Friday, 23 March 2012

Why I'm loving a small japanese fish

Today I got a lovely tour of the Fish Facility at Karlsruhr Institute of Technology (KIT). Here Felix Loosli showed me the fish tanks for our Medaka fish reference panel. This is a simple, but very powerful idea - but first off to introduce Medaka fish.


Medaka is a small fish that lives all across Japan, Korea and the eastern seaboard of China. It is found in Rice paddies, and so is often called "Japanese Rice paddy fish". It has a long history in genetics - some of the earliest genetic strains come from this fish. Unsurisingly given its geographical location it has long been established in Japan and that's where most people doing research on this work. Compared to the main "western" laboratory fish, Zebrafish, there are both upsides to Medaka - in particular, for some funky reason, transient transgenics work better in Medaka fish and downsides - its embryos are not naturally opaque (you have to remove glycoproteins on the outside) and it only has ~30 eggs at a time, whereas Zebrafish have 1000 eggs each time.

But that's not why I am really excited about Medaka fish. Interestingly it is one of the few vertebrates known to go isogenic from the wild. Kiyoshi Naruse (in Nagoya) has regularly made new isogenic lines from the wild. This means that Medaka fish joins a select set of species that one can make isogenic from the wild - Arabidopsis, Drosophila are the only multicellular organisms with large wild isogenic populations - there are other species where one gets isogenic laboratory animals - most famously Mice - but this is not the same as a large set of wild isogenic strains.


We - and by we I mean Felix Loosli, Kiyoshi Naruse, Jochen Wittbrodt and myself have tasked ourselves to set up isogenic panel in Medaka fish. This will end up being similar to Arabidopsis or Drosophila panels - both of which are generating interesting results (read here and here). Not only will the fish be ideal for genetic mapping of any phenotype of interest (I always like skeletal phenotypes myself, but behavioural phenotypes are very interesting) but also the isogenic panel is perfect for looking at Gene X Environment lines. The first 130 lines have made it from Nagoya to Karlsruhr, and we're now into the 2nd generation of inbreeding - we reckon we need to make it to 7 or 8 generations of inbreeding before they are isogenic enough. That means we're about 6 months into a 2 year inbreeding project.


Finally I get to see the fish in real life. I've taken some pictures of the F2 set and a video of them moving about.


This is one of these scientific projects which is really about logistics - once we've set this up, and sequenced their genomes (you will only do this at the end - it only makes sense to do on the isogenic lines, and in anycase, sequencing keeps getting cheaper), then each time we phenotype these fish we will be able to do a genomewide association study. I've been listening all day to interesting phenotyping methods in fish - mainly in zebrafish - but by 2015 we will be able to apply many of these techniques to this panel.


In the meantime I took a iPhone video of the fish moving around. Perhaps I will play about with the image processing of this :)



video