The Zebrafish, Danio rerio, is tropical freshwater fish and a very popular model organism for scientific research in the fields of development, vertebrate processes, genetics, and more.

The Zebrafish is an omnivorous vertebrates and consumes zooplankton, insects, insect larvae and phytoplankton.


Female zebrafish spawn every 2-3 days and produce several hundred eggs in each clutch. Males must be present at spawning and for successful ovulation. Zebrafish eggs are relatively transparent--a characteristic that makes it a very desirable model organism for development biology study. Also, the zebrafish development is quite fast, with precursors to all major organs developing within 36 post-fertilization. Eggs hatch within 48-72 hours post-fertilization. With five days of fertilization, larvae display food seeking and avoidance behaviors.The generation time of zebrafish is approximately 3-4 months, which is convenient for selection experiments.

Basic stuff about Zebrafish

Zebrafish embryo development

Webb and Miller 2007 Figure 1. Schematic representation of zebrafish development from the Zygote Period to the mid-Segmentation Period.

Video: Zebrafish embryogenesis nuclear divisions, from Keller et al. 2008.

Gilbert 6th ed. Fig. 11.2 Fish blastula. (A) Prior to gastrulation, the deep cells are surrounded by the EVL. The animal surface of the yolk cell is flat and contains the nuclei of the YSL. Microtubules extend through the yolky cytoplasm and through the external region of the YSL. (B) Late-blastula stage embryo of the minnow Fundulus, showing the external YSL. The nuclei of these cells were derived from cells at the margin of the blastoderm, which released their nuclei into the yolky cytoplasm. (C) Fate map of the deep cells after cell mixing has stopped. The lateral view is shown, and not all organ fates are labeled (for the sake of clarity). (A and C after Langeland and Kimmel 1997; B from Trinkaus 1993, photograph courtesy of the author.)

Gilbert 6th ed. Fig. 11.3 Cell movements during gastrulation of the zebrafish. (A) The blastoderm at 30% completion of epiboly (about 4.7 hours). (B) Formation of the hypoblast, either by involution of cells at the margin of the epibolizing blastoderm or by delamination of cells from the epiblast (6 hours). (C) Close-up of the marginal region. (D) At 90% epiboly (9 hours), mesoderm can be seen surrounding the yolk, between the endoderm and ectoderm. (E) Completion of gastrulation (10.3 hours). (After Driever 1995; Langeland and Kimmel 1997.)

Fish embryonic shield

Gilbert, 6th ed. Fig. 11.4 Convergence and extension in the zebrafish gastrula. (A) Dorsal view of the convergence and extension movements during zebrafish gastrulation. Epiboly spreads the blastoderm over the yolk; involution or ingression generates the hypoblast; convergence and extension bring the hypoblast and epiblast cells to the dorsal side to form the embryonic shield. Within the shield, intercalation extends the chordamesoderm toward the animal pole. (B) Convergent extension of chordamesoderm is shown by those cells expressing the gene no tail, a gene that is expressed by notochord cells. (C) Convergent extension of paraxial mesodermal cells (marked by their expression of the snail gene) to flank the notochord. (From Langeland and Kimmel 1997; photographs courtesy of the authors.)

Gilbert, 6th ed. Fig. 11.5 The embryonic shield as organizer in the fish embryo. A donor embryonic shield (about 100 cells from a stained embryo) is transplanted into a host embryo at the same early-gastrula stage. The result is two embryonic axes joined to the host’s yolk cell. In the photograph, both axes have been stained for sonic hedgehog mRNA, which is expressed in the ventral midline. (The embryo to the right is the secondary axis.) (After Shinya et al. 1999; photograph courtesy of the authors.)

Resources about Zebrafish

Current research questions

  • New studies are being done in order to understand the impact inhibitors have on Zebrafish. One such inhibitor is SP600125 which is a JNK inhibitor. This inhibitor has a profound impact on the Zebrafish. Studies are being done in order to understand how and why this inhibitor has such harsh effects on the Zebrafish. (Link)
  • New studies have been done to understand the involvement of Delta/Notch signaling in zebrafish adult pigment stripe patterning. Studies have been done with xanthophores and melanophores. (Link)

Agnathans (jawless fish)


Keller PJ, AD Schmidt, J Wittbrodt, EHK Stelzer 2008. Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy, Science 322:1065-1069
DOI: 10.1126/science.1162493

Shinya M, Furutani-Seiki M, Kuroiwa A, Takeda H 1999. Mosaic analysis with oep mutant reveals a repressive interaction between floor-plate and non-floor-plate mutant cells in the zebrafish neural tube, Dev Growth Differ. 41:135-42 DOI: 10.1046/j.1440-169x.1999.00417.x

Webb SE and Miller AL 2007.  Ca2+ signaling and early embryonic patterning during zebrafish development, Proc Austral Physiol Soc 38:43-51

Spence, R., G. Gerlach, C. Lawrence, and C. Smith. 2007. The behaviour and ecology of the Zebrafish, Danio rerio. Biological Review 83: 13-34.

5 Responses to Zebrafish

  1. Jung Choi says:

    New paper showing that organization of zebrafish embryos can be accomplished with just opposing gradients of BMP and Nodal! http://www.sciencemag.org/content/344/6179/87.full The difference between their experiments and Spemann-Mangold is that they look at the ability to create an embryonic axis from animal cap. Spemann-Mangold implanted the dorsal lip into the ventral side, at mesendodermal site.

  2. Pingback: MURAL CELL | biochemwithleme

  3. Jung Choi says:

    I think we are going to need a separate home page for agnathans. There is a sea lamprey genome paper out: http://www.nature.com/ng/journal/v45/n4/full/ng.2568.html
    The genome paper provides insights into various aspects of vertebrate evolution, such as that a key limb-specific enhancer for SHH expression is missing in sea lampreys, but present in jawed fish.
    Moreover, genomic DNA undergoes programmed rearrangement during sea lamprey embryonic development, such that pluripotency genes are retained in the germline, but eliminated in many, most, or all somatic tissues! http://www.cell.com/current-biology/retrieve/pii/S0960982212006732

  4. Jung Choi says:

    A paper in PNAS shows that in the Patagonian pejerrey (Odontesthes hatcheri), a teleost fish, a Y-linked copy of the Anti-Mullerian Hormone gene that is required for testis determination and may be the master determinant of chromosomal sex in this species.

    Hattori, RS, Y Murai, M Oura, S Masuda, SK Majhi, T Sakamoto, JL Fernandino, GM Somoza, M Yokota, CA Strussmann, 2012. A Y-linked anti-Mullerian hormone duplicaiton takes over a critical role in sex determination. Proc. Natl. Acad. Sci. USA 109:2955-2959
    doi: 10.1073/pnas.1018392109

  5. Jung Choi says:

    New paper by Neil Shubin’s group (discoverer of the transitional fossil Tiktaalik) shows that CsB, a gene regulating limb development, is present in zebrafish and skate, and that the zebrafish and skate versions of this gene can function in mouse limb development and the mouse version can function in fish fin development.

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