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DNA Research Advance Access originally published online on February 23, 2006
DNA Research 2005 12(6):417-427; doi:10.1093/dnares/dsi019
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© The Author 2006. 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

Genome-wide Investigation of Intron Length Polymorphisms and Their Potential as Molecular Markers in Rice (Oryza sativa L.)

Xusheng Wang {dagger}, Xiangqian Zhao {dagger}, Jun Zhu and Weiren Wu*

Institute of Bioinformatics, Huajiachi Campus, Zhejiang University Hangzhou, 310029, P. R. China

Intron length polymorphisms (ILPs) have been used as genetic markers in some studies. However, a systematic investigation and large-scale exploitation of ILP markers has not been reported. In this study, we performed a genome-wide search of ILPs between two subspecies (indica and japonica) in rice using the draft genomic sequences of cultivars 93-11 (indica) and Nipponbare (japonica) and 32 127 full-length cDNA sequences of Nipponbare obtained from public databases. We identified 13 308 putative ILPs. Based on these putative ILPs, we developed 5811 candidate ILP markers via electronic-PCR with primers designed in flanking exons. We further conducted experiment to verify the candidate ILP markers. Out of 215 candidate ILP markers tested on 93-11, Nipponbare and their hybrid, we successfully exploited 173 codominant ILP markers. Further analyses on 10 rice accessions showed that these ILP markers were widely applicable and most (71.1%) exhibited subspecies specificity. This feature suggests that ILPs would be useful for the studies of genome evolution and inter-subspecies heterosis and for cross-subspecies marker-assisted selection in rice. In addition, by testing 51 pairs of the ILP primers on five Gramineae plants and three dicot plants, we found another desirable characteristic of rice ILP markers that they have high transferability to other plants.

Key words: rice (Oryza sativa L.); intron length polymorphism (ILP); molecular marker; genome

*To whom correspondence should be addressed. Tel/Fax. +86-571-86971910, E-mail: wuwr{at}zju.edu.cn

{dagger}These authors contributed equally to this work.

Communicated by Satoshi Tabata


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