Recent Advances in Rice Genome and Chromosome Structure Research by Fluorescence in Situ Hybridization (FISH)

Overview

Journal Proc Jpn Acad Ser B Phys Biol Sci

Specialties Biology
Science

Date 2010 Feb 16

PMID 20154468

Citations 6

Authors

Nobuko Ohmido

Kiichi Fukui

Toshiro Kinoshita

Affiliations

Soon will be listed here.

Abstract

Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.

Citing Articles

Allopolyploidy enhances survival advantages for urban environments in the native plant genus Commelina.

Shimomai H, Taichi N, Katsuhara K, Kato S, Ushimaru A, Ohmido N Ann Bot. 2024; 134(6):1055-1066.

PMID: 39175163 PMC: 11687629. DOI: 10.1093/aob/mcae141.

Molecular combing and its application in clinical settings.

Wang Y, Kumar K, Liehr T Mol Cytogenet. 2022; 15(1):50.

PMID: 36384693 PMC: 9670602. DOI: 10.1186/s13039-022-00628-8.

Production and First Assessment of Iranian Secondary Tritipyrum Genotypes by GISH and AFLP Markers.

Shahsavand Hassani H, Blattner F, Houben A, Brner A Iran J Biotechnol. 2020; 17(4):e1796.

PMID: 32671119 PMC: 7357698. DOI: 10.30498/IJB.2019.91760.

Physical mapping of black spot disease resistance/susceptibility-related genome regions in Japanese pear (Pyrus pyrifolia) by BAC-FISH.

Yamamoto M, Terakami S, Takada N, Yamamoto T Breed Sci. 2016; 66(3):444-9.

PMID: 27436955 PMC: 4902454. DOI: 10.1270/jsbbs.15085.

Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes.

Yang L, Liu T, Li B, Sui Y, Chen J, Shi J PLoS One. 2012; 7(11):e50236.

PMID: 23185584 PMC: 3503983. DOI: 10.1371/journal.pone.0050236.

References

Ma J, Wing R, Bennetzen J, Jackson S . Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 2007; 23(3):134-9. DOI: 10.1016/j.tig.2007.01.004. View

Zhang Y, Huang Y, Zhang L, Li Y, Lu T, Lu Y . Structural features of the rice chromosome 4 centromere. Nucleic Acids Res. 2004; 32(6):2023-30. PMC: 390372. DOI: 10.1093/nar/gkh521. View

Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K . Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol. 1998; 35(6):791-9. DOI: 10.1023/a:1005823124989. View

Ohmido N, Fukui K, Kinoshita T . Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). Proc Jpn Acad Ser B Phys Biol Sci. 2010; 86(2):103-16. PMC: 3417561. DOI: 10.2183/pjab.86.103. View

Wu J, Mizuno H, Hayashi-Tsugane M, Ito Y, Chiden Y, Fujisawa M . Physical maps and recombination frequency of six rice chromosomes. Plant J. 2003; 36(5):720-30. DOI: 10.1046/j.1365-313x.2003.01903.x. View

Ananiev E, Phillips R, Rines H . Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci U S A. 1998; 95(22):13073-8. PMC: 23713. DOI: 10.1073/pnas.95.22.13073. View

Lysak M, Fransz P, Schubert I . Cytogenetic analyses of Arabidopsis. Methods Mol Biol. 2006; 323:173-86. DOI: 10.1385/1-59745-003-0:173. View

Pardue M, Gall J . Chromosomal localization of mouse satellite DNA. Science. 1970; 168(3937):1356-8. DOI: 10.1126/science.168.3937.1356. View

Ohmido N, Kijima K, Ashikawa I, de Jong J, Fukui K . Visualization of the terminal structure of rice chromosomes 6 and 12 with multicolor FISH to chromosomes and extended DNA fibers. Plant Mol Biol. 2001; 47(3):413-21. DOI: 10.1023/a:1011632111845. View

10.

Dong F, Miller J, Jackson S, Wang G, Ronald P, Jiang J . Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc Natl Acad Sci U S A. 1998; 95(14):8135-40. PMC: 20942. DOI: 10.1073/pnas.95.14.8135. View

11.

Ohmido N, Ishimaru A, Kato S, Sato S, Tabata S, Fukui K . Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res. 2010; 18(2):287-99. DOI: 10.1007/s10577-009-9103-5. View

12.

Suzuki G, Kai N, Hirose T, Fukui K, Nishio T, Takayama S . Genomic organization of the S locus: Identification and characterization of genes in SLG/SRK region of S(9) haplotype of Brassica campestris (syn. rapa). Genetics. 1999; 153(1):391-400. PMC: 1460755. DOI: 10.1093/genetics/153.1.391. View

13.

Ma Y, Lee J, Li L, Uchiyama S, Ohmido N, Fukui K . Fluorescent labeling of plant chromosomes in suspension by FISH. Genes Genet Syst. 2005; 80(1):35-9. DOI: 10.1266/ggs.80.35. View

14.

Dubcovsky J, Dvorak J . Ribosomal RNA multigene loci: nomads of the Triticeae genomes. Genetics. 1995; 140(4):1367-77. PMC: 1206700. DOI: 10.1093/genetics/140.4.1367. View

15.

Wang C, Harper L, Cande W . High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell. 2006; 18(3):529-44. PMC: 1383631. DOI: 10.1105/tpc.105.037838. View

16.

Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N . Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science. 2003; 301(5631):376-9. DOI: 10.1126/science.1081288. View

17.

Langer P, Waldrop A, Ward D . Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc Natl Acad Sci U S A. 1981; 78(11):6633-7. PMC: 349103. DOI: 10.1073/pnas.78.11.6633. View

18.

Ohtsubo H, Umeda M, Ohtsubo E . Organization of DNA sequences highly repeated in tandem in rice genomes. Jpn J Genet. 1991; 66(3):241-54. DOI: 10.1266/jjg.66.241. View

19.

Howell E, Kearsey M, Jones G, King G, Armstrong S . A and C genome distinction and chromosome identification in brassica napus by sequential fluorescence in situ hybridization and genomic in situ hybridization. Genetics. 2008; 180(4):1849-57. PMC: 2600926. DOI: 10.1534/genetics.108.095893. View

20.

Wako T, Fukuda M, Furushima-Shimogawara R, Belyaev N, Fukui K . Cell cycle-dependent and lysine residue-specific dynamic changes of histone H4 acetylation in barley. Plant Mol Biol. 2002; 49(6):645-53. DOI: 10.1023/a:1015554124675. View