Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice ( Oryza sativa , Oryza rufipogon ) and Establishment of SNP Markers (original) (raw)

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Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

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Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

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Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

Search for other works by this author on:

,

Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

Search for other works by this author on:

,

Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

Search for other works by this author on:

,

Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

Search for other works by this author on:

,

Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

* To whom correspondence should be addressed. Tel. +81-298-39-4823, Fax. +81-298-39-4824, E-mail: monna@pgcdna.co.jp

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Plant Genome Center

1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

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Revision received:

18 September 2002

Published:

01 October 2002

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Shinobu Nasu, Junko Suzuki, Rieko Ohta, Kana Hasegawa, Rika Yui, Noriyuki Kitazawa, Lisa Monna, Yuzo Minobe, Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice ( Oryza sativa , Oryza rufipogon ) and Establishment of SNP Markers , DNA Research, Volume 9, Issue 5, 2002, Pages 163–171, https://doi.org/10.1093/dnares/9.5.163
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Abstract

We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice ( O. rufipogon ). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars ‘Nipponbare’ and ‘Koshihikari’ can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice.

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Kazusa DNA Research Institute

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