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Short answer: Medaka (Oryzias latipes, also called Japanese medaka or Japanese rice fish) is a small freshwater teleost used in laboratories as a vertebrate model organism. Its embryos are transparent, it tolerates inbreeding, and stock centres supply defined inbred, mutant and transgenic lines. This guide covers the laboratory use of the species, not the aquarium trade.
Definition and scope
Medaka is an egg-laying fish from East Asia. According to the 2015 review by Kirchmaier, Naruse, Wittbrodt and Loosli in Genetics, adults reach up to about 4 cm, and the eggs and embryos are transparent, which allows detailed in vivo analysis of development. The same review places medaka about 150 million years of divergent evolution from zebrafish, so the two are complementary teleost models rather than interchangeable ones.
Searches for “medaka fish” mostly return ornamental varieties sold to hobbyists. Those colour morphs are not the standardised research lines described below, and nothing on this page concerns buying fish for display.
How medaka is used in practice
The review describes a mature toolbox: a completed genome sequence, cDNA, BAC and fosmid libraries, and transgenesis by plasmid injection, I-SceI meganuclease (reported 25-50% efficiency, against 1-10% for plain plasmid injection) or Tol2 vectors. Site-directed mutagenesis with CRISPR/Cas9 has been used, with modifications transmitted to the F1 generation at reported frequencies of 42.9 to 100%.
Inbred strains and the reference genome
Medaka tolerates inbreeding. The review reports strains inbred for more than 100 generations of brother-sister crosses, with heterozygosity around 3 × 10-5, roughly 100-fold lower than in wild-caught fish. The EMBL-EBI medaka reference panel page states that the reference genome comes from the inbred HdrR strain (southern Japanese origin) and that the inbred HNI, Kaga, HSOK and Nilan strains were sequenced against it. It also notes two divergent wild populations, northern and southern, separated by the Japanese Alps, that remain fertile together in the laboratory.
Sex determination (DMY)
In O. latipes the sex-determining gene on the Y chromosome is DMY, also called DMRT1Yb; the review cites Matsuda et al. (2002, 2003) for this. Related medaka species use other genes, for example gsdfY or Sox3. Check which species your stock actually is before assuming a sex-determination mechanism.
Medaka at a glance: figures traced to the review
| Property | Reported value | Source |
|---|---|---|
| Haploid genome size | about 800 Mb (the EBI panel page gives about 700 MB for the HdrR reference, so quote the assembly you use) | Kirchmaier et al. 2015; EMBL-EBI medaka panel |
| Generation time | 8-12 weeks, depending on strain and husbandry | Kirchmaier et al. 2015 |
| Temperature tolerance | 4-40 °C, adults and embryos | Kirchmaier et al. 2015 |
| Embryo hatching | 7-8 days at 28 °C; temperature controls developmental speed | Kirchmaier et al. 2015 |
| Adult length | up to about 4 cm | Kirchmaier et al. 2015 |
| Divergence from zebrafish | about 150 million years | Kirchmaier et al. 2015 |
Zebrafish values are deliberately not tabulated here, because the review’s text does not state them. When you compare the two models for a project, take the zebrafish numbers from ZFIN or the zebrafish literature and record the source alongside each one; see the comparison of model organism databases for where those resources sit.
Where it matters for labs: sourcing strains and resources
The Japanese Medaka Stock Center under the National BioResource Project (NBRP) Medaka, started in 2002, is the central repository. As of 2014 the review lists 548 strains, including 373 mutants and 74 transgenic lines, plus more than 60 wild strains and about 14 derived inbred strains. These are 2014 figures; confirm current holdings with the centre.
Strain-sourcing checklist
- Record the stock centre and its stock identifier for every line, and the species (O. latipes or a related Oryzias species).
- Record whether the line is a wild-derived stock, an inbred strain (for example HdrR, HNI, Kaga) or a mutant or transgenic line, and its genotype.
- State the temperature and husbandry conditions, since generation time depends on both.
- Where a registry assigns one, report an RRID so the organism can be identified unambiguously in the methods section; this supports the authentication of key resources expected by many funders.
- Check whether your institution’s animal care and use committee covers fish in your jurisdiction, and report the work using the ARRIVE 2.0 items.
Reference resources named in the review
- Medaka Book: an online lab manual for maintenance and husbandry.
- Medaka Atlas: brain anatomy and blood vascular system.
- Medaka Tree: phylogeny of wild populations from mitochondrial DNA.
- Medaka Map: a genome browser with physical maps, alignment view and BLAST.
For other organisms, see the guide to Drosophila and the dictionary entry on the research animal.
Common misunderstandings
- Pet medaka are research strains. Hobby varieties are bred for colour; laboratory work depends on documented strains from a stock centre.
- Medaka and zebrafish are the same model. They diverged roughly 150 million years ago, and each has its own community resources.
- One genome size applies everywhere. Sources quote about 700 Mb and about 800 Mb; name the assembly.
FAQ
What is Oryzias latipes?
It is the scientific name of the Japanese medaka, the species used as a laboratory fish model. Other Oryzias species exist and use different sex-determining genes.
What is a Japanese medaka used for in research?
Developmental biology, genetics and genomics, using transparent embryos, inbred strains, a reference genome and transgenic and CRISPR/Cas9 tools.
How long is the medaka generation time?
8-12 weeks depending on strain and husbandry, per Kirchmaier et al. (2015).
Sources
- Kirchmaier S, Naruse K, Wittbrodt J, Loosli F. The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes). Genetics 2015;199(4):905-918. doi:10.1534/genetics.114.173849 (PMC4391551), read 2026-11-07.
- EMBL-EBI, About medaka (medaka reference panel), ebi.ac.uk, read 2026-11-07.
