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DNA Research Advance Access originally published online on March 6, 2009
DNA Research 2009 16(2):131-140; doi:10.1093/dnares/dsp004
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© The Author 2009. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

High Potential of a Transposon mPing as a Marker System in japonica x japonica Cross in Rice

Yuki Monden1, Ken Naito2, Yutaka Okumoto1, Hiroki Saito1, Nobuhiko Oki1, Takuji Tsukiyama1, Osamu Ideta3, Tetsuya Nakazaki1, Susan R. Wessler2 and Takatoshi Tanisaka1,*

1 Plant Breeding Laboratory, Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
2 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
3 National Agricultural Research Center for Western Region, National Agricultural Research Organization, Fukuyama, Hiroshima 721-8514, Japan

Received 21 November 2008 ; accepted 15 February 2009.

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 x 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 x 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.

Key words: Linkage mapping; Transposon; japonica; Oryza sativa L.; QTL analysis

* To whom correspondence should be addressed. Tel. +81 75 753 6045. Fax. +81 75 753 6047. E-mail: tanisaka{at}kais.kyoto-u.ac.jp


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