High potential of a transposon mPing as a marker system in japonica × japonica cross in rice

Yuki Monden, Ken Naito, Yutaka Okumoto, Hiroki Saito, Nobuhiko Oki, Takuji Tsukiyama, Osamu Ideta, Tetsuya Nakazaki, Susan R. Wessler, Takatoshi Tanisaka

Research output: Contribution to journalArticlepeer-review

41 Citations (Scopus)


Although quantitative traits loci (QTL) analysis has been widely performed to isolate agronomically important genes, it has been difficult to obtain molecular markers between individuals with similar phenotypes (assortative mating). Recently, the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies. In contrast, most other japonicas, including Nipponbare, have 50 or fewer mPing insertions in their genome. In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas, Nipponbare × Gimbozu (EG4). These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism (150 of 183) than all other molecular markers tested including short sequence repeat markers (46 of 661). In addition, we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare × Gimbozu EG4, and successfully mapped a locus involved in heading date on the short arm of chromosome 6. Moreover, we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10.

Original languageEnglish
Pages (from-to)131-140
Number of pages10
JournalDNA Research
Issue number2
Publication statusPublished - Apr 2009
Externally publishedYes


  • Japonica
  • Linkage mapping
  • Oryza sativa L.
  • QTL analysis
  • Transposon

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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