Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes-Reference-Cited by-同舟云学术

Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes

Published:2004-07-01 Issue:3 Volume:135 Page:1198-1205
ISSN:1532-2548
Container-title:Plant Physiology
language:en
Short-container-title:

Author:

Shen Ying-Jia¹,Jiang Hua¹,Jin Jian-Peng¹,Zhang Zai-Bao¹,Xi Biao¹,He You-Yu¹,Wang Guan¹,Wang Chen¹,Qian Lily¹,Li Xiang¹,Yu Qing-Bo¹,Liu Hui-Juan¹,Chen De-Hui¹,Gao Jian-Hua¹,Huang Hai¹,Shi Tie-Liu¹,Yang Zhong-Nan¹

Affiliation:

1. 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 Institu

Abstract

Abstract 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).

Publisher

Oxford University Press (OUP)

Subject

Plant Science,Genetics,Physiology

Link

http://academic.oup.com/plphys/article-pdf/135/3/1198/38703518/plphys_v135_3_1198.pdf

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