Transposon display for active DNA transposons in rice

Kyoko Takagi, Naoko Ishikawa, Masahiko Maekawa, Kazuo Tsugane, Shigeru Iida

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Transposon display (TD) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function. Although active endogenous DNA transposons have been used extensively for gene tagging in maize, only two active endogenous DNA transposons in rice have been identified, the 0.43-kb element mPing of the MITE family and the 0.6-kb nDart element of the hAT family. The nDart transposition was shown to be induced by crossing with a line containing its autonomous element aDart and stabilized by segregating aDart under natural growth conditions, while mPing-related elements were shown to transpose in cultured cells, plants regenerated from an anther culture, and ?-ray-irradiated plants. No somaclonal variation should occur in nDart-promoted gene tagging because no tissue culture was involved in nDart activation. As an initial step to develop an effective tagging system using nDart in rice, we tried to visualize GC-rich nDart-related elements comprising 18 nDart-related sequences of 0.6-kb and 63 nDart-related elements longer than 2 kb in Nipponbare by TD. Comparing the observed bands in TD with the anticipated virtual bands of the nDart-related elements based upon the available rice genome sequence, we have improved our TD protocol by optimizing the PCR amplification conditions and are able to visualize approximately 87% of the anticipated bands produced from the nDart-related elements. To compare the visualization efficiency of these nDart-related elements with that of 50 mPing elements and a unique Ping sequence in Nipponbare, we also tried to visualize the mPing-related elements; all mPing-related elements are easily visualized. Based on these results, we discuss the parameters affecting the visualization efficiencies of these rice DNA transposons. We also discuss the utilization of nDart elements in gene tagging for functional genomics in rice.

Original languageEnglish
Pages (from-to)109-122
Number of pages14
JournalGenes and Genetic Systems
Volume82
Issue number2
DOIs
Publication statusPublished - 2007

Fingerprint

DNA Transposable Elements
transposons
Genes
rice
DNA
Visualization
genes
Tissue culture
Genomics
Zea mays
miniature inverted repeat transposable elements
Cultured Cells
genomics
somaclonal variation
Amplification
anther culture
Oryza
transposition (genetics)
Genome
Polymerase Chain Reaction

Keywords

  • DNA transposon
  • Functional genomics
  • Gene tagging
  • Rice genome
  • Transposon display

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Genetics
  • Genetics(clinical)

Cite this

Takagi, K., Ishikawa, N., Maekawa, M., Tsugane, K., & Iida, S. (2007). Transposon display for active DNA transposons in rice. Genes and Genetic Systems, 82(2), 109-122. https://doi.org/10.1266/ggs.82.109

Transposon display for active DNA transposons in rice. / Takagi, Kyoko; Ishikawa, Naoko; Maekawa, Masahiko; Tsugane, Kazuo; Iida, Shigeru.

In: Genes and Genetic Systems, Vol. 82, No. 2, 2007, p. 109-122.

Research output: Contribution to journalArticle

Takagi, K, Ishikawa, N, Maekawa, M, Tsugane, K & Iida, S 2007, 'Transposon display for active DNA transposons in rice', Genes and Genetic Systems, vol. 82, no. 2, pp. 109-122. https://doi.org/10.1266/ggs.82.109
Takagi K, Ishikawa N, Maekawa M, Tsugane K, Iida S. Transposon display for active DNA transposons in rice. Genes and Genetic Systems. 2007;82(2):109-122. https://doi.org/10.1266/ggs.82.109
Takagi, Kyoko ; Ishikawa, Naoko ; Maekawa, Masahiko ; Tsugane, Kazuo ; Iida, Shigeru. / Transposon display for active DNA transposons in rice. In: Genes and Genetic Systems. 2007 ; Vol. 82, No. 2. pp. 109-122.
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