Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish
INVESTIGATION Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish Mikhail Spivakov,*,1,2 Thomas O. Auer,†,1,3 Ravindra Peravali,‡ Ian Dunham,* Dirk Dolle,*,† Asao Fujiyama,§ Atsushi Toyoda,§ Tomoyuki Aizu,§ Yohei Minakuchi,§ Felix Loosli,‡,4 Kiyoshi Naruse,**,4 Ewan Birney,*,4 and Joachim Wittbrodt†,4 *European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK, †Centre for Organismal Studies, Heidelberg University, Germany, ‡Karslruhe Institute of § Technology, Karlsruhe, Germany, Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, Japan, and **National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan ABSTRACT Oryzias latipes (medaka) has been established as a vertebrate genetic model for more than KEYWORDS a century and recently has been rediscovered outside its native Japan. The power of new sequencing Medaka methods now makes it possible to reinvigorate medaka genetics, in particular by establishing a near- inbreeding isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka population catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of genomics a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and strain specific has advantageous linkage
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