Abstract
A genome is a collection of chromosomes and visible chromosomes under a photomicroscope that provide a unique and effective approach to genome analysis. In situ hybridization (ISH) is one of the most effective methods to analyze the essential characteristics of genomes, because the method is based on the structural constituent of genomes that is sometimes overlooked by biochemical means. The method requires that the structure of DNA fibers, chromosomes and nuclei is maintained as much as possible in order to utilize the morphological components as the key information for specifying and/or interpreting the location and biological significance of the signals detected. It could also be pointed out that the information from single chromosomal spreads sometimes gives satisfactory and essential information on the localization of certain nucleotide sequences on the target chromosomes and their biological significance. Therefore, genome analysis by ISH provides unique information different from the ordinary biochemical means which handle the mass of DNA fragments as the target in most cases.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Aggarwal, R.K., Brar, D.S., and Khush, G.S., 1997, Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization, Mol. Gen. Genet. 254:1.
Arumaganathan, K., and Earle, E.D., 1991, Nuclear DNA content of some important plant species, Plant Mol. Biol. Rep. 9:208.
Bennett, M.D., and Leitch, I.J., 1995, Nuclear DNA amounts in angiosperms, Ann. Bot. 76:113.
Causse, M.A., Fulton, T.M., Cho, Y.G., Ahn, S.N., Chunwongse, J., Wu, K., **ao, J., Yu, Z., Ronald, P.C., Harrington, S.E., Second, G., McCouch, S.R., and Tanksley, S.D., 1994, Saturated molecular map of the rice genome based on an interspecific backcross population, Genetics 138:1251.
Chen, J.H., Song, Y.C., and Liu, L.H., 1994, Studies on G-banded karyotype among fourOryza species, in: Plant Chromosome Research 1992, R. Tanaka, ed., pp. 133, International Academic Publishers, Bei**g.
Dally, A.M., and Second, G., 1990, Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza, section Oryza). Cladistic mutation and genetic-distance analysis, Theor. Appl. Genet. 80:209.
De Kochko, A., Kiefer, M.C., Cordesse, F., Reddy, A.S., and Delseny, M, 1991, Distribution organization of a tandemly repeated 352-bp sequence in theOryza family, Theor. Appl. Genet. 82:57.
Deshpande, V.G., and Ranjekar, P.K., 1980, Repetitive DNA in three Gramineae species with low DNA content, in: Physiological Chemistry 361, Z. Hoppe-Seyler ed., pp.1223, Walter de Gruyter & Co., Berlin.
Fransz, P.F., Alonso-Blanco, C., Liharska, T.B., Peeters, A.J.M., Zabel, P., and de Jong, J.H., 1996, High resolution physical map** in Arabidopsis thaliana and tomato by fluorescence in situ hybridisation to extended DNA fibres, Plant J. 9:421.
Fukui, K., 1986a, Standardization of karyoty** plant chromosomes by a newly developed chromosome image analyzing system (CHIAS), Theor. Appl. Genet. 72:27.
Fukui, K., 1986b, Comparison between Giemsa and orcein staining methods in rice chromosomes, La Kromosomo 11-43-44:1398.
Fukui, K., 1988, analysis and utility of chromosome information by using the chromosome image analyzing system, CHIAS, Bull. Natl. Inst. Agrobiol. Resour. 4:154.
Fukui, K., 1990, Localization of rRNA genes on rice chromosomes, Rice Biotech. Quart. 1:18.
Fukui, K., 1996a, Plant chromosomes at mitosis, in: Plant Chromosomes: Laboratory Methods, K. Fukui and S. Nakayama eds., pp.1, CRC Press, Boca Raton.
Fukui, K., 1996b, Recent advances in rice chromosome research, in: Rice Genetics 111, Proceedings of the 3rd International Rice Genetics Symposium, G. S. Khush ed., pp. 117, International Rice Research Institute, Los Banos, Philippines.
Fukui, K., and Iijima, K., 1991, Somatic chromosome map of rice by imaging methods. Theor. Appl. Genet. 81:589.
Fukui, K., and Iijima, K., 1992, Manual on rice chromosomes, (2nd ed.) Misc. Pub. Natl. Inst. Agrobiol. Resour. 4:1.
Fukui, K. and Ohmido, N., 2000, Smallness: gain and loss in chromosome research, in: Chromosome Today 13, P. Redi and E. Olmo eds., Birkhäuser Verlag AG, Basel (in press).
Fukui, K., Kakeda, K., Hashimoto, J., and Matsuoka, S. 1987, In situ hybridization of 125I-labeled rRNA to rice chromosomes, Rice Genet. Newsl. 4:114.
Fukui, K., Minezawa, M., Kamisugi, Y., Ishikawa, M., Ohmido, M., Yanagisawa, T., Fujishita M., Sakai, F., 1992, Microdissection of plant chromosomes by argon-ion laser beam, Theor. Appl. Genet. 84:787.
Fukui, K., Nakayama, S., Ohmido, N., Yoshiaki, H.2 and Yamabe, M., 1998, Quantitative karyoty** of three diploid Brassica species by imaging methods and localization of 45s rDNA loci on the identified chromosomes, Theor. Appl. Genet. 96:325.
Fukui, K., Ohmido, N., and Khush, G. S., 1994, Variability in rDNA loci in genus Oryza detected through fluorescence in situ hybridization, Theor. Appl. Genet. 87:893.
Fukui, K., Shishido, R., and Kinoshita, T., 1997, Identification of the rice D-genome chromosomes by genomic in situ hybridization, Theor. Appl. Genet. 95:1239.
Gustafson, J.P., and Dillé, J.E., 1992, Chromosome location of Oryza sativa recombination linkage groups, Proc. Natl. Acad. Sci. USA 89:8646.
Ha, S., Moore, P.H., Heinz, D., Kato, S., Ohmido, N. and Fukui, K. 1999, Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor fluorescence in situ hybridization and immaging methods, Plant Mol. Biol. 39:1165.
Hu, C.H., 1964, Further studies on the chromosome morphology of Oryza sativa L., in: Rice Genetics and Cytogenettcs, pp. 51, Elsevier Publishing Co., Amsterdam.
Iijima, K., Kakeda, K., and Fukui, K. 1991, Identification and characterization of somatic rice chromosomes by imaging methods, Theor. Appl. Genet. 81:597.
Islam-Faridi, M.N., Ishii, T., Kumar, V., Sitch, L.A., and Brar, D.S., 1990, Chromosomal location of ribosomal RNA genes in rice by in situ hybridization, Rice Genet Newsl. 7:143.
Jiang, J., Gill, B.S., Wang, G.L., Ronald, P.C., Ward, D.C., 1995, Metaphase and interphase fluorescence in situ hybridisation map** of rice genome with bacterial artificial chromosomes, Proc. Natl. Acad. Sci. USA 92:4487.
Kamisugi, Y., Furuya, N., Iijima, K., and Fukui, K., 1993, Computer-aided automatic identification of rice chromosomes by image parameters, Chromosome Res. 1:189.
Kamisugi, Y., Nakayama, S., O’Neill, CM., Mathias, R.J., Trick, M., and Fukui, K., 1998, Visualization of the Brassica self-incompatibility S-locus on identified oilseed rape chromosomes, Plant Mol. Biol. 38:29.
Kamisugi, Y., Sakai, F., Minezawa, M., Fujishita, M., and Fukui, K., 1993, Recovery of dissected C-band regions in Crepis chromosomes, Theor. Appl. Genet. 85:825.
Kato, S., and Fukui, K., 1998, Condensation pattern (CP) analysis of plant chromosomes by an improved chromosome image analyzing system, CHIAS III, Chromosome Res. 6:473.
Kato, S., Hirose, T., Akiyama, Y., O’Neill, CM., and Fukui, K., 1997, Manual on the chromosome image analyzing system HI, CHIAS III, Res. Rep. Agr. Devel. Hokuriku Area 36:1.
Khush, G.S., and Kinoshita, T., 1991, Rice karyotype, marker genes and linkage groups, in: Rice Biotechnology, G.S. Khush and G.H. Toennieson, eds., pp. 83, CAB International, Oxford.
Kurata, N., and Omura, T., 1978, Karyotype analysis in rice. A new method for identifying all chromosome pairs, Jpn. J. Genet. 53:251.
Kurata, N., Nagamura, Y., Yamamoto, K., Harushima, Y., Sue, N., Wu, J., Antonio, B.A., Shomura, A., Shimizu, T., Lin, S.Y., Inoue, T., Fukuda, A., Shimano, T., Kuboki, Y., Toyama, T., Miyamoto, Y., Kirihara, T., Hayasaka, K., Miyao, A., Monna, L., Zhong, H.S., Tamura, Y., Wang, Z.X., Momma, T., Umehara, Y., Yano, M., Sasaki, T., and Minobe, Y., 1994, A 300 kilobase interval genetic map of rice including 883 expressed sequences, Nature Genet. 8:365.
Kuwada, Y., 1910, A cytological study of Oryza sativa L., Bot. Mag. Tokyo 26:267.
Lawrence, J.B., Singer, R.H., and McNeil, J.A., 1990, Interphase and metaphase resolution of different distance within the human dystrophin gene, Science 249:928.
Li, H.W., Weng, T.S., Chen, C.C., and Wang, W.H., 1961, Cytogenetical studies of Oryza sativa L. and its related species. 1. Hybrids O. paraguaiensis Wedd. x O. brachyantha Chev. et Roehr., O. paraguaiensis Wedd. x O. australiensis Domin. and O. australiensis Domin. x O. aha Swallen, Bot. Bull. Acad. Sinica 2:79.
Martinez, C.P., Arumaganathan, K., Kikuchi, H., and Earle, E.D., 1994, Nuclear DNA content often rice species as determined by flow cytometry, Jpn. J. Genet. 69:513.
Morinaga, T., 1939, Cyto-genetics on rice (Oryza sativa L.), Bot. Zool. 7:179.
Nakamura, S., Asakawa, S., Ohmido, N., Fukui, K., Shimizu, N., and Kawasaki, S., 1997, Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta 2 using a highly repetitive rice BAC library, Mol. Gen. Genet. 254:611.
Nakamura, M., and Fukui, K., 1997, A chromosome-oriented approach to genome analysis in a woody plant-Sequoiadendron giganteum (Lindl.) Buchholz, in: Cytogenetic Studies of Forest Trees and Shrub Species, Z. Borzan and S. E. Schlarbaum, eds, pp.89, University of Zagreb, Zagreb, Croatia.
Ohmido, N., Akiyama, Y., and Fukui, K., 1998, Physical map** of unique nucleotide sequences on identified rice chromosomes, Plant Mol. Biol. 38:1043.
Ohmido, N., and Fukui, K., 1997, Visual verification of close disposition of rice A genome specific tandem repeat sequence (TrsA) and telomere sequence, Plant Mol. Biol. 35:963.
Ohmido, N., Kijima, K., Akiyama, Y., de Jong, J.H. and Fukui, K. Quantification of total genomic DNA and repetitive sequences in rice reveals concurrent changes of different DNA families in indica and japonica rice, Mol. Gen. Genet, (in press).
Ohmido, N., Kijima, K., Ashikawa, I., de Jong, H.J. and Fukui, K. Visualization of the terminal structure of rice chromosomes using multicolor FISH on chromosomes and extended DNA fibers. Theor. Appl. Genet, (submitted).
Ohtsubo, H., Umeda, M., and Ohtsubo, E., 1991, Organization of DNA sequences highly repeated in tandem in rice genomes, Jpn. J. Genet. 66:241.
Schriml, L.M., Padilla-Nash, H.M., Colemn, A., Moen, P., Nash, W.G., Menninger, J., Jones, G., Ried, T. and Dean M. 1999, Tyramide signal amplification (TSA)-FISH applied to map** PCR-labeled probes less than lkb in size, Biotechniques 27:608.
Schrock, E., du Manior, S., Veldman, T., Schoell, B., Wienberg, J., Ferguson-Smith, M.A., Ning, Y., Ledbetter, D.H., Bar-Am, I., Soenksen, D., Garini, Y., and Ried, T., 1996, Multicolor spectral karyoty** of human chromosomes, Science 273:494.
Shishido, R., Apistwanich, S., Ohmido, N., Okinaka, Y., Mori, K., and Fukui, K., 1998, Detection of specific chromosome reduction in nce somatic hybrids with A, B, and C genomes by multicolor genomic in situ hybridization. Theor. Appl. Genet, (in press).
Singh, K., Ishii, T., Parco, A., Huang, N., Brar, D.S., and Khush, G.S., 1996, Centromere map** and orientation of the molecular linkage map of rice (Oryza sativa L.), Proc. Nati Acad. Sci USA 93:6163.
Song, Y.C., and Gustafson, J.P, 1995, The physical location of fourteen RFLP markers in nce. (Oryza sativa L.), Theor. Appl. Genet. 90:113.
Speicher, M.R., Ballard, S.G., and Ward, D.C., 1996, Karyoty** human chromosomes by combinatorial multi-fluor FISH, Nature Genet. 12:368.
Stebbins, G.L., 1950, Variation and Evolution in Plants, pp. 300, Columbia University Press, New York.
Swanson, C.P., 1957, Polyploidy and evolution, in: Cytology and Cytogenetics, pp. 500, Prentice-Hall, Inc., Englewood Cliffs.
Uozu, S., Ohmido, N., Ohtsubo, H., Ohtsubo, E., and Fukui, K., 1997, Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza, Plant Mol. Biol. 35:791.
Van den Engh, G., Sachs, R., and Trask, B.J. 1992, Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model, Science 257:1410.
Wiegant, J., Kalle, W., Mullenders, L., Brookes, S., Hoovers, J.M.N., Dauwerse, J.G., van Ommen, G.J.B., Raap, A.K., 1992, High-resolution in situ hybridization using DNA halo preparations. Hum. Mol. Genet. 1.587.
Wu, H.K., Chung, M.C., Wu, T., Nmg, C.N., and Wu, R., 1991, Localization of specific repetitive DNA sequences in individual rice chromosomes, Chromosoma 100:330.
Wu, K.S., and Tanksley, S.D., 1993, Genetic and physical map** of telqmeres and macrosatellites of rice. Plant Mol. Biol. 22:861.
Wu, T., Wang, Y., and Wu, R. 1994, Transcribed repetitive DNA sequence in telomeric regions of rice (Oryza sativa). Plant Mol. Biol. 26:363.
Wu, T., and Wu, R.A., 1987, A new rice repetitive DNA shows sequence homology to both 5S RNA and tRNA, Nucl. Acids Res. 15 5913.
Yanagisawa, T., Tano, S., Fukui, K., and Harada, H., 1991, Marker chromosomes commonly observed in the genus Glycine, Theor. Appl. Genet. 81:606.
Zwick, M.S., Hanson, R.E., McKmght, T.D., Islam-Fandi, M.N., Stelly, D.M., Wing, R.A., and Price, H.L., 1997, A rapid procedure for the isolation of Cot-1 DNA for plants, Genome 40:138.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Springer Science+Business Media New York
About this chapter
Cite this chapter
Fukui, K., Ohmido, N. (2000). Rice Genome Research: An Alternative Approach Based on Molecular Cytology. In: Gustafson, J.P. (eds) Genomes. Stadler Genetics Symposia Series. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-4235-3_10
Download citation
DOI: https://doi.org/10.1007/978-1-4615-4235-3_10
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-6902-8
Online ISBN: 978-1-4615-4235-3
eBook Packages: Springer Book Archive