Zebrafish as an Experimental Organism


Over the last 20 years, the popularity of the zebrafish model has grown more rapidly than any other vertebrate model, and by now the zebrafish is used for virtually all disciplines of biological and medical research. New sophisticated advances in gene editing, transgenesis, 3D‐imaging and behavioural assay design have been established successfully and complemented the ‘tool box’ to make the zebrafish one of the most powerful vertebrate model organisms. There is now information available on expression of over 12 000 genes and about 1000 mutant phenotypes. The latest high‐quality sequence assembly of the zebrafish genome allows in‐depth comparative genomic analysis which will further enhance the use of zebrafish as a model for human diseases. Together with the previously established techniques such as forward genetics, cell‐transplantation, ‐ablation and ‐extraction, which can now be used for new generation sequencing analysis with temporal‐spatial precision, the zebrafish provides an outstanding in vivo vertebrate model to study development and human disease.

Key Concepts

  • The advantages of the zebrafish model include rapid development, short generation time, large number of offspring and transparency of the embryos
  • The zebrafish has become an excellent genetic model organism, amenable to forward genetic screens, targeted mutagenesis and efficient transgenesis
  • Using the zebrafish as a research model for developmental biology, regeneration, chemical screens and disease will expand our knowledge in basic and clinical research

Keywords: zebrafish; model organism; development; genetics; disease model

Figure 1. (a) One‐day‐old zebrafish embryo, lateral view. (b) Dorsal view of the anterior neural plate, emx3 (blue) and rx3 (red) in situ RNA double hybridisation. (c) Mosaic overexpression of GFP (green), rx3 (red) in situ, dorsal view of the anterior neural plate. (d) Primary axonal tracts in a 2‐day‐old zebrafish brain. (e) m‐cherry‐injected rx3:GFP transgenic embryos at 18 somite stage, frontal view. (f) Row of green donor cells transplanted into a shield stage host embryo. (g) Lateral view of the zebrafish brain showing telencephalic emx3 gene expression (blue) and transplanted cells in the eye (brown). (h) Rescue of a telencephalon (expressing emx3 in blue) in a brain mutant after transplant of wild‐type anterior neural plate cells (brown). (i) Axonal staining (brown) of a forebrain mutant masterblind (left) and wild‐type (right) 2‐day‐old embryos.


Ahrens MB, Orger MB, Robson DN, Li JM and Keller PJ (2013) Whole‐brain functional imaging at cellular resolution using light‐sheet microscopy. Nature Methods 10: 413–420.

Bassett DI and Currie PD (2003) The zebrafish as a model for muscular dystrophy and congenital myopathy. Human Molecular Genetics 12 Spec No: R265–R270.

Bielen H and Houart C (2012) BMP signaling protects telencephalic fate by repressing eye identity and its Cxcr4‐dependent morphogenesis. Developmental Cell 23: 812–822.

Boniface EJ, Lu J, Victoroff T, Zhu M and Chen W (2009) FlEx‐based transgenic reporter lines for visualization of Cre and Flp activity in live zebrafish. Genesis 47: 484–491.

Brownlie A, Donovan A, Pratt SJ, et al. (1998) Positional cloning of the zebrafish sauternes gene: a model for congenital sideroblastic anaemia. Nature Genetics 20: 244–250.

Carmany‐Rampey A and Moens CB (2006) Modern mosaic analysis in the zebrafish. Methods 39: 228–238.

Chang N, Sun C, Gao L, et al. (2013) Genome editing with RNA‐guided Cas9 nuclease in zebrafish embryos. Cell Research 23: 465–472.

Chung K and Deisseroth K (2013) CLARITY for mapping the nervous system. Nature Methods 10: 508–513.

Collins RT, Linker C and Lewis J (2010) MAZe: a tool for mosaic analysis of gene function in zebrafish. Nature Methods 7: 219–223.

Doyon Y, McCammon JM, Miller JC, et al. (2008) Heritable targeted gene disruption in zebrafish using designed zinc‐finger nucleases. Nature Biotechnology 26: 702–708.

Feldman B, Dougan ST, Schier AF and Talbot WS (2000) Nodal‐related signals establish mesendodermal fate and trunk neural identity in zebrafish. Current Biology 10: 531–534.

Gerety SS and Wilkinson DG (2011) Morpholino artifacts provide pitfalls and reveal a novel role for pro‐apoptotic genes in hindbrain boundary development. Developmental Biology 350: 279–289.

Griffin KJ, Amacher SL, Kimmel CB and Kimelman D (1998) Molecular identification of spadetail: regulation of zebrafish trunk and tail mesoderm formation by T‐box genes. Development 125: 3379–3388.

Gross‐Thebing T, Paksa A and Raz E (2014) Simultaneous high‐resolution detection of multiple transcripts combined with localization of proteins in whole‐mount embryos. BMC Biology 12: 55.

Hans S, Freudenreich D, Geffarth M, et al. (2011) Generation of a non‐leaky heat shock‐inducible Cre line for conditional Cre/lox strategies in zebrafish. Developmental Dynamics 240: 108–115.

Hatta K, Kimmel CB, Ho RK and Walker C (1991) The cyclops mutation blocks specification of the floor plate of the zebrafish central nervous system. Nature 350: 339–341.

Ho RK and Kane DA (1990) Cell‐autonomous action of zebrafish spt‐1 mutation in specific mesodermal precursors. Nature 348: 728–730.

Houart C, Westerfield M and Wilson SW (1998) A small population of anterior cells patterns the forebrain during zebrafish gastrulation. Nature 391: 788–792.

Howe K, Clark MD, Torroja CF, et al. (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496: 498–503.

Hwang WY, Fu Y, Reyon D, et al. (2013) Efficient genome editing in zebrafish using a CRISPR‐Cas system. Nature Biotechnology 31: 227–229.

Karlstrom RO, Talbot WS and Schier AF (1999) Comparative synteny cloning of zebrafish you‐too: Mutations in the Hedgehog target gli2 affect ventral forebrain patterning. Genes and Development 13: 388–393.

Kawakami K, Abe G, Asada T, et al. (2010) zTrap: zebrafish gene trap and enhancer trap database. BMC Developmental Biology 10: 105.

Keller PJ, Schmidt AD, Wittbrodt J and Stelzer EHK (2008) Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322: 1065–1069.

Kimmel CB, Hatta K and Eisen JS (1991) Genetic control of primary neuronal development in zebrafish. Development Suppl 2: 47–57.

Kwan KM, Fujimoto E, Grabher C, et al. (2007) The Tol2kit: a multisite gateway‐based construction kit for Tol2 transposon transgenesis constructs. Developmental Dynamics 236: 3088–3099.

Laird AS and Robberecht W (2011) Modeling neurodegenerative diseases in zebrafish embryos. Methods in Molecular Biology 793: 167–184.

Lauter G, Söll I and Hauptmann G (2011) Two‐color fluorescent in situ hybridization in the embryonic zebrafish brain using differential detection systems. BMC Developmental Biology 11: 43.

Lun K and Brand M (1998) A series of no isthmus (noi) alleles of the zebrafish pax2.1 gene reveals multiple signaling events in development of the midbrain‐hindbrain boundary. Development 125: 3049–3062.

Meng X, Noyes MB, Zhu LJ, Lawson ND and Wolfe SA (2008) Targeted gene inactivation in zebrafish using engineered zinc‐finger nucleases. Nature Biotechnology 26: 695–701.

Mosimann C and Zon LI (2011) Advanced zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments. Methods in Cell Biology 104: 173–194.

Nasevicius A and Ekker SC (2000) Effective targeted gene “knockdown” in zebrafish. Nature Genetics 26: 216–220.

Norton WHJ, Stumpenhorst K, Faus‐Kessler T, et al. (2011) Modulation of Fgfr1a signaling in zebrafish reveals a genetic basis for the aggression‐boldness syndrome. Journal of Neuroscience 31: 13796–13807.

Peterson RT and Fishman MC (2011) Designing zebrafish chemical screens. Methods in Cell Biology 105: 525–541.

Reifers F, Böhli H, Walsh EC, et al. (1998) Fgf8 is mutated in zebrafish acerebellar (ace) mutants and is required for maintenance of midbrain‐hindbrain boundary development and somitogenesis. Development 125: 2381–2395.

Ronneberger O, Liu K, Rath M, et al. (2012) ViBE‐Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nature Methods 9: 735–742.

Schulte‐Merker S and Stainier DYR (2014) Out with the old, in with the new: reassessing morpholino knockdowns in light of genome editing technology. Development 141: 3103–3104.

Sehnert AJ, Huq A, Weinstein BM, et al. (2002) Cardiac troponin T is essential in sarcomere assembly and cardiac contractility. Nature Genetics 31: 106–110.

Staudt N and Houart C (2007) The prethalamus is established during gastrulation and influences diencephalic regionalization. PLoS Biology 5: 878–888.

Stemple DL (2004) TILLING–a high‐throughput harvest for functional genomics. Nature Reviews. Genetics 5: 145–150.

Streisinger G, Walker C, Dower N, Knauber D and Singer F (1981) Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291: 293–296.

Thermes V, Grabher C, Ristoratore F, et al. (2002) I‐SceI meganuclease mediates highly efficient transgenesis in fish. Mechanisms of Development 118: 91–98.

Turner KJ, Bracewell TG and Hawkins TA (2014) Anatomical dissection of zebrafish brain development. Methods in Molecular Biology 1082: 197–214.

Walker C and Streisinger G (1983) Induction of Mutations by gamma‐Rays in Pregonial Germ Cells of Zebrafish Embryos. Genetics 103: 125–136.

White R, Rose K and Zon L (2013) Zebrafish cancer: the state of the art and the path forward. Nature Reviews. Cancer 13: 624–636.

Wyart C and Del Bene F (2011) Let there be light: zebrafish neurobiology and the optogenetic revolution. Reviews in the Neurosciences 22: 121–130.

Wyart C, Del Bene F, Warp E, et al. (2009) Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature 461: 407–410.

Xi Y, Noble S and Ekker M (2011) Modeling neurodegeneration in zebrafish. Current Neurology and Neuroscience Reports 11: 274–282.

Xiao A, Wang Z, Hu Y, et al. (2013) Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Research 41: e141.

Zebrafish Issue (1996) Development 123: 1–460.

Further Reading

Feierstein CE, Portugues R and Orger MB (2014) Seeing the whole picture: a comprehensive imaging approach to functional mapping of circuits in behaving zebrafish. Neuroscience. (article in press, epub ahead of print)

Feitsma H and Cuppen E (2008) Zebrafish as a cancer model. Molecular Cancer Research 6: 685–94.

Haesemeyer M and Schier AF (2015) The study of psychiatric disease genes and drugs in zebrafish. Current Opinion in Neurobiology 30C: 122–130.

Howe DG, Bradford YM, Conlin T, et al. (2013) ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Research 41: D854–60.

Newman M, Ebrahimie E and Lardelli M (2014) Using the zebrafish model for Alzheimer's disease research. Frontiers in Genetics 5: 189.

Ota S and Kawahara A (2014) Zebrafish: a model vertebrate suitable for the analysis of human genetic disorders. Congenit Anom (Kyoto) 54: 8–11.

Varshney GK and Burgess SM (2014) Mutagenesis and phenotyping resources in zebrafish for studying development and human disease. Briefings in Functional Genomics 13: 82–94.

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Bielen, Holger(Apr 2015) Zebrafish as an Experimental Organism. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002094.pub2]