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Background Oryzias latipes (Medaka) has been established as a vertebrategenetic model for over a century, and has recently been rediscovered outsideits native Japan. The power of new sequencing methods now makes it possible toreinvigorate Medaka genetics, in particular by establishing a near-isogenicpanel derived from a single wild population. Results Here we characterise thegenomes of wild Medaka catches obtained from a single Southern Japanesepopulation in Kiyosu as a precursor for the establishment of a near isogenicpanel of wild lines. The population is free of significant detrimentalpopulation structure, and has advantageous linkage disequilibrium propertiessuitable for establishment of the proposed panel. Analysis of morphometrictraits in five representative inbred strains suggests phenotypic mapping willbe feasible in the panel. In addition high throughput genome sequencing ofthese Medaka strains confirms their evolutionary relationships on lines ofgeographic separation and provides further evidence that there has been littlesignificant interbreeding between the Southern and Northern Medaka populationsince the Southern/Northern population split. The sequence data suggest thatthe Southern Japanese Medaka existed as a larger older population which wentthrough a relatively recent bottleneck around 10,000 years ago. In addition wedetect patterns of recent positive selection in the Southern population.Conclusions These data indicate that the genetic structure of the Kiyosu Medakasamples are suitable for the establishment of a vertebrate near isogenic paneland therefore inbreeding of 200 lines based on this population has commenced.Progress of this project can be tracked athttp://www.ebi.ac.uk/birney-srv/medaka-ref-panel

Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish