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

TL;DR

This study characterizes the genome and phenotypic traits of a wild Medaka population to establish a near-isogenic genetic resource, enabling advanced genetic mapping and research in this vertebrate model.

Contribution

It provides the first comprehensive genomic and phenotypic analysis of a wild Medaka population, supporting the development of a near-isogenic panel for genetic studies.

Findings

Population is genetically homogeneous with suitable linkage disequilibrium.

Phenotypic traits are measurable for mapping in the panel.

Little interbreeding between Southern and Northern Medaka populations.

Abstract

Background Oryzias latipes (Medaka) has been established as a vertebrate genetic model for over a century, and has recently been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate Medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Results Here we characterise the genomes of wild Medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near isogenic panel of wild lines. The population is free of significant detrimental population structure, and has advantageous linkage disequilibrium properties suitable for establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition high throughput genome sequencing of these Medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern Medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese Medaka existed as a larger older population which went through a relatively recent bottleneck around 10,000 years ago. In addition we detect patterns of recent positive selection in the Southern population. Conclusions These data indicate that the genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel