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PMID: 15266053 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.

Plant physiology ·Vol. 135 ·No. 3 ·2004-07-00 ·Pages 1198-205

Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN

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).

MeSH Terms
Base Sequence Chromosome Mapping Chromosomes, Plant/genetics Cloning, Molecular DNA, Plant/genetics Genome, Plant Oryza/genetics Polymorphism, Genetic/genetics Reproducibility of Results
Chemicals
DNA, Plant
Authors & Affiliations
17 authors, click to expand affiliations / ORCID
Shen Ying-Jia
College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
Jiang Hua
Jin Jian-Peng
Zhang Zai-Bao
Xi Biao
He You-Yu
Wang Guan
Wang Chen
Qian Lily
Li Xiang
Yu Qing-Bo
Liu Hui-Juan
Chen De-Hui
Gao Jian-Hua
Huang Hai
Shi Tie-Liu
Yang Zhong-Nan
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.103.038463
Published
2004-07-00
Pages
1198-205
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC519040
Subset
IM
External Links
PubMed source DOI: 10.1104/pp.103.038463 PMC Full Text View journal details
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