Chromosome painting in plants

  • Ingo Schubert
  • Paul F. Fransz
  • Jörg Fuchs
  • J. Hans de Jong


The current ‘state-of-art’ as to chromosome painting in plants is reviewed. We define different situations described as painting so far: i) Genomic in situ hybridisation (GISH) with total genomic DNA to distinguish alien chromosomes on the basis of divergent dispersed repeats, ii) ‘Chromosomal in situ suppression’ (CISS) hybridisation with chromosome-derived DNA probes and blocking of interchromosomally dispersed repeats by total genomic or C0 t-1 DNA in excess, iii) exceptional cases of single chromosome painting by probes containing chromosome-specific dispersed repeats, and iv) Fluorescence in situ hybridisation (FISH) with extended contigs of large insert clones for painting of those chromosomes of a euploid complement which harbour the cloned sequences. While GISH was successfully applied in most plant hybrids and/or their derivatives, painting of individual chromosomes by CISS hybridisations of chromosome-specific DNA probes have so far not revealed convincing results in plants. The reason for this failure and the use of possible alternative approaches are discussed. At least for small plant genomes, painting by large insert single sequence clones provides a promising alternative tool to solve cytogenetic questions, which up to now could not be tackled otherwise. An example of such a painting is described in detail for Arabidopsis thaliana.

Key words

Chromosomal in situ suppression hybridisation Chromosome painting Genomic in situ hybridisation Large insert clones Plants 


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  1. 01.
    Ambros P, Schweizer D (1976). The Giemsa C-banded karyotype of Arabidopsis thaliana (L.) Heynh. Arabidopsis Inf Serv 13: 161–171.Google Scholar
  2. 02.
    Anamthawat-Jónsson K, Reader SM (1995). Pre-annealing of total genomic DNA probes for simultaneous genomic in situ hybridization. Genome 38: 814–816.PubMedCrossRefGoogle Scholar
  3. 03.
    Aragón-Alcaide L, Reader S, Beven A, Shaw P, Miller T, Moore G (1997). Association of homologous chromosomes during floral development. Curr Biol 7: 905–908.PubMedCrossRefGoogle Scholar
  4. 04.
    Breneman JW, Ramsey MJ, Lee DA, Eveleth GG, Minkler JL, Tucker JD (1993). The development of chromosome-specific composite DNA probes for the mouse and their application to chromosome painting. Chromosoma 102: 591–598.PubMedCrossRefGoogle Scholar
  5. 05.
    Camilleri C, Lafleuriel J, Macadré C, Varoquaux F, Parmentier Y, Picard G, Caboche M, Bouchez D (1998). A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J 14: 633–642.PubMedCrossRefGoogle Scholar
  6. 06.
    Carter NP, Ferguson-Smith MA, Perryman MT, Telenius H, Pelmear AH, Leversha MA, Glancy MT, Wood SL, Cook K, Dyson HM, Ferguson-Smith ME, Willatt LR (1992). Reverse chromosome painting: a method for rapid analysis of aberrant chromosomes in clinical cytogenetics. J Med Genet 29: 299–307.PubMedCrossRefGoogle Scholar
  7. 07.
    Choi S, Creelman RA, Mullet JE, Wing R (1995). Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Reporter 13: 124–128.CrossRefGoogle Scholar
  8. 08.
    de Jong JH, Fransz P, Zabel P (1999). High resolution FISH in plants — techniques and applications. Trends Plant Sci 4: 258–263.CrossRefGoogle Scholar
  9. 09.
    de Jong JH, Zhong X-B, Fransz PF, Wennekes-van Eden J, Jacobsen E, Zabel P (2000). High resolution FISH reveals the molecular and chromosomal organisation of repetitive sequences of individual tomato chromosomes. Chromosomes Today 13: 267–275.Google Scholar
  10. 10.
    Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G (1998). Cytogenetics for the model system Arabidopsis thaliana. Plant J 13: 867–876.PubMedCrossRefGoogle Scholar
  11. 11.
    Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen C, Dean C, Zabel P, Bisseling T, Jones GH (2000). Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100: 367–376.PubMedCrossRefGoogle Scholar
  12. 12.
    Fuchs J, Houben A, Brandes A, Schubert I (1996a). Chromosome ‘painting’ in plants — a feasible technique? Chromosoma 104: 315–320.PubMedGoogle Scholar
  13. 13.
    Fuchs J, Kloos D-U, Ganal MW, Schubert I (1996b). In situ localization of yeast artificial chromosome sequences on tomato and potato metaphase chromosomes. Chromosome Res 4: 277–281.PubMedCrossRefGoogle Scholar
  14. 14.
    Fuchs J, Kuhfittig S, Reuter G, Schubert I (1998). Chromosome painting in Drosophila. Chromosome Res 6: 335–336.PubMedCrossRefGoogle Scholar
  15. 15.
    Garriga-Calderé F, Huigen DJ, Filotico F, Jacobsen E, Ramanna MS (1997). Identification of alien chromosomes through GISH and RFLP analysis and the potential for the establishment of potato lines with monosomic additions of tomato chromosomes. Genome 40: 666–673.PubMedCrossRefGoogle Scholar
  16. 16.
    Gelvin SB, Schilperoort RA, Verma DPS, eds, (1988). Plant Molecular Biology Manual. Dordrecht: Kluwer Akad Publ.Google Scholar
  17. 17.
    Hake S, Walbot V (1980). The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79: 251–270.CrossRefGoogle Scholar
  18. 18.
    Hanson RE, Zwick MS, Choi S, Islam-Faridi MN, McKnight TD, Wing RA, Price HJ, Stelly DM (1995). Fluorescent in situ hybridization of a bacterial artificial chromosome. Genome 38: 646–651.PubMedCrossRefGoogle Scholar
  19. 19.
    Hoebee B, de Stoppelaar JM, Suijkerbuijk RF, Monard S (1994). Isolation of rat chromosome-specific paint probes by bivariate flow sorting followed by degenerate oligonucleotide primed-PCR. Cytogenet Cell Genet 66: 277–282.PubMedCrossRefGoogle Scholar
  20. 20.
    Houben A, Kynast RG, Heim U, Hermann H, Jones RN, Forster JW (1996). Molecular cytogenetic characterization of the terminal heterochromatic segment of the B-chromosome of rye (Secale cereale). Chromosoma 105: 97–103.PubMedCrossRefGoogle Scholar
  21. 21.
    Jacobsen E, de Jong JH, Kamstra SA, van den Berg PMMM, Ramanna MS (1995). Genomic in situ hybridization (GISH) and RFLP analysis for the identification of alien chromosomes in the backcross progeny of potato (+) tomato fusion hybrids. Heredity 74: 250–257.CrossRefGoogle Scholar
  22. 22.
    Jiang J, Gill BS, Wang G-L, Ronald PC, Ward DC (1995). Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92: 4487–4491.PubMedCrossRefGoogle Scholar
  23. 23.
    Johnson DH (1990). Molecular cloning of DNA from specific chromosomal regions by microdissection and sequence-independent amplification of DNA. Genomics 6: 243–251.PubMedCrossRefGoogle Scholar
  24. 24.
    Kallioniemi A, Kallioniemi O-P, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992). Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821.PubMedCrossRefGoogle Scholar
  25. 25.
    Keller ERJ, Schubert I, Fuchs J, Meister A (1996). Interspecific crosses of onion with distant Allium species and characterization of the presumed hybrids by means of flow cytometry, karyotype analysis and genomic in situ hybridization. Theor Appl Genet 92: 417–424.CrossRefGoogle Scholar
  26. 26.
    Kenton A, Parokonny AS, Gleba YY, Bennett MD (1993). Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Mol Gen Genet 240: 159–169.PubMedCrossRefGoogle Scholar
  27. 27.
    Khrustaleva LI, Kik C (1998). Cytogenetical studies in the bridge cross Allium cepa x (A. fistulosum × A. roylei). Theor Appl Genet 96: 8–14.CrossRefGoogle Scholar
  28. 28.
    Khrustaleva LI, Kik C (2000). Introgression of Allium fistulosum into A. cepa mediated by A. roylei. Theor Appl Genet 100: 17–26.CrossRefGoogle Scholar
  29. 29.
    Khrustaleva LI, Kik C (2000). Localization of single-copy T-DNA insertion in transgenic shallots (Allium cepa L.) by using ultra-sensitive FISH with tyramide signal amplification. Plant J 25: 699–707.CrossRefGoogle Scholar
  30. 30.
    Kohne DE, Levison SA, Byers MJ (1977). Room temperature method for increasing the rate of DNA reassociation by many thousandfold: the phenol emulsion reassociation technique. Biochemistry 16: 5329–5341.PubMedCrossRefGoogle Scholar
  31. 31.
    Langford CF, Telenius H, Carter NP, Miller NGA, Tucker EM (1992). Chromosome painting using chromosome-specific probes from flow-sorted pig chromosomes. Cytogenet Cell Genet 61: 221–223.PubMedCrossRefGoogle Scholar
  32. 32.
    Lengauer C, Luedecke H-J, Wienberg J, Cremer T, Horsthemke B (1991). Comparative chromosome band mapping in primates by in situ suppression hybridization of band specific DNA microlibraries. Human Evol 1991;6:67–71.CrossRefGoogle Scholar
  33. 33.
    Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1998). Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Human Genet 80: 224–234.CrossRefGoogle Scholar
  34. 34.
    Lin X, Kaul S, Rounsley S, Shea TP, Benito M-I, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Fraser CM, Venter JC (1999). Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761–769.PubMedCrossRefGoogle Scholar
  35. 35.
    Maluszynska J, Heslop-Harrison JS (1991). Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J 1: 159–166.CrossRefGoogle Scholar
  36. 36.
    Mayer K, Schüller C, Wambutt R, Fransz P, Martienssen R, McCombie WR (1999). Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402: 769–777.PubMedCrossRefGoogle Scholar
  37. 37.
    Menke M, Fuchs J, Schubert I (1998). A comparison of sequence resolution on plant chromosomes: PRINS versus FISH. Theor Appl Genet 97: 1314–1320.CrossRefGoogle Scholar
  38. 38.
    Mesbah M, de Bock TSM, Sandbrink JM, Klein-Lankhorst RM, Lange W (1997). Molecular and morphological characterization of monosomic additions in Beta vulgaris, carrying extra chromosomes of B. procumbens or B. patellaris. Mol Breed 3: 147–157.CrossRefGoogle Scholar
  39. 39.
    Mesbah M, Wennekes-van Eden J, de Jong JH, de Bock TSM, Lange W (2000). FISH to mitotic chromosomes and extended DNA fibres of Beta procumbens in a series of monosomic additions to beet (Beta vulgaris). Chromosome Res 8: 285–293.PubMedCrossRefGoogle Scholar
  40. 40.
    Mikhailova EI, Naranjo T, Sheperd K, Wennekes-van Eden J, Heyting C, de Jong JH (1998). The effect of the wheat Ph1 locus on chromatin organisation and meiotic chromosome pairing analysed by genome painting. Chromosoma 107: 339–350.PubMedCrossRefGoogle Scholar
  41. 41.
    Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T (1999). A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet 22: 271–275.PubMedCrossRefGoogle Scholar
  42. 42.
    Mukai Y, Friebe B, Hatchett JH, Yamamoto M, Gill BS (1993). Molecular cytogenetic analysis of radiation-induced wheat-rye terminal and intercalary chromosomal translocations and the detection of rye chromatin specifying resistance to Hessian fly. Chromosoma 102: 88–95.CrossRefGoogle Scholar
  43. 43.
    Murata M, Heslop-Harrison JS, Motoyoshi F (1997). Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones. Plant J 12: 31–37.PubMedCrossRefGoogle Scholar
  44. 44.
    Pich U, Houben A, Fuchs J, Meister A, Schubert I (1994). Utility of DNA amplified by degenerate oligonucleotide-primed PCR (DOP-PCR) from the total genome and defined chromosomal regions of field beans. Mol Gen Genet 243: 173–177.PubMedGoogle Scholar
  45. 45.
    Pickering RA, Malyshev S, Künzel G, Johnston PA, Korzun V, Menke M, Schubert I (2000). Locating introgressions of Hordeum bulbosum chromatin within the H. vulgare genome. Theor Appl Genet 100: 27–31.CrossRefGoogle Scholar
  46. 46.
    Pinkel D, Landegent J, Collins C, Fuscoe J, Segraves R, Lucas J, Gray J (1988). Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 and translocations of chromosome 4. Proc Natl Acad Sci USA 85: 9138–9142.PubMedCrossRefGoogle Scholar
  47. 47.
    Poggio L, Confalonieri V, Comas C, Cuadrado A, Jouve N, Naranjo CA (1999). Genomic in situ hybridization (GISH) of Tripsacum dactyloides and Zea mays B chromosomes. Genome 42: 687–691.Google Scholar
  48. 48.
    Poggio L, Confalonieri V, Comas C, Gonzalez G, Naranjo CA (1999). Genomic affinities of Zea luxurans, Z. diploperennis, and Z. perennis: meiotic behavior of their F, hybrids and genomic in situ hybridization (GISH). Genome 42: 993–1000.Google Scholar
  49. 49.
    Raap AK, van de Corput MPC, Vervenne RAW, van Gijlskwijk RPM, Tanke HJ, Wiegant J (1995). Ultrasensitive FISH using peroxidase-mediated deposition of biotin-or fluorochrome tyramides. Human Mol Genet 4: 529–534.CrossRefGoogle Scholar
  50. 50.
    Ross KJ, Fransz P, Jones GH (1996). A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosome Res 4: 507–516.PubMedCrossRefGoogle Scholar
  51. 51.
    Sadder MT, Ponelies N, Born U, Weber G (2000). Physical localization of single-copy sequences on pachytene chromosomes in maize (Zea mays L.) by chromosome in situ suppression hybridization. Genome 43: 1081–1083.PubMedGoogle Scholar
  52. 52.
    Sambrook J, Fritsch EF, Maniatis T (1989). Molecular Cloning: A Laboratory Manual. 2nd. edition. Cold Spring Harbor: Cold Spring Harbor Lab Press.Google Scholar
  53. 53.
    Scherthan H, Loidl J, Schuster T, Schweizer D (1992). Meiotic chromosome condensation and pairing in Saccharomyces cerevisiae studied by chromosome painting. Chromosoma 101: 590–595.PubMedCrossRefGoogle Scholar
  54. 54.
    Scherthan H, Cremer T, Arnason U, Weier H-U, Lima-de-Faria A, Frönicke L (1994). Comparative chromosome painting discloses homologous segments in distantly related mammals. Nature Genet 6: 342–347.PubMedCrossRefGoogle Scholar
  55. 55.
    Schmidt R, West J, Cnops G, Love K, Balestrazzi A, Dean C (1996). Detailed description of four YAC contigs representing 17 Mb of chromosome 4 of Arabidopsis thaliana ecotype Columbia. Plant J 9: 755–765.PubMedCrossRefGoogle Scholar
  56. 56.
    Schmidt R, Love K, West J, Lenehan Z, Dean C (1997). Description of 31 YAC contigs spanning the majority of Arabidopsis thaliana chromosome 5. Plant J 11: 563–572.PubMedCrossRefGoogle Scholar
  57. 57.
    Schmidt T, Heslop-Harrison JS (1998). Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3: 195–199.CrossRefGoogle Scholar
  58. 58.
    Schubert I, Shi F, Fuchs J, Endo TR (1998). An efficient screening for terminal deletions and translocations of barley chromosomes added to common wheat. Plant J 14: 489–495.CrossRefGoogle Scholar
  59. 59.
    Schwarzacher T, Leitch AR, Bennett MD, Heslop-Harrison JS (1989). In situ localization of parental genomes in a wide hybrid. Ann Bot 64: 315–324.Google Scholar
  60. 60.
    Schwarzacher T, Wang ML, Leitch AR, Miller N, Moore G, Heslop-Harrison JS (1997). Flow cytometric analysis of the chromosomes and stability of a wheat cell-culture line. Theor Appl Genet 94: 91–97.PubMedCrossRefGoogle Scholar
  61. 61.
    Schwarzacher T (1997). Three stages of meiotic homologous chromosome pairing in wheat: cognition, alignment and synapsis. Sex Plant Reprod 10: 324–331.CrossRefGoogle Scholar
  62. 62.
    Shibata F, Hizume M, Kuroki Y (1999). Chromosome painting of Y chromosomes and isolation of a Y chromosome-specific repetitive sequence in the dioecious plant Rumex acetosa. Chromosoma 108: 266–270.PubMedCrossRefGoogle Scholar
  63. 63.
    Stein N, Ponelies N, Musket T, McMullen M, Weber G (1998). Chromosome micro-dissection and region-specific libraries from pachytene chromosomes of maize (Zea mays L.). Plant J 13: 281–289.CrossRefGoogle Scholar
  64. 64.
    Takahashi C, Marshall JA, Bennett MD, Leitch IJ (1999). Genomic relationships between maize and its wild relatives. Genome 42: 1201–1207.PubMedCrossRefGoogle Scholar
  65. 65.
    Telenius H, Carter NP, Bebb CE, Nordenskjôld M, Ponder BAJ, Tunnacliffe A (1992). Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13: 718–725.PubMedCrossRefGoogle Scholar
  66. 66.
    Unfried K, Schiebel K, Hemleben V (1991). Subrepeats of rDNA intergenic spacer present as prominent independent satellite DNA in Vigna radiata but not in Vigna angularis. Gene 99: 63–68.PubMedCrossRefGoogle Scholar
  67. 67.
    Van Devanter DR, Choongkrittaworn NM, Dyer KA, Aten J, Otto P, Behler C, Bryant EM, Rabinovitch PS (1994). Pure chromosome-specific PCR libraries from single sorted chromosomes. Proc Natl Acad Sci USA 91: 5858–5862.CrossRefGoogle Scholar
  68. 68.
    Vega JM, Abbo S, Feldman M, Levy AA (1994). Chromosome painting in plants: In situ hybridization with a DNA probe from a specific microdissected chromosome arm of common wheat. Proc Natl Acad Sci USA 91: 12041–12045.PubMedCrossRefGoogle Scholar
  69. 69.
    Wienberg J, Jauch A, Stanyon R, Cremer T (1990). Molecular cytotaxonomy of primates by chromosomal in situ suppression hybridization. Genomics 8: 347–350.PubMedCrossRefGoogle Scholar
  70. 70.
    Woo S-S, Jiang J, Gill BS, Paterson AH, Wing RA (1994). Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22: 4922–4931.PubMedCrossRefGoogle Scholar
  71. 71.
    Zachgo EA, Wang ML, Dewdney J, Bouchez D, Camilleri C, Belmonte S, Huang L, Dolan M, Goodman HM (1996). A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res 6: 19–25.PubMedCrossRefGoogle Scholar
  72. 72.
    Zhong X-B, de Jong JH, Zabel P (1996). Preparation of tomato meiotic pachytene and mitotic metaphase chromosomes suitable for fluorescence in situ hybridization (FISH). Chromosome Res 4: 24–28.PubMedCrossRefGoogle Scholar
  73. 73.
    Zhong X-B, Fransz PF, Wennekes-van Eden J, Ramanna MS, van Kammen A, Zabel P, de Jong HJ (1998). FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato. Plant J 13: 507–517.PubMedCrossRefGoogle Scholar
  74. 74.
    Zhou Y, Hu Z, Dang B, Wang H, Deng X, Wang L, Chen Z (1999). Microdissection and microcloning of rye (Secale cereale L.) chromosome 1R. Chromosoma 108: 250–255.PubMedCrossRefGoogle Scholar
  75. 75.
    Zimmer R, King WA, Verrinder Gibbins AM (1997). Generation of chicken Z-chromosome painting probes by microdissection for screening large-insert genomic libraries. Cytogenet Cell Genet 78: 124–130.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2001

Authors and Affiliations

  • Ingo Schubert
    • 1
  • Paul F. Fransz
    • 1
    • 2
  • Jörg Fuchs
    • 1
    • 3
  • J. Hans de Jong
    • 4
  1. 1.Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Swammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
  3. 3.Institute of BotanyUniversity of ViennaViennaAustria
  4. 4.Department of Plant Sciences, Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands

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