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DNA Research Advance Access published online on April 23, 2007
DNA Research, doi:10.1093/dnares/dsm005
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© The Author 2007. 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

A Genome-wide Microsatellite Polymorphism Database for the Indica and Japonica Rice

Zhonghua Zhang1,5 {dagger}, Yajun Deng2 {dagger}, Jun Tan4 {dagger}, Songnian Hu1,2, Jun Yu1,2,3 and Qingzhong Xue1,6,*

1 James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
2 Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
3 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 101300, China
4 Institute of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
5 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
6 Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China

Received 27 July 2006 ; revised 11 March 2007

Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR.

Key words: polymorphism; microsatellite or MS; database; whole-genome sequences; rice

* To whom correspondence should be addressed. Tel. +86-571-86971611. Fax. +86-571-86971117, E-mail: qzhxue{at}hotmail.com

{dagger} These authors contributed equally to this paper.

Communicated by Masahiro Yano


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