A Medaka Genetic Reference Panel
We have established a project to generate an inbred Medaka Genetic Reference Panel to exploit the advantages of this flexible vertebrate model organism. As part of this project we have:
- characterized molecular, genetic and phenotypic variation in a single Southern Japanese population of Medaka (Kiyosu population)
- begun the inbreeding cycles of 200 lines from the Kiyosu population to establish the panel
- used high throughput sequencing to improve the HdrR genome sequence
- used high throughput sequencing to characterise existing inbred lines from diverse geographic locations
- published this analysis and released the data to the public repositories.
Motivation
Defined genetic reference panels of inbred lines are an important resource for mapping traits in animal and plant genetics. One approach is to sample wild individuals from a population and inbreed them to give near isogenic wild lines. Compared to recombinant inbred lines, near isogenic wild lines have higher diversity of alleles and recombination patterns that allow finer mapping of loci.
The genetics of Japanese Rice Fish or medaka fish (Oryzias latipes) have been studied for over 100 years (see more on Medaka). Over the last decade, medaka as a model orgainism has been rediscovered beyond Japan for its developmental genetics, genomics and evolutionary biology (Wittbrodt et al. 2002; Takeda and Shimada 2010). Wild medaka are easily accessible from their natural habitat and inbreeding of wild caught medaka to give stable inbred lines has a long and established history.
For these reasons we have undertaken development of a reference Medaka inbred panel from a wild population sampled in Southern Japan.
Development of an Inbred Panel
Medaka inbred lines have been established from wild caught individuals and maintained by single brother-sister mating extensively for many years. Inbreeding from the wild can produce a near-isogenic wild panel, similar to the panels that have already been developed for quantitative genetics in Arabidopsis and Drosophila. These panels are powerful mapping resources and are one of the few ways to study gene-environment effects since phenotyping experiments can be repeated over the same genotypes but in differing laboratory environments. Being able to have such a panel with a vertebrate such as Medaka will be very powerful.
We sampled a wild Medaka population from Kiyosu in Southern Japan and have begun establishing a near isogenic panel. Since a good genetic panel should be free of population structure and have appropriate linkage disequilibrium (LD) properties, we have characterised the Kiyosu population using high throughput sequencing to assess suitablility. We set up 8 breeding pairs and sequenced the two parents and one child. We chose this sequencing structure so we could phase the parental genotypes using the child’s genotype, and in effect sample 16 haplotypes. Extensive analysis of population genetic parameters, LD and phenotypes convinced us move ahead with the rounds of inbreeding to produce the panel.
Current Progress
We have initiated the fourth generation of the inbreeding program for 200 independent medaka lines derived from this Kiyosu population. Please see Inbred panel for up to date details. This work is described in full in the G3 paper
News
Contact Us
Contact the project at EBI.
Fun Fish Facts
Medaka feature in Japanese art. To the right is a Woodblock by the celebrated artist, Ando Hiroshige, (安藤 広重) depicting Goldfish and the much smaller Medaka.
