Plant Physiology 135:1198-1205 (2004)
© 2004 American Society of Plant Biologists
GENOME ANALYSIS
Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes1,[w]
Ying-Jia Shen2,
Hua Jiang2,
Jian-Peng Jin2,
Zai-Bao Zhang,
Biao Xi,
You-Yu He,
Guan Wang,
Chen Wang,
Lily Qian,
Xiang Li,
Qing-Bo Yu,
Hui-Juan Liu,
De-Hui Chen,
Jian-Hua Gao,
Hai Huang,
Tie-Liu Shi* and
Zhong-Nan Yang*
College of Life and Environment Sciences (Y.-J.S., H.J., Z.-B.Z., G.W., C.W., Q.-B.Y., H.-J.L., D.-H.C., Z.-N.Y.) and Mathematics and Sciences College (J.-P.J., X.L., J.-H.G.), Shanghai Normal University, Shanghai 200234, China; College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China (B.X.); Shanghai Information Center for Life Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China (Y.-Y.H., T.-L.S.); Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90024 (L.Q.); and Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China (H.H., Z.-N.Y.)
DNA polymorphism is the basis to develop molecular markers that are widely used in genetic mapping today. A genome-wide rice (Oryza sativa) DNA polymorphism database has been constructed in this work using the genomes of Nipponbare, a cultivar of japonica, and 93-11, a cultivar of indica. This database contains 1,703,176 single nucleotide polymorphisms (SNPs) and 479,406 Insertion/Deletions (InDels), approximately one SNP every 268 bp and one InDel every 953 bp in rice genome. Both SNPs and InDels in the database were experimentally validated. Of 109 randomly selected SNPs, 107 SNPs (98.2%) are accurate. PCR analysis indicated that 90% (97 of 108) of InDels in the database could be used as molecular markers, and 68% to 89% of the 97 InDel markers have polymorphisms between other indica cultivars (Guang-lu-ai 4 and Long-te-pu B) and japonica cultivars (Zhong-hua 11 and 9522). This suggests that this database can be used not only for Nipponbare and 93-11, but also for other japonica and indica cultivars. While validating InDel polymorphisms in the database, a set of InDel markers with each chromosome 3 to 5 marker was developed. These markers are inexpensive and easy to use, and can be used for any combination of japonica and indica cultivars used in this work. This rice DNA polymorphism database will be a valuable resource and important tool for map-based cloning of rice gene, as well as in other various research on rice (http://shenghuan.shnu.edu.cn/ricemarker).
1 This work was supported by the Shu-Guang Program of the Shanghai Education and Development Board (grant to Z.-N.Y.), by the Shanghai Education Committee (grant to Z.-N.Y.), and by the Shanghai Science and Technology Committee (grant no. 03DJ14015 to Z.-N.Y.).
2 These authors contributed equally to the paper.
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.103.038463.
* Corresponding authors; e-mail znyang{at}shtu.edu.cn or tlshi{at}sibs.ac.cn; fax 86–21–64322142.
Received December 25, 2003;
returned for revision May 9, 2004;
accepted May 23, 2004.
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