Open Access Short Report

Medaka: a promising model animal for comparative population genomics

Yoshifumi Matsumoto17, Hiroki Oota1*, Yoichi Asaoka2, Hiroshi Nishina2, Koji Watanabe3, Janusz M Bujnicki456, Shoji Oda1, Shoji Kawamura1 and Hiroshi Mitani1*

Author Affiliations

1 Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan

2 Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan

3 FUJIYA CO., LTD., Kanagawa, Japan

4 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan

5 International Institute of Molecular and Cell Biology, Warsaw, Poland

6 Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland

7 Laboratory for Behavioral and Developmental Disorders, Brain Science Institute, RIKEN, Saitama, Japan

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BMC Research Notes 2009, 2:88  doi:10.1186/1756-0500-2-88

Published: 10 May 2009



Within-species genome diversity has been best studied in humans. The international HapMap project has revealed a tremendous amount of single-nucleotide polymorphisms (SNPs) among humans, many of which show signals of positive selection during human evolution. In most of the cases, however, functional differences between the alleles remain experimentally unverified due to the inherent difficulty of human genetic studies. It would therefore be highly useful to have a vertebrate model with the following characteristics: (1) high within-species genetic diversity, (2) a variety of gene-manipulation protocols already developed, and (3) a completely sequenced genome. Medaka (Oryzias latipes) and its congeneric species, tiny fresh-water teleosts distributed broadly in East and Southeast Asia, meet these criteria.


Using Oryzias species from 27 local populations, we conducted a simple screening of nonsynonymous SNPs for 11 genes with apparent orthology between medaka and humans. We found medaka SNPs for which the same sites in human orthologs are known to be highly differentiated among the HapMap populations. Importantly, some of these SNPs show signals of positive selection.


These results indicate that medaka is a promising model system for comparative population genomics exploring the functional and adaptive significance of allelic differentiations.