions. M9RHs with 1 to 10 radiation-induced breaks per chromosome were identified. We estimated that a panel of 100 informative M9RHs (with an average of 3 breaks per chromosome) would allow mapping at the 0.5- to 1.0-Mb level of resolution. Because mapping with maize chromosome addition lines and radiation hybrid derivatives involves assays for the presence or absence of a given marker, monomorphic markers can be quickly and efficiently mapped to a chromosome region. Radiation hybrid derivatives also represent sources of region-specific DNA for cloning of genes or DNA markers.
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Bedo, D. G. "Polytene chromosome mapping in Ceratitis capitata (Diptera: Tephritidae)". Genome 29, nr 4 (1.08.1987): 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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Nelson, J. C., M. E. Sorrells, A. E. Van Deynze, Y. H. Lu, M. Atkinson, M. Bernard, P. Leroy, J. D. Faris i J. A. Anderson. "Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7." Genetics 141, nr 2 (1.10.1995): 721–31. http://dx.doi.org/10.1093/genetics/141.2.721.
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Abstract A molecular-marker linkage map of hexaploid wheat (Triticum aestivum L. em. Thell) provides a framework for integration with teh classical genetic map and a record of the chromosomal rearrangements involved in the evolution of this crop species. We have constructed restriction fragment length polymorphism (RFLP) maps of the A-, B-, and D-genome chromosomes of homoeologous groups 4, 5, and 7 of wheat using 114 F7 lines from a synthetic X cultivated wheat cross and clones from 10 DNA libraries. Chromosomal breakpoints for known ancestral reciprocal translocations involving these chromosomes and for a known pericentric inversion on chromosome 4A were localized by linkage and aneuploid analysis. Known genes mapped include the major vernalization genes Vrn1 and Vrn3 on chromosome arms 5AL and 5DL, the red-coleoptile gene Rc1 on 7AS, and presumptively the leaf-rust (Puccinia recondita f.sp. tritici) resistance gene Lr34 on 7DS and the kernel-hardness gene Ha on 5DS. RFLP markers previously obtained for powdery-mildew (Blumeria graminis f.sp. tritici) resistance genes Pm2 and Pm1 were localized on chromosome arms 5DS and 7AL.
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Sarma, R. N., L. Fish, B. S. Gill i 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, nr 1 (1.02.2000): 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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Cheng, Zhukuan, Gernot G. Presting, C. Robin Buell, Rod A. Wing i 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, nr 4 (1.04.2001): 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 i Pawel Michalak. "Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila". Cytogenetic and Genome Research 152, nr 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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Gschwend, Andrea R., Qingyi Yu, Paul Moore, Christopher Saski, Cuixia Chen, Jianping Wang, Jong-Kuk Na i Ray Ming. "Construction of Papaya Male and Female BAC Libraries and Application in Physical Mapping of the Sex Chromosomes". Journal of Biomedicine and Biotechnology 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/929472.
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Papaya is a major fruit crop in the tropics and has recently evolved sex chromosomes. Towards sequencing the papaya sex chromosomes, two bacterial artificial chromosome (BAC) libraries were constructed from papaya male and female genomic DNA. The female BAC library was constructed using restriction enzymeBstY I and consists of 36,864 clones with an average insert size of 104 kb, providing 10.3x genome equivalents. The male BAC library was constructed using restriction enzymeEcoR I and consists of 55,296 clones with an average insert size of 101 kb, providing 15.0x genome equivalents. The male BAC library was used in constructing the physical map of the male-specific region of the male Y chromosome (MSY) and in filling gaps and extending the physical map of the hermaphrodite-specific region of the Yhchromosome (HSY) and the X chromosome physical map. The female BAC library was used to extend the X physical map gap. The MSY, HSY, and X physical maps offer a unique opportunity to study chromosomal rearrangements, Y chromosome degeneration, and dosage compensation of the papaya nascent sex chromosomes.
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Luo, Chao-Xi, Liang-Fen Yin, Satomi Koyanagi, Mark L. Farman, Motoaki Kusaba i Hiroshi Yaegashi. "Genetic Mapping and Chromosomal Assignment of Magnaporthe oryzae Avirulence Genes AvrPik, AvrPiz, and AvrPiz-t Controlling Cultivar Specificity on Rice". Phytopathology® 95, nr 6 (czerwiec 2005): 640–47. http://dx.doi.org/10.1094/phyto-95-0640.
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A genetic map including three avirulence (Avr) genes, AvrPik, AvrPiz, and AvrPiz-t, was constructed in a genetic cross of two rice field isolates, 84R-62B and Y93-245c-2. The chromosomal locations of the Avr genes were determined by using selected markers to probe Southern blots of the parental chromosomes that had been separated by contour-clamped homogenous electric fields electrophoresis. Electrophoretic karyotyping showed that both parental isolates 84R-62B and Y93-245c-2 contained seven chromosomes greater than 3.5 megabases (Mb) in size and 84R-62B possessed a small chromosome of ≈1.6 Mb. The linkage groups containing AvrPiz and AvrPiz-t were assigned to chromosomes 3 and 7, respectively. Some markers from the linkage group that contained AvrPik hybridized with chromosome 1 and the 1.6-Mb chromosome, yet all of the cloned RAPD markers that were closely linked to AvrPik hybridized exclusively to the 1.6-Mb chromosome in 84R-62B, the parent that possesses AvrPik. Thus, we conclude that AvrPik is located on the 1.6-Mb chromosome in 84R-62B.
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Orosová, Martina, Anna Marková, Magda Zrzavá, František Marec i Mikuláš Oros. "Chromosome analysis and the occurrence of B chromosomes in fish parasite Acanthocephalus anguillae (Palaeacanthocephala: Echinorhynchida)". Parasite 30 (2023): 44. http://dx.doi.org/10.1051/parasite/2023045.
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The cytogenetics of Acanthocephala is a neglected area in the study of this group of endoparasites. Chromosome number and/or karyotypes are known for only 12 of the 1,270 described species, and molecular cytogenetic data are limited to rDNA mapping in two species. The standard karyological technique and mapping of 18S rRNA and H3 histone genes on the chromosomes of Acanthocephalus anguillae individuals from three populations, one of which originated from the unfavorable environmental conditions of the Zemplínska Šírava reservoir in eastern Slovakia, were applied for the first time. All specimens had 2n = 7/8 (male/female); n = 1m + 1m-sm + 1a + 1a (X). Fluorescence in situ hybridization (FISH) revealed three loci of 18S rDNA on two autosomes and dispersion of H3 histone genes on all autosomes and the X chromosome. In addition to the standard A chromosome set, 34% of specimens from Zemplínska Šírava possessed a small acrocentric B chromosome, which was always found to be univalent, with no pairing observed between the B chromosome and the A complement. The B chromosome had a small amount of heterochromatin in the centromeric and telomeric regions of the chromosomal arms and showed two clusters of H3 genes. It is well known that an environment permanently polluted with chemicals leads to an increased incidence of chromosomal rearrangements. As a possible scenario for the B chromosome origin, we propose chromosomal breaks due to the mutagenic effect of pollutants in the aquatic environment. The results are discussed in comparison with previous chromosome data from Echinorhynchida species.
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Allen, Sally Lyman, Dawn Zeilinger i Eduardo Orias. "Mapping Three Classical Isozyme Loci in Tetrahymena: Meiotic Linkage of EstA to the ChxA Linkage Group". Genetics 144, nr 4 (1.12.1996): 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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Scardino, Rita, Vanessa Milioto, Anastasia A. Proskuryakova, Natalia A. Serdyukova, Polina L. Perelman i Francesca Dumas. "Evolution of the Human Chromosome 13 Synteny: Evolutionary Rearrangements, Plasticity, Human Disease Genes and Cancer Breakpoints". Genes 11, nr 4 (1.04.2020): 383. http://dx.doi.org/10.3390/genes11040383.
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The history of each human chromosome can be studied through comparative cytogenetic approaches in mammals which permit the identification of human chromosomal homologies and rearrangements between species. Comparative banding, chromosome painting, Bacterial Artificial Chromosome (BAC) mapping and genome data permit researchers to formulate hypotheses about ancestral chromosome forms. Human chromosome 13 has been previously shown to be conserved as a single syntenic element in the Ancestral Primate Karyotype; in this context, in order to study and verify the conservation of primate chromosomes homologous to human chromosome 13, we mapped a selected set of BAC probes in three platyrrhine species, characterised by a high level of rearrangements, using fluorescence in situ hybridisation (FISH). Our mapping data on Saguinus oedipus, Callithrix argentata and Alouatta belzebul provide insight into synteny of human chromosome 13 evolution in a comparative perspective among primate species, showing rearrangements across taxa. Furthermore, in a wider perspective, we have revised previous cytogenomic literature data on chromosome 13 evolution in eutherian mammals, showing a complex origin of the eutherian mammal ancestral karyotype which has still not been completely clarified. Moreover, we analysed biomedical aspects (the OMIM and Mitelman databases) regarding human chromosome 13, showing that this autosome is characterised by a certain level of plasticity that has been implicated in many human cancers and diseases.
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Watkins, PC, R. Eddy, Y. Fukushima, MG Byers, EH Cohen, WR Dackowski, RM Wydro i TB Shows. "The gene for protein S maps near the centromere of human chromosome 3". Blood 71, nr 1 (1.01.1988): 238–41. http://dx.doi.org/10.1182/blood.v71.1.238.238.
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Abstract Two different mapping approaches were used to determine the human chromosomal location of the gene for protein S. A human protein S cDNA was used as a hybridization probe to analyze a panel of somatic cell hybrids containing different human chromosomes. Cosegregation of protein S-specific DNA restriction fragments with human chromosome 3 was observed. Three cell hybrids containing only a portion of chromosome 3 were analyzed in order to further localize protein S. Based on the somatic cell hybrid analysis, protein S is assigned to a region of chromosome 3 that contains a small part of the long arm and short arm of the chromosome including the centromere (3p21----3q21). In situ hybridization of the protein S cDNA probe to human metaphase chromosomes permitted a precise localization of protein S to the region of chromosome 3 immediately surrounding the centromere (3p11.1---- 3q11.2). Protein S is the first protein involved in blood coagulation that has been mapped to human chromosome 3.
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Watkins, PC, R. Eddy, Y. Fukushima, MG Byers, EH Cohen, WR Dackowski, RM Wydro i TB Shows. "The gene for protein S maps near the centromere of human chromosome 3". Blood 71, nr 1 (1.01.1988): 238–41. http://dx.doi.org/10.1182/blood.v71.1.238.bloodjournal711238.
Pełny tekst źródłaStreszczenie:
Two different mapping approaches were used to determine the human chromosomal location of the gene for protein S. A human protein S cDNA was used as a hybridization probe to analyze a panel of somatic cell hybrids containing different human chromosomes. Cosegregation of protein S-specific DNA restriction fragments with human chromosome 3 was observed. Three cell hybrids containing only a portion of chromosome 3 were analyzed in order to further localize protein S. Based on the somatic cell hybrid analysis, protein S is assigned to a region of chromosome 3 that contains a small part of the long arm and short arm of the chromosome including the centromere (3p21----3q21). In situ hybridization of the protein S cDNA probe to human metaphase chromosomes permitted a precise localization of protein S to the region of chromosome 3 immediately surrounding the centromere (3p11.1---- 3q11.2). Protein S is the first protein involved in blood coagulation that has been mapped to human chromosome 3.
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Westbrook, CA, CM Rubin, JJ Carrino, MM Le Beau, A. Bernards i JD Rowley. "Long-range mapping of the Philadelphia chromosome by pulsed-field gel electrophoresis". Blood 71, nr 3 (1.03.1988): 697–702. http://dx.doi.org/10.1182/blood.v71.3.697.697.
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Abstract The Philadelphia chromosome (Ph1) of chronic myelogenous leukemia (CML) contains sequences from chromosome 9, including the ABL protooncogene, that have been translocated to the breakpoint cluster region (bcr) of chromosome 22, giving rise to a bcr-ABL fusion gene, whose product has been implicated in the genesis of CML. Although chromosome 22 translocation breakpoints in CML virtually always occur within the 5.8- kilobase (kb) bcr, chromosome 9 breakpoints have been identified within the known limits of ABL in only a few instances. For a better understanding of the variability of the breakpoints on chromosome 9, we studied the CML cell line BV173. Using pulsed-field gel electrophoresis (PFGE), large-scale maps of the t(9;22) junctions were constructed. The chromosome 9 breakpoint was shown to have occurred within an ABL intron, 160 kb upstream of the v-abl homologous sequences, but still 35 kb downstream of the 5′-most ABL exon. bcr-ABL and ABL-bcr fusion genes were demonstrated on the Ph1 and the 9q+ chromosomes, respectively; both of these genes are expressed. These results suggest that the 9;22 translocation breakpoints in CML consistently occur within the limits of the large ABL gene. RNA splicing, sometimes of very large regions, appears to compensate for the variability in breakpoint location. These studies show that PFGE is a powerful new tool for the analysis of chromosomal translocations in human malignancies.
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Westbrook, CA, CM Rubin, JJ Carrino, MM Le Beau, A. Bernards i JD Rowley. "Long-range mapping of the Philadelphia chromosome by pulsed-field gel electrophoresis". Blood 71, nr 3 (1.03.1988): 697–702. http://dx.doi.org/10.1182/blood.v71.3.697.bloodjournal713697.
Pełny tekst źródłaStreszczenie:
The Philadelphia chromosome (Ph1) of chronic myelogenous leukemia (CML) contains sequences from chromosome 9, including the ABL protooncogene, that have been translocated to the breakpoint cluster region (bcr) of chromosome 22, giving rise to a bcr-ABL fusion gene, whose product has been implicated in the genesis of CML. Although chromosome 22 translocation breakpoints in CML virtually always occur within the 5.8- kilobase (kb) bcr, chromosome 9 breakpoints have been identified within the known limits of ABL in only a few instances. For a better understanding of the variability of the breakpoints on chromosome 9, we studied the CML cell line BV173. Using pulsed-field gel electrophoresis (PFGE), large-scale maps of the t(9;22) junctions were constructed. The chromosome 9 breakpoint was shown to have occurred within an ABL intron, 160 kb upstream of the v-abl homologous sequences, but still 35 kb downstream of the 5′-most ABL exon. bcr-ABL and ABL-bcr fusion genes were demonstrated on the Ph1 and the 9q+ chromosomes, respectively; both of these genes are expressed. These results suggest that the 9;22 translocation breakpoints in CML consistently occur within the limits of the large ABL gene. RNA splicing, sometimes of very large regions, appears to compensate for the variability in breakpoint location. These studies show that PFGE is a powerful new tool for the analysis of chromosomal translocations in human malignancies.
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Kubaláková, M., M. Valárik, J. Barto, J. Vrána, J. Cíhalíková, M. Molnár-Láng i J. Dolezel. "Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry". Genome 46, nr 5 (1.10.2003): 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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Anokhin, Boris A., i Valentina G. Kuznetsova. "FISH-based karyotyping of Pelmatohydra oligactis (Pallas, 1766), Hydra oxycnida Schulze, 1914, and H. magnipapillata Itô, 1947 (Cnidaria, Hydrozoa)". Comparative Cytogenetics 12, nr 4 (20.12.2018): 539–48. http://dx.doi.org/10.3897/compcytogen.v12i4.32120.
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An account is given of the karyotypes of Hydramagnipapillata Itô, 1947, H.oxycnida Schulze, 1914, and Pelmatohydraoligactis (Pallas, 1766) (Cnidaria, Hydrozoa, Hydridae). A number of different techniques were used: conventional karyotype characterization by standard staining, DAPI-banding and C-banding was complemented by the physical mapping of the ribosomal RNA (18S rDNA probe) and H3 histone genes, and the telomeric (TTAGGG)n sequence by fluorescence in situ hybridization (FISH). We found that the species studied had 2n = 30; constitutive heterochromatin was present in the centromeric regions of the chromosomes; the “vertebrate” telomeric (TTAGGG)n motif was located on both ends of each chromosome and no interstitial sites were detected; 18S rDNA was mapped on the largest chromosome pair in H.magnipapillata and on one of the largest chromosome pairs in H.oxycnida and P.oligactis; in H.magnipapillata, the major rRNA and H3 histone multigene families were located on the largest pair of chromosomes, on their long arms and in the centromeric areas respectively. This is the first chromosomal mapping of H3 in hydras.
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Konerat, Jocicléia Thums, Vanessa Bueno, Lucas Baumgartner, Isabel Cristina Martins-Santos i Vladimir Pavan Margarido. "B chromosome and NORs polymorphism in Callichthys callichthys (Linnaeus, 1758) (Siluriformes: Callichthyidae) from upper Paraná River, Brazil". Neotropical Ichthyology 12, nr 3 (23.06.2014): 603–9. http://dx.doi.org/10.1590/1982-0224-20130189.
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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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Tishakova, Katerina V., Dmitry Yu Prokopov, Guzel I. Davletshina, Alexander V. Rumyantsev, Patricia C. M. O’Brien, Malcolm A. Ferguson-Smith, Massimo Giovannotti, Artem P. Lisachov i Vladimir A. Trifonov. "Identification of Iguania Ancestral Syntenic Blocks and Putative Sex Chromosomes in the Veiled Chameleon (Chamaeleo calyptratus, Chamaeleonidae, Iguania)". International Journal of Molecular Sciences 23, nr 24 (13.12.2022): 15838. http://dx.doi.org/10.3390/ijms232415838.
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The veiled chameleon (Chamaeleo calyptratus) is a typical member of the family Chamaeleonidae and a promising object for comparative cytogenetics and genomics. The karyotype of C. calyptratus differs from the putative ancestral chameleon karyotype (2n = 36) due to a smaller chromosome number (2n = 24) resulting from multiple chromosome fusions. The homomorphic sex chromosomes of an XX/XY system were described recently using male-specific RADseq markers. However, the chromosomal pair carrying these markers was not identified. Here we obtained chromosome-specific DNA libraries of C. calyptratus by chromosome flow sorting that were assigned by FISH and sequenced. Sequence comparison with three squamate reptiles reference genomes revealed the ancestral syntenic regions in the C. calyptratus chromosomes. We demonstrated that reducing the chromosome number in the C. calyptratus karyotype occurred through two fusions between microchromosomes and four fusions between micro-and macrochromosomes. PCR-assisted mapping of a previously described Y-specific marker indicates that chromosome 5 may be the sex chromosome pair. One of the chromosome 5 conserved synteny blocks shares homology with the ancestral pleurodont X chromosome, assuming parallelism in the evolution of sex chromosomes from two basal Iguania clades (pleurodonts and acrodonts). The comparative chromosome map produced here can serve as the foundation for future genome assembly of chameleons and vertebrate-wide comparative genomic studies.
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Lukaszewski, Adam J. "Genetic mapping in the 1R.1D wheat–rye translocated chromosomes". Genome 37, nr 6 (1.12.1994): 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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Proskuryakova, Kulemzina, Perelman, Yudkin, Lemskaya, Okhlopkov, Kirillin i in. "Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species". Genes 10, nr 11 (29.10.2019): 857. http://dx.doi.org/10.3390/genes10110857.
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: Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, and three inversions. We discuss changes in pecoran ancestral karyotype in the light of new painting data. Variations in the X chromosome structure of four bovid species nilgai bull (Boselaphus tragocamelus), saola (Pseudoryx nghetinhensis), gaur (Bos gaurus), and Kirk’s Dikdik (Madoqua kirkii) were further analyzed using 26 cattle BAC-clones. We found the duplication on the X in saola. We show main rearrangements leading to the formation of four types of bovid X: Bovinae type with derived cattle subtype formed by centromere reposition and Antilopinae type with Caprini subtype formed by inversion in XSB3.
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Iannuzzi, Alessandra, Leopoldo Iannuzzi i Pietro Parma. "Molecular Cytogenetics in Domestic Bovids: A Review". Animals 13, nr 5 (6.03.2023): 944. http://dx.doi.org/10.3390/ani13050944.
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The discovery of the Robertsonian translocation (rob) involving cattle chromosomes 1 and 29 and the demonstration of its deleterious effects on fertility focused the interest of many scientific groups on using chromosome banding techniques to reveal chromosome abnormalities and verify their effects on fertility in domestic animals. At the same time, comparative banding studies among various species of domestic or wild animals were found useful for delineating chromosome evolution among species. The advent of molecular cytogenetics, particularly the use of fluorescence in situ hybridization (FISH), has allowed a deeper investigation of the chromosomes of domestic animals through: (a) the physical mapping of specific DNA sequences on chromosome regions; (b) the use of specific chromosome markers for the identification of the chromosomes or chromosome regions involved in chromosome abnormalities, especially when poor banding patterns are produced; (c) better anchoring of radiation hybrid and genetic maps to specific chromosome regions; (d) better comparisons of related and unrelated species by comparative FISH mapping and/or Zoo-FISH techniques; (e) the study of meiotic segregation, especially by sperm-FISH, in some chromosome abnormalities; (f) better demonstration of conserved or lost DNA sequences in chromosome abnormalities; (g) the use of informatic and genomic reconstructions, in addition to CGH arrays, to predict conserved or lost chromosome regions in related species; and (h) the study of some chromosome abnormalities and genomic stability using PCR applications. This review summarizes the most important applications of molecular cytogenetics in domestic bovids, with an emphasis on FISH mapping applications.
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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 i Gregory Grabowski. "Combined Genetic and Physical Map of the Complex Genome of Agrobacterium tumefaciens". Journal of Bacteriology 181, nr 17 (1.09.1999): 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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Gallego, Francesca, Catherine Feuillet, Monika Messmer, Anja Penger, Andreas Graner, Masahiro Yano, Takuji Sasaki i Beat Keller. "Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley". Genome 41, nr 3 (1.06.1998): 328–36. http://dx.doi.org/10.1139/g98-024.
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The wheat genome is large, hexaploid, and contains a high amount of repetitive sequences. In order to isolate agronomically important genes from wheat by map-based cloning, a simpler model of the genome must be used for identifying candidate genes. The objective of this study was to comparatively map the genomic regions of two wheat leaf rust disease resistance loci, Lr1 and Lr10, in the putative model genomes of rice and barley. Two probes cosegregating with the Lr1 gene on chromosome 5DL of wheat were studied. The rice sequences corresponding to the two probes were isolated and mapped. The two probes mapped to two different rice chromosomes, indicating that the organization of the region orthologous to Lr1 is different in rice and wheat. In contrast, synteny was conserved between wheat and barley in this chromosomal region. The Lrk10 gene cosegregated with Lr10 on chromosome 1AS in wheat. The rice gene corresponding to Lrk10 was mapped on rice chromosome 1, where it occurred in many copies. This region on rice chromosome 1 corresponds to the distal part of the group 3S chromosomes in Triticeae. The synteny is conserved between rice chromosome 1 and the Triticeae group 3S chromosomes up to the telomere of the chromosomes. On group 3S chromosomes, we found a gene that is partially homologous to Lrk10. We conclude that in the genomic regions studied, there is limited and only partially useful synteny between wheat and rice. Therefore, barley should also be considered as a model genome for isolating the Lr1 and Lr10 genes from wheat.Key words: barley, comparative mapping, leaf rust, resistance genes, rice, synteny, wheat.
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Malimpensa, Geovana C., Josiane B. Traldi, Danyelle Toyama, Flávio Henrique-Silva, Marcelo R. Vicari i Orlando Moreira-Filho. "Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes". Cytogenetic and Genome Research 154, nr 2 (2018): 99–106. http://dx.doi.org/10.1159/000487652.
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The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with clusters (microsatellite accumulation) in some chromosome regions. The telomeric probe revealed no signs of chromosomal rearrangements in the genome of B. westermanni. The 45S rDNA sites were detected in the terminal region of pair 27; these sites corresponded to a GC-rich heterochromatin block. In addition, 3 of the 4 B chromosomes also contained 45S rDNA copies. Silver nitrate staining in interphase nuclei provided indirect evidence of the expression of these rRNA genes in B chromosomes, indicating the probable origin of these elements. This report shows plasticity in the chromosomal localization of repeat DNA in B. westermanni and features a discussion of genomic diversification.
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SHARMA, UPASNA, PRIYANKA BANERJEE, JYOTI JOSHI, PRERNA KAPOOR i RAMESH KUMAR VIJH. "Identification of quantitative trait loci for milk yield in Murrah buffaloes". Indian Journal of Animal Sciences 88, nr 5 (23.05.2018): 550–57. http://dx.doi.org/10.56093/ijans.v88i5.79972.
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A reference family consisting of 12 half sib sire families were created for the identification of QTLs for milk yield in buffaloes. Daughters were recorded for monthly test day milk yield. The number of daughters per sire varied from 50 to 335 daughters per sire. Seventy nine polymorphic microsatellite markers located on 8 chromosomes were genotyped for 2281 daughters of the 12 sires. Whole chromosome scanning was done using single marker analysis and interval mapping using three different algorithms. The analysis was carried out sire family wise. QTLs (63) were identified in single marker analysis and 32 QTLs were identified using interval mapping. The significance of LOD score was tested using permutation tests. The metaQTL analysis was carried out to find out the consensus chromosomal regions associated with milk yield in buffaloes. Five models were utilised and the best was selected on the basis of Akaike Information content. Total 23 chromosomal regions were identified for milk yield in buffaloes. 2 metaQTL chromosomal regions were identified on buffalo chromosome BBU2q; 3 metaQTLs each on buffalo chromosomes BBU8, BBU10 and BBU15 and 4 metaQTL regions each on BBU1q, BBU6, BBU9.
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Kurtz, T. W., i E. M. St Lezin. "Gene mapping in experimental hypertension." Journal of the American Society of Nephrology 3, nr 1 (lipiec 1992): 28–34. http://dx.doi.org/10.1681/asn.v3128.
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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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Gutierrez, Juana, Gael Aleix-Mata, Juan A. Marchal, María Arroyo, Riccardo Castiglia i Antonio Sánchez. "Molecular Cytogenetic Analysis of Karyotype and Y Chromosome Conservation in Species of the Genus Talpa (Insectivora)". Cytogenetic and Genome Research 160, nr 5 (2020): 264–71. http://dx.doi.org/10.1159/000507836.
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The Talpidae family has a highly stable karyotype. Most of the chromosome studies in this mammal group, however, employed classical cytogenetic techniques. Molecular cytogenetic analyses are still scarce and, for example, no repeated DNA sequences have been described to date. In this work, we used sequence analysis, chromosomal mapping of a LINE1 retroelement sequence, as well as chromosome painting with a whole Y chromosome probe of T. occidentalis to compare the karyotypes of 3 species of the genus Talpa (T. occidentalis, T. romana, and T. aquitania). Our results demonstrate that in Talpa genomes LINE1 sequences are widely distributed on all chromosomes but are enriched in pericentromeric C-band-positive regions. In addition, these LINE1 accumulate on the Y chromosomes of the 3 Talpa species regardless of their euchromatic or heterochromatic condition. Chromosome painting shows that the Y chromosomes in these 3 species are highly conserved. Interestingly, they share sequences with heterochromatic blocks on chromosome pairs 14 and 16 and, to a lesser degree, with the pericentromeric regions of other autosomes. Together, our analyses demonstrate that the repetitive DNA content of chromosomes from Talpa species is highly conserved.
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Bilgic, Hatice, Seungho Cho, David F. Garvin i Gary J. Muehlbauer. "Mapping barley genes to chromosome arms by transcript profiling of wheat–barley ditelosomic chromosome addition lines". Genome 50, nr 10 (październik 2007): 898–906. http://dx.doi.org/10.1139/g07-059.
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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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Luo, Xiaomei, Yunke Liu, Xiao Gong, Meng Ye, Qiangang Xiao i Zhen Zeng. "Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 42 Species". Genes 15, nr 5 (20.05.2024): 647. http://dx.doi.org/10.3390/genes15050647.
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This study was conducted to evaluate the 5S rDNA site number, position, and origin of signal pattern diversity in 42 plant species using fluorescence in situ hybridization. The species were selected based on the discovery of karyotype rearrangement, or because 5S rDNA had not yet been explored the species. The chromosome number varied from 14 to 160, and the chromosome length ranged from 0.63 to 6.88 μm, with 21 species having small chromosomes (<3 μm). The chromosome numbers of three species and the 5S rDNA loci of nineteen species are reported for the first time. Six 5S rDNA signal pattern types were identified. The 5S rDNA varied and was abundant in signal site numbers (2–18), positions (distal, proximal, outside of chromosome arms), and even in signal intensity. Variation in the numbers and locations of 5S rDNA was observed in 20 species, whereas an extensive stable number and location of 5S rDNA was found in 22 species. The potential origin of the signal pattern diversity was proposed and discussed. These data characterized the variability of 5S rDNA within the karyotypes of the 42 species that exhibited chromosomal rearrangements and provided anchor points for genetic physical maps.
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Leitch, I. J., i 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, nr 3 (1.06.1993): 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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Ziolkowski, Piotr A., i Jan Sadowski. "FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas". Genome 45, nr 1 (1.02.2002): 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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Koo, Dal-Hoe, Vijay K. Tiwari, Eva Hřibová, Jaroslav Doležel, Bernd Friebe i Bikram S. Gill. "Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat". Cytogenetic and Genome Research 148, nr 4 (2016): 314–21. http://dx.doi.org/10.1159/000447471.
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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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Ingles, Emory D., i Janine E. Deakin. "Comparative Cytogenetic Mapping and Telomere Analysis Provide Evolutionary Predictions for Devil Facial Tumour 2". Genes 11, nr 5 (28.04.2020): 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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Jiang, Jiming, i Bikram S. Gill. "Nonisotopic in situ hybridization and plant genome mapping: the first 10 years". Genome 37, nr 5 (1.10.1994): 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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Moore, Richard C., Olga Kozyreva, Sabine Lebel-Hardenack, Jiri Siroky, Roman Hobza, Boris Vyskot i Sarah R. Grant. "Genetic and Functional Analysis of DD44, a Sex-Linked Gene From the Dioecious Plant Silene latifolia, Provides Clues to Early Events in Sex Chromosome Evolution". Genetics 163, nr 1 (1.01.2003): 321–34. http://dx.doi.org/10.1093/genetics/163.1.321.
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Abstract Silene latifolia is a dioecious plant with heteromorphic sex chromosomes. The sex chromosomes of S. latifolia provide an opportunity to study the early events in sex chromosome evolution because of their relatively recent emergence. In this article, we present the genetic and physical mapping, expression analysis, and molecular evolutionary analysis of a sex-linked gene from S. latifolia, DD44 (Differential Display 44). DD44 is homologous to the oligomycin sensitivity-conferring protein, an essential component of the mitochondrial ATP synthase, and is ubiquitously expressed in both sexes. We have been able to genetically map DD44 to a region of the Y chromosome that is genetically linked to the carpel-suppressing locus. Although we have physically mapped DD44 to the distal end of the long arm of the X chromosome using fluorescence in situ hybridization (FISH), DD44 maps to the opposite arm of the Y chromosome as determined by our genetic map. These data suggest that chromosomal rearrangements have occurred on the Y chromosome, which may have contributed to the genetic isolation of the Y chromosome. We discuss the implications of these results with respect to the structural and functional evolution of the S. latifolia Y chromosome.
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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 i Rod A. Wing. "FISH of a maize sh2-selected sorghum BAC to chromosomes of Sorghum bicolor". Genome 40, nr 4 (1.08.1997): 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.