Journal Article

Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of <i>Japonica</i> Rice by Whole-Genome Sequencing

Yuko Arai-Kichise, Yuh Shiwa, Hideki Nagasaki, Kaworu Ebana, Hirofumi Yoshikawa, Masahiro Yano and Kyo Wakasa

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 52, issue 2, pages 274-282
Published in print February 2011 | ISSN: 0032-0781
Published online January 2011 | e-ISSN: 1471-9053 | DOI:

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry


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Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions–deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7% of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi (

Keywords: Deletion; DNA marker; Insertion; Next-generation sequencer; SNP; SNP array

Journal Article.  5116 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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