Abstract
For a long time, Arabidopsis thaliana was not a favorite of cytogeneticists because of its small chromosomes. Nevertheless, most cytogenetic approaches have become applicable to this model plant during the past decade. Recently, the very small genome, the low content, and strong clustering of repetitive sequences even turned out to be advantageous for the first establishment of chromosome painting in a euploid plant. Chromosome painting together with the high-resolution fluorescence in situ hybridization (FISH) mapping on Arabidopsis pachytene chromosomes has opened new perspectives for plant cytogenetics.
In this chapter, we describe standard cytogenetic methods including preparation of chromosomes and chromatin fibers, isolation of interphase nuclei, FISH and immunostaining, painting of Arabidopsis chromosomes, and comparative chromosome painting in other Brassicaceae species.
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References
The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815.
Hosouchi, T., Kumekawa, N., Tsuruoka, H., and Kotani, H. (2002) Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3. DNA Res. 9, 117–121.
Bennett, M. D., Leitch, I. J., Price, H. J., and Johnston, J. S. (2003) Comparisons with Caenorhabditis (∼100 Mb) and Drosophila (∼175 Mb) using flow cytometry show genome size in Arabidopsis to be ∼157 Mb and thus ∼25% larger than the Arabidopsis genome initiative estimate of ∼125 Mb. Ann. Bot. 91, 547–557.
Leutwiler, L. S., Hough-Evans, B. R., and Meyerowitz, E. M. (1984) The DNA of Arabidopsis thaliana. Mol. Gen. Genet. 194, 15–23.
Laibach, F. (1907) Zur Frage nach der Individualität der Chromosomen im Pflanzenreich. Beih. Bot. Centralbl. Abt. 1 22, 191–210.
Ambros, P. and Schweizer, D. (1976) The Giemsa C-banded karyotype of Arabidopsis thaliana (L.) Heynh. Arabidopsis Inf. Serv. 13, 167–171.
Maluszynska, J. and Heslop-Harrison, J. S. (1991) Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J. 1, 159–166.
Maluszynska, J. and Heslop-Harrison, J. S. (1993) Molecular cytogenetics of the genus Arabidopsis: in situ localization of rDNA sites, chromosome numbers and diversity in centromeric heterochromatin. Ann. Bot. 71, 479–484.
Steinitz-Sears, L. M. (1963) Chromosome studies in Arabidopsis thaliana. Genetics 48, 483–490.
Röbbelen, G. and Kribben, F. J. (1966) Erfahrungen bei der Auslese von Trisomen. Arabidopsis Inf. Serv. 3, 16–17.
Samoylova, T. I., Meister, A., and Miséra, S. (1996) The flow karyotype of Arabidopsis thaliana interphase chromosomes. Plant J. 10, 949–954.
Ross, K. J., Fransz, P., and Jones, G. H. (1996) A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosome Res. 4, 507–516.
Fransz, P., Armstrong, S., Alonso-Blanco, C., Fischer, T. C., Torres-Ruiz, R. A., and Jones, G. (1998) Cytogenetics for the model system Arabidopsis thaliana. Plant J. 13, 867–876.
Fransz, P. F., Armstrong, S., de Jong, J. H., et al. (2000) Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100, 367–376.
Fransz, P., de Jong, J. H., Lysak, M., Ruffini Castiglione, M., and Schubert, I. (2002) Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. USA 99, 14584–14589.
Koornneef, M., Fransz, P., and de Jong, H. (2003) Cytogenetic tools for Arabidopsis thaliana. Chromosome Res. 11, 183–194.
Jones, G. H., Armstrong, S. J., Caryl, A. P., and Franklin, F. C. H. (2003) Meiotic chromosome synapsis and recombination in Arabidopsis thaliana; an integration of cytological and molecular approaches. Chromosome Res. 11, 205–215.
Fransz, P. F., Alonso-Blanco, C., Liharska, T. B., Peeters, A. J. M., Zabel, P., and de Jong, J. H. (1996) High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J. 9, 421–430.
Soppe, W. J. J., Jasencakova, Z., Houben, A., et al. (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549–6559.
Jasencakova, Z., Soppe, W. J. J., Meister, A., Gernand, D., Turner, B. M., and Schubert, I. (2003) Histone modifications in Arabidopsis—high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J. 33, 471–480.
Probst, A. V., Fransz, P. F., Paszkowki, J., and Mittelsten Scheid, O. (2003) Two means of transcriptional reactivation within heterochromatin. Plant J. 33, 743–749.
Chytilova, E., Macas, J., and Galbraith, D. W. (1999) Green fluorescent protein targeted to the nucleus, a transgenic phenotype useful for studies in plant biology. Ann. Bot. 83, 645–654.
Kato, N. and Lam, E. (2001) Detection of chromosome tagged with green fluorescent protein in live Arabidopsis thaliana plants. Genome Biol. 2, research 0045.
Lysak, M. A., Fransz, P. F., Ali, H. B. M., and Schubert, I. (2001) Chromosome painting in Arabidopsis thaliana. Plant J. 28, 689–697.
Lysak, M. A., Pecinka, A., and Schubert, I. (2003) Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Res. 11, 195–204.
Ali, H. B. M., Lysak, M. A. and Schubert, I. (2004) Genomic in situ hybridization in plants with small genomes is feasible and elucidates the chromosomal parentage in interspecific Arabidopsis hybrids. Genome 47, 954–960.
Menke, M., Chen, I. P., Angelis, K. J., and Schubert, I. (2001) DNA damage and repair in Arabidopsis thaliana as measured by the comet assay after treatment with different classes of genotoxins. Mutat. Res. 493, 87–93.
Siroky, J., Zluvova, J., Riha, K., Shippen, D. E., and Vyskot, B. (2003) Rearrangements of ribosomal DNA clusters in late generation telomerase-deficient Arabidopsis. Chromosoma 112, 116–123.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory. Press, Cold Spring Harbor, NY.
Dolezel, J., Lysak, M. A., Kubaláková, M., Simková, H., Macas, J., and Lucretti, S. (2001) Sorting of plant chromosomes. Methods Cell Biol. 64, 3–31.
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Lysak, M., Fransz, P., Schubert, I. (2006). Cytogenetic Analyses of Arabidopsis . In: Salinas, J., Sanchez-Serrano, J.J. (eds) Arabidopsis Protocols. Methods in Molecular Biology™, vol 323. Humana Press. https://doi.org/10.1385/1-59745-003-0:173
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DOI: https://doi.org/10.1385/1-59745-003-0:173
Publisher Name: Humana Press
Print ISBN: 978-1-58829-395-4
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