Theoretical and Applied Genetics

, Volume 109, Issue 8, pp 1586–1596 | Cite as

Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers

  • Z. Hashimoto
  • N. MoriEmail author
  • M. Kawamura
  • T. Ishii
  • S. Yoshida
  • M. Ikegami
  • S. Takumi
  • C. Nakamura
Original Paper


Japanese rice (Oryza sativa L.) cultivars that are strictly used for the brewing of sake (Japanese rice wine) represent a unique and traditional group. These cultivars are characterized by common traits such as large grain size with low protein content and a large, central white-core structure. To understand the genetic diversity and phylogenetic characteristics of sake-brewing rice, we performed amplified fragment length polymorphism and simple sequence repeat analyses, using 95 cultivars of local and modern sake-brewing rice together with 76 cultivars of local and modern cooking rice. Our analysis of both nuclear and chloroplast genome polymorphisms showed that the genetic diversity in sake-brewing rice cultivars was much smaller than the diversity found in cooking rice cultivars. Interestingly, the genetic diversity within the modern sake-brewing cultivars was about twofold higher than the diversity within the local sake-brewing cultivars, which was in contrast to the cooking cultivars. This is most likely due to introgression of the modern cooking cultivars into the modern sake-brewing cultivars through breeding practices. Cluster analysis and chloroplast haplotype analysis suggested that the local sake-brewing cultivars originated monophyletically in the western regions of Japan. Analysis of variance tests showed that several markers were significantly associated with sake-brewing traits, particularly with the large white-core structure.


Quantitative Trait Locus Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Rice Cultivar Amplify Fragment Length Polymorphism Marker 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank Dr. Kazuo Kawano, Food Resources Education and Research Center, Kobe University, for his critical comments. The work was supported in part by a grant-in-aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan (to CN, no. 11794003, 1638006). Contribution No. 151 from the Laboratory of Plant Genetics, Kobe University.


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Z. Hashimoto
    • 1
  • N. Mori
    • 1
    Email author
  • M. Kawamura
    • 1
  • T. Ishii
    • 2
  • S. Yoshida
    • 3
  • M. Ikegami
    • 3
  • S. Takumi
    • 1
  • C. Nakamura
    • 1
  1. 1.Laboratory of Plant Genetics, Department of Biological and Environmental Science, Faculty of Agriculture, and Graduate School of Science and TechnologyKobe UniversityKobeJapan
  2. 2.Laboratory of Plant Breeding, Department of Plant Resources Science, Faculty of AgricultureKobe UniversityKobeJapan
  3. 3.Hyogo Institute of Agriculture, Forestry and FisheryHyogoJapan

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