Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH)

Proceedings of the Japan Academy Series B: Physical and Biological Sciences

Volumn 86, Issue 2, 2010, Pages 103-106

  Ohmido, Nobuko ^a   Fukui, Kiichi ^b   Kinoshita, Toshiro ^c  

^a KOBE UNIVERSITY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Chromosome; Extended DNA fibers (EDFs); Fluorescence in situ hybridization (FISH); Genomic in situ hybridization (GISH); Oryza sativa L.

Indexed keywords

ORYZA SATIVA;

RIBOSOME RNA;

FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; METHODOLOGY; PLANT CHROMOSOME; PLANT GENOME; REVIEW; RICE;

CHROMOSOMES, PLANT; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; ORYZA SATIVA; RNA, RIBOSOMAL;

EID: 77951925184     PISSN: 03862208     EISSN: 13492896     Source Type: Journal    
DOI: 10.2183/pjab.86.103     Document Type: Review

References (89)

1. Gill, B.S. and Friebe, B. (1998) Plant cytogenetics at the dawn of the 21st century. Curr. Opin. Plant Biol. 1, 109-115.
2. Mukai, Y. (1996) In situ hybridization. In Plant Chromosomes Laboratory Methods (eds. Fukui, K. and Nakayama, S.). CRC Press, New York, pp. 155-170.
3. Mukai, Y. (2005) Perspectives in molecular cytogenetics of wheat. Frontiers of Wheat Bioscience. Memorial Issue, Wheat Inf. Serv. 100, 17-31.
4. de Jong, H. (2003) Visualizing DNA domains and sequences by microscopy: a fifty-year history of molecular cytogenetics. Genome 46, 943-946.
5. Lysak, M.A., Pecinka, A. and Schubert, I. (2003) Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Res. 11, 195-204.
6. Jiang, J. and Gill, B.S. (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49, 1057-1068.
7. Lysak, M., Fransz, P. and Schubert, I. (2006) Cytogenetic analyses of Arabidopsis. Methods Mol. Biol. 323, 173-186.
8. Harper, L.C. and Cande, W.Z. (2000) Mapping a new frontier: development of integrated cytogenetic maps in plants. Funct. Integr. Genomics 1, 89-98.
9. Fukui, K. (1990) Localization of rRNA genes on rice chromosomes. Rice Biotech. Quart. 1, 18-19.
10. Fukui, K. and Iijima, K. (1991) Somatic chromosome map of rice by imaging methods. Theor. Appl. Genet. 81, 589-596.
11. Langer, P.R., Waldrop, A.A. and Ward, D.C. (1981) Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. USA 78, 6633-6637.
12. Pardue, M.L. and Gall, J.G. (1970) Chromosomal localization of mouse satellite DNA. Science 168, 1356-1358.
13. Schwarzacher, T., Leitch, A.R., Bennett, M.D. and Heslop-Harrison, J.S. (1989) In situ hybridization of parental genomes in a wide hybrid. Ann. Bot. (London) 64, 315-324.
14. Yamamoto, M. and Mukai, Y. (1989) Application of fluorescence in situ hybridization to molecular cytogenetics of wheat. Wheat Inf. Serv. 69, 30-32.
15. 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, 893-899.
16. Ohmido, N. and Fukui, K. (1995) Cytological studies of African cultivated rice, Oryza glaberrima. Theor. Appl. Genet. 91, 212-217.
17. Shishido, R., Sano, Y. and Fukui, K. (2000) Ribosomal DNAs: an exception to the conservation of gene order in rice genomes. Mol. Gen. Genet. 263, 586-591.
18. Chung, M.C., Lee, Y.I., Cheng, Y.Y., Chou, Y.J. and Lu, C.F. (2008) Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor. Appl. Genet. 116, 745-753.
19. Dubcovsky, J. and Dvorák, J. (1995) Ribosomal RNA multigene loci: nomads of the Triticeae genomes. Genetics 140, 1367-1377.
20. Schubert, I. and Wobus, U. (1985) In situ hybridization confirms jumping nucleolus organizing regions in Allium. Chromosoma 92, 143-148.
21. Dolezel, J., Kubaláková, M., Bartos, J. and Macas, J. (2004) Flow cytogenetics and plant genome mapping. Chromosome Res. 12, 77-91.
22. Ma, Y., Lee, J.H., Li, L.C., Uchiyama, S., Ohmido, N. and Fukui, K. (2005) Fluorescent labeling of plant chromosomes in suspension by FISH. Genes Genet. Syst. 80, 35-39.
23. International Rice Genome Sequence Project: http://rgp.dna.affrc.go.jp/E/IRGSP/index.html
24. Moore, G., Foote, T., Helentjaris, T., Devos, K., Kurata, N. and Gale, M. (1995) Was there a single ancestral cereal chromosome? Trends Genet. 11, 81-82.
25. National Institute of Agribiological Sciences Rice Full-Length cDNA Project Team (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376-379.
26. Ohtsubo, H., Umeda, M. and Ohtsubo, E. (1991) Organization of DNA sequences highly repeated in tandem in rice genomes. Jpn. J. Genet. 66, 241-254.
27. Wu, H.K., Chung, M.C., Wu, T.Y., Ning, C.N. and Wu, R. (1991) Localization of specific repetitive DNA sequences in individual rice chromosomes. Chromosoma 100, 330-338.
28. Ohmido, N. and Fukui, K. (1997) Visual verification of close disposition between a rice A genome-specific DNA sequence (TrsA) and the telomere sequences. Plant Mol. Biol. 35, 963-968.
29. Ohmido, N., Kijima, K., Ashikawa, I., de Jong, H.J. and Fukui, K. (2001) Visualization of the terminal structure of rice chromosomes 6 and 12 using multicolor FISH to chromosomes and extended DNA fibers. Plant Mol. Biol. 47, 413-421.
30. Mizuno, H., Wu, J., Kanamori, H., Fujisawa, M., Namiki, N., Saji, S. et al. (2006) Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L, and 8S. Plant J. 46, 206-217.
31. Ohmido, N. and Fukui, K. (2004) Recent advances in FISH analysis of plant chromosomes. Recent Res. Devel. Biochem. 5, 267-279.
32. Heslop-Harrison, J.S., Brandes, A., Taketa, S., Schmidt, T., Vershinin, A.V., Alkhimova, E.G. et al. (1997) The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica 100, 197-204.
33. Nakajima, R., Noma, K., Ohtsubo, H. and Ohtsubo, E. (1996) Identification and characterization of two tandem repeat sequences (TrsB and TrsC) and a retrotransposon (RIRE1) as genome-general sequences in rice. Genes Genet. Syst. 71, 373-382.
34. Uozu, S., Ikehashi, H., 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, 791-799.
35. Suoniemi, A., Anamthawat-Jónsson, K., Arna, T. and Schulman, A.H. (1996) Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol. Biol. 30, 1321-1329.
36. Tang, X., Bao, W., Zhang, W. and Cheng, Z. (2007) Identification of chromosomes from multiple rice genomes using a universal molecular cytogenetic system. J. Integr. Plant Biol. 49, 953-960.
37. Heslop-Harrison, J.S., Brandes, A. and Schwarzacher, T. (2003) Tandemly repeated DNA sequences and centromeric chromosomal regions of Arabidopsis species. Chromosome Res. 11, 241-253.
38. Ananiev, E.V., Phillips, R.L. and Rines, H.W. (1998) Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc. Natl. Acad. Sci. USA 95, 13073-13078.
39. Dong, F., Miller, J.T., Jackson, S.A., Wang, G.L., Ronald, P.C. and Jiang, J. (1998) Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc. Natl. Acad. Sci. USA 95, 8135-8140.
40. Kumekawa, N., Ohmido, N., Fukui, K., Ohtsubo, E. and Ohtsubo, H. (2001) A new gypsy-type retrotransposon, RIRE7: preferential insertion into the tandem repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes. Mol. Gen. Genomics 265, 480-488.
41. Ma, J., Wing, R.A., Bennetzen, J.L. and Jackson, S.A. (2007) Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 23, 134-139.
42. Fukui, K.N., Suzuki, G., Lagudah, E.S., Rahman, R., Appels, R., Yamamoto, M. and Mukai, Y. (2001) Physical arrangement of retrotransposon-related repeats in centromeric regions of wheat. Plant Cell Physiol. 42, 189-196.
43. Cheng, Z.J. and Murata, M. (2003) A centromeric tandem repeat family originating from a part of Ty3/gypsy-retroelement in wheat and its relatives. Genetics 164, 665-672.
44. Ohmido, N., Ishimaru, A., Kato, S., Sato, S., Tabata S. and Fukui, K. (2009) Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res. (in press)
45. Zhang, Y., Huang, Y., Zhang, L., Li, Y., Lu, T., Lu, Y. et al. (2004) Structural features of the rice chromosome 4 centromere. Nucleic Acids Res. 32, 2023-2030.
46. Cheng, Z., Dong, F., Langdon, T., Ouyang, S., Buell, C.R., Gu, M. et al. (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14, 1691-1704.
47. Zhang, W., Yi, C, Bao, W., Liu, B., Cui, J., Yu, H. et al. (2005) The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol. 139, 306-315.
48. Jiang, J., Birchle, J.A., Parrott, W.A. and Dawe, R.K. (2003) A molecular view of plant centromeres. Trends Plant Sci. 8, 570-575.
49. Palmer, D.K., O'Day, K., Trong, H.L., Charbonneau, H. and Margolis, R.L. (1991) Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proc. Natl. Acad. Sci. USA 88, 3734-3738.
50. Talbert, P.B., Masuelli, R., Tyagi, A.P., Comai, L. and Henikoff, S. (2002) Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14, 1053-1066.
51. Nagaki, K., Neumann, P., Zhang, D., Ouyang, S., Buell, C.R., Cheng, Z. et al. (2005) Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice. Mol. Biol. Evol. 22, 845-855.
52. Houben, A., Demidov, D., Gernand, D., Meister, A., Leach, C.R. and Schubert, I. (2003) Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J. 33, 967-973.
53. Iwata, I. (2008) Cytological research of rice chromosomes. Kobe University Graduation thesis, pp. 1-51.
54. Ohmido, N., Akiyama, Y. and Fukui, K. (1998) Physical mapping of unique nucleotide sequences on identified rice chromosomes. Plant Mol. Biol. 38, 1043-1052.
55. Rajyashiri, K.R., Nair, S., Ohmido, N., Fukui, K., Kurata, N., Sasaki, T. et al. (1998) Isolation and FISH mapping of Yeast Artificial Chromosomes (YACs) encompassing an allele of the Gm2 gene for gall midge resistance in rice. Theor. Appl. Genet. 97, 507-514.
56. Jiang, J., Gill, B.S., Wang, G.L., Ronald, P.C. and Ward, D.C. (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.
57. 2 using a highly representative rice BAC library. Mol. Gen. Genet. 254, 611-620.
58. Szinay, D., Chang, S.B., Khrustaleva, L., Peters, S., Schijlen, E., Bai, Y. et al. (2008) High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. Plant J. 56, 627-637.
59. Wang, C.J., Harper, L. and Cande, W.Z. (2006) High-resolution single-copy fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18, 529-544.
60. Cheng, Z., Buell, C.R., Wing, R.A., Gu, M. and Jiang, J. (2001) Toward a cytological characterization of the rice genome. Genome Res. 11, 2133-2141.
61. Tang, X., Bao, W., Zhang, W. and Cheng, Z. (2007) Identification of chromosomes from multiple rice genomes using a universal molecular cytogenetic marker system. J. Integr. Plant Biol. 49, 953-960.
62. Wu, J., Mizuno, H., Hayashi-Tsugane, M., Ito, Y., Chiden, Y., Fujisawa, M. et al. (2003) Physical maps and recombination frequency of six rice chromosomes. Plant J. 36, 720-730.
63. Kato, S., Ohmido, N. and Fukui, K. (2003) Development of a quantitative pachytene chromosome map in Oryza sativa by imaging methods. Genes Genet. Syst. 78, 155-161.
64. Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y. et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420, 316-320.
65. Schubert, I., Fransz, P.F., Fuchs, J. and de Jong, J.H. (2001) Chromosome painting in plants. Methods Cell Sci. 23, 57-69.
66. Mukai, Y. and Gill, B.S. (1991) Detection of barley chromatin added to wheat by genomic in situ hybridization. Genome 34, 448-452.
67. Mukai, Y., Nakahara, Y. and Yamamoto, M. (1993) Simultaneous discrimination on the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome 36, 489-494.
68. Fukui, K., Shishido, R. and Kinoshita, T. (1997) Identification of the rice D-genome chromosomes by genomic in situ hybridization. Theor. Appl. Genet. 95, 1239-1245.
69. Shishido, R., Apisitwanich, S., Ohmido, N., Okinaka, Y., Mori, K. and Fukui, K. (1998) Detection of specific chromosome reduction in rice somatic hybrids with the A, B, and C genomes by multi-color genomic in situ hybridization. Theor. Appl. Genet. 97, 1013-1018.
70. Tan, G., Jin, H., Li, G., He, R., Zhu, L. and He, G. (2005) Production and characterization of a complete set of individual chromosome additions from Oryza officinalis to Oryza sativa using RFLP and GISH analyses. Theor. Appl. Genet. 111, 1585-1595.
71. Yan, H., Liu, G., Cheng, Z., Min, S. and Zhu, L. (2001) Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by restriction fragment length polymorphism (RFLP) analysis and genomic in situ hybridization (GISH). Genome 44, 86-95.
72. Shishido, R., Ohmido, N. and Fukui, K. (2001) Chromosome painting as a tool for rice genetics and breeding. Methods Cell Sci. 23, 125-132.
73. Escalante, A., Imanishi, S., Hossain, M., Ohmido, N. and Fukui, K. (1998) RFLP analysis and genomic in situ hybridization (GISH) in somatic hybrids and their progenies between Lycopersicon esculentum and Solanum lycopersicoides. Theor. Appl. Genet. 96, 719-726.
74. Iwamoto, Y., Hirai, M., Ohmido, N., Fukui, K. and Ezura, H. (2007) Fertile somatic hybrids between Solanum integrifolium and S. sanitwongsei (syn. S. kurzii) as candidates for bacterial wilt-resistant rootstock of eggplant. Plant Biotech. 24, 179-184.
75. Snowdon, R.J., Kohler, W., Friedt, W. and Kohler, A. (1997) Genomic in situ hybridization in Brassica amphidiploids and interspecific hybrids. Theor. Appl. Genet. 95, 1320-1324.
76. Howell, E.C., Kearsey, M.J., Jones, G.H., King, G.J. and Armstrong, S.J. (2008) A and C genome distinction and chromosome identification in Brassica napus by sequential fluorescence in situ hybridization and genomic in situ hybridization. Genetics 180, 1849-1857.
77. de Jong, H.J., Fransz, P. and Zabel, P. (1999) High-Resolution FISH in plants: techniques and applications. Trends Plant Sci. 4, 258-263.
78. Fransz, P., Alonso-Blanco, C., Liharska, T., 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 fibers. Plant J. 9, 421-430.
79. Ohmido, N., Kijima, K., Akiyama, Y., de Jong, J.H. and Fukui, K. (2000) Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol. Gen. Genet. 263, 388-394.
80. Mukai, Y. (1996) Multicolor fluorescence in situ hybridization: a new tool for genome analysis. In Methods of Genome Analysis in Plants (ed. Jauhar P.P.). CRC Press, New York, pp. 181-192.
81. Henegariu, O., Grober, L., Haskins, W., Bowers, P.N., State, M.W., Ohmido, N. et al. (2001) Rapid DNA fiber technique for size measurements of linear and circular DNA probes. Biotechniques 31, 246-250.
82. Jackson, S.A., Wang, M.L., Goodman, H.M. and Jiang, J. (1998) Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 41, 566-572.
83. Cheng, Z., Buell, C.R., Wing, R.A. and Jiang, J. (2002) Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes, and extended DNA fibers. Chromosome Res. 10, 379-387.
84. Yuan, Q., Hill, J., Hsiao, J., Moffat, K., Ouyang, S., Cheng, Z. et al. (2002) Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol. Genet. Genomics 267, 713-720.
85. Suzuki, G., Kai, N., Hirose, T., Fukui, K., Nishio, T., Takayama, S. et al. (1999) Genomic organization of the S locus: identification and characterization of genes in SLG/SRK region of S9 haplotype of Brassica campestris (syn. rapa). Genetics 153, 391-400.
86. Morishima, H. (1984) Wild plants and domestication. In Biology of Rice (eds. Tsunoda, S. and Takahashi, N.). Japan Sci. Soc. Press, Amsterdam, pp. 3-30.
87. Ohmido, N., Fukui, K. and Kinoshita, T. (2005) Advances in rice chromosomes research. Proc. Jpn. Acad., Ser. B 81, 382-392.
88. Wako, T., Fukuda, M., Furushima-Shimogawara, R., Belyaev, N.D. and Fukui, K. (2002) Cell cycle-dependent and lysine residue-specific dynamic changes of histone H4 acetylation in barley. Plant Mol. Biol. 49, 645-653.
89. Ohmido, N., Wako, T. and Fukui, K. (2008) Nuclear organization analyzed by visualization. The Nucleus 50, 473-489.