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Interphase fluorescence in situ hybridization mapping: a physical mapping strategy for plant species with large complex genomes

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Abstract

The chromatin in interphase nuclei is much less condensed than are metaphase chromosomes, making the resolving power of fluorescence in situ hybridization (FISH) two orders of magnitude higher in interphase nuclei than on metaphase chromosomes. In mammalian species it has been demonstrated that within a certain range the interphase distance between two FISH sites can be used to estimate the linear DNA distance between the two probes. The intephase mapping strategy has never been applied in plant species, mainly because of the low sensitivity of the FISH technique on plant chromosomes. Using a CCD (charge-coupled device) camera system, we demonstrate that DNA probes in the 4 to 8 kb range can be detected on both metaphase and interphase chromosomes in maize. DNA probes pA1-Lc and pSh2.5·SstISalI, which contain the maize locia1 andsh2, respectively, and are separated by 140 kb, completely overlapped on metaphase chromosomes. However, when the two probes were mapped in interphase nuclei, the FISH signals were well separated from each other in 86% of the FISH sites analyzed. The average interphase distance between the two probes was 0.50 µm. This result suggests that the resolving power of interphase FISH mapping in plant species can be as little as 100 kb. We also mapped the interphase locations of another pair of probes, ksu3/4 and ksu16, which span theRp1 complex controlling rust resistance of maize. Probes ksu3/4 and ksu16 were mapped genetically approximately 4 cM apart and their FISH signals were also overlapped on metaphase chromosomes. These two probes were separated by an average of 2.32 µm in interphase nuclei. The possibility of estimating the linear DNA distance between ksu3/4 and ksu16 is discussed.

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References

  • Brandriff BF, Gordon LA, Tynan KT, Olsen AS, Mohrenweiser HW, Fertitta A, Carrano AV, Trask BJ (1992) Order and genomic distances among members of the carcinoembryonic antigen (CEA) gene family determined by fluorescence in situ hybridization. Genomics 12:773–779

    PubMed  Google Scholar 

  • Civardi L, Xia Y, Edwards KJ, Schnable PS, Nikolau BJ (1994) The relationship between genetic and physical distances in the cloneda1-sh2 interval of theZea mays L. genome. Proc Natl Acad Sci USA 91:8268–8272

    PubMed  Google Scholar 

  • Florijn RJ, Bonden LAJ, Vrolijk H, Wiegant J, Vaandrager JW, Baas F, den Dunnen JT, Tanke HJ, van Ommen GJB, Raap AK (1995) High-resolution DNA fiber-FISH for genomic DNA mapping and color bar-coding of large genes. Hum Mol Genet 4:831–836

    PubMed  Google Scholar 

  • Fransz PF, Alonso-Blanco C, Liharska TB, Peeters AJM, Zabel P, de Jong JH (1996) High-resolution physical mapping inArabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibers. Plant J 9:421–430

    PubMed  Google Scholar 

  • Ganal MW, Young ND, Tanksley SD (1989) Pulsed field gel electrophoresis and physical mapping of large DNA fragments in theTm-2a region of chromosome 9 in tomato. Mol Gen Genet 215:395–400

    Google Scholar 

  • Gill KS, Gill BS, Endo TR (1993) A chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat. Chromosoma 102:374–381

    Google Scholar 

  • Haaf T, Ward DC (1994) High resolution ordering of YAC contigs using extended chromatin and chromosomes. Hum Mol Genet 3:629–633

    PubMed  Google Scholar 

  • Hong KS, Richter TE, Bennetzen JL, Hulbert SH (1993) Complex duplications in maize lines. Mol Gen Genet 239:115–121

    PubMed  Google Scholar 

  • Houseal TW, Dackowski WR, Landes GM, Klinger KW (1994) High resolution mapping of overlapping cosmids by fluorescence in situ hybridization. Cytometry 15:193–198

    PubMed  Google Scholar 

  • Hulbert SH, Bennetzen JL (1991) Recombination at theRp1 locus of maize. Mol Gen Genet 226:377–382

    PubMed  Google Scholar 

  • Jiang J, Gill BS (1994) Nonisotopic in situ hybridization and plant genome mapping: the first 10 years. Genome 37:717–725

    Google Scholar 

  • Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase FISH mapping of the rice genome using bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487–4491

    PubMed  Google Scholar 

  • Lawrence JB, Singer RH, McNeil JA (1990) Interphase and metaphase resolution of different distance within the human dystrophin gene. Science 249:928–932

    PubMed  Google Scholar 

  • Lichter P, Tang CC, Call K, Hermanson G, Evans GA, Housman D, Ward DC (1990) High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247:64–69

    PubMed  Google Scholar 

  • Parra I, Windle B (1993) High resolution visual mapping of stretched DNA by fluorescent hybridization. Nature Genet 5:17–21

    PubMed  Google Scholar 

  • Richter TE, Pryor TJ, Bennetzen JL, Hulbert SH (1995) New rust resistance specificities associated with recombination in theRp1 complex in maize. Genetics 141:373–381

    PubMed  Google Scholar 

  • Schwarz-Sommer Z, Shepherd N, Tacke E, Gierl A, Rohde W, Leclercq L, Mattes M, Berndtgen R, Peterson PA, Saedler H (1987) Influence of transposable elements on the structure and function of theA1 gene ofZea mays. EMBO J 6:287–294

    PubMed  Google Scholar 

  • Segal G, Sarfatti M, Schaffer A, Ovi N, Zamir D, Fluhr R (1992) Correlation of genetic and physical structure in the region surrounding theI 2 Fusarium oxysporum resistance locus in tomato. Mol Gen Genet 231:179–185

    PubMed  Google Scholar 

  • Senger G, Ragoussis J, Trowsdale J, Sheer D (1993) Fine mapping of the human MHC class II region within chromosome band 6p21 and evaluation of probe ordering using interphase fluorescencein situ hybridization. Cytogenet Cell Genet 64:49–53

    PubMed  Google Scholar 

  • Senger G, Jones TA, Fidlerová H, Sanséau P, Trowsdale J, Duff M, Sheer D (1994) Released chromatin: linearized DNA for high resolution fluorescence in situ hybridization. Hum Mol Genet 3:1275–1280

    PubMed  Google Scholar 

  • Shaw JR, Hannah LC (1992) Genomic nucleotide sequences of a wild-typeshrunken-2 allele ofZea mays. Plant Physiol 98:1214–1216

    Google Scholar 

  • Staskawicz BJ, Ausubel FM, Baker BJ, Ellis JG, Jones JDG (1995) Molecular genetics of plant disease resistance. Science 268:661–667

    PubMed  Google Scholar 

  • Sudupak MA, Bennetzen JL, Hulbert SH (1993) Unequal exchange and meiotic instability of disease-resistance genes in theRp1 region of maize. Genetics 133:119–125

    PubMed  Google Scholar 

  • Trask BJ (1991) Mapping of human chromosome Xq28 by two-color fluorescence in situ hybridization of DNA sequences to interphase cell nuclei. Am J Hum Genet 48:1–15

    PubMed  Google Scholar 

  • Trask BJ, Pinkel D, van den Engh G (1989) The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs. Genomics 5:710–717

    PubMed  Google Scholar 

  • Umehara Y, Inagaki A, Tanoue H, Yasukochi T, Nagamura Y, Saji S, Otsuki Y, Fujimura T, Kurata N, Minobe Y (1994) Construction and characterization of a rice YAC library for physical mapping. Mol Breed 1:79–89

    Google Scholar 

  • van den Engh G, Sachs R, Trask BJ (1992) Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science 257:1410–1412

    PubMed  Google Scholar 

  • Werner JE, Endo TR, Gill BS (1992) Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci USA 89:11307–11311

    PubMed  Google Scholar 

  • Wu KS, Tanksley SD (1993) Genetic and physical mapping of telomeres and microsatellites of rice. Plant Mol Biol 22:861–872

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin-Madison, 53706, Madison, WI, USA

    J. Jiang

  2. Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA

    S. H. Hulbert & B. S. Gill

  3. Department of Genetics, YaleUniversity School of Medicine, 06510, New Haven, CT, USA

    D. C. Ward

Authors
  1. J. Jiang
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  2. S. H. Hulbert
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  3. B. S. Gill
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  4. D. C. Ward
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Communicated by R. G. Herrmann

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Jiang, J., Hulbert, S.H., Gill, B.S. et al. Interphase fluorescence in situ hybridization mapping: a physical mapping strategy for plant species with large complex genomes. Molec. Gen. Genet. 252, 497–502 (1996). https://doi.org/10.1007/BF02172395

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  • DOI: https://doi.org/10.1007/BF02172395

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