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Learning Developmental Biology
Collaborative Resources for Learning Developmental Biology
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Fate Map of the Zebrafish Embryo
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David Kimelman

Additional Author(s): Benjamin L. Martin

Published on SDB CoRe: Mar 8 2012

Organisms: Model Organisms; Vertebrates
Morphogenic Movements: Gastrulation
Embryonic Patterning: Axis Formation; Compartments/Boundaries
Signaling: Signaling Pathways
Endoderm-derived: Digestive (Gut) Tract
Mesoderm-derived: Notochord; Cardiovascular System; Somites; Reproductive & Excretory; Muscle
Ectoderm-derived: Nervous System; Epidermis
Extraembryonic: Extraembryonic Tissues
Organism: Zebrafish
Stage of Development: Embryo

Object Description

At the top is a fate map of the zebrafish embryo at the start of gastrulation (which is called the shield stage because of a slight thickening in the shape of a shield in the region that will become the head and notochord).  At this stage, the cells of the embryo (approximately 4000 cells) sit atop a large yolk cell (yellow).  The fate map shows the tendencies of cells in regions of the embryo to contribute to a certain fate, but any individual cell will not necessarily follow the fate of the region it is in.

At the bottom are sagittal sections—lateral and midline—of a 31-hour post-fertilization embryo.   The arrows above the sagittal sections indicate the position of the transverse section on the right. WIREs Dev Biol DOI: 10.1002/wdev.25

Fate Map of the Zebrafish Embryo

The fates of cells in the early zebrafish embryo differ along both the animal-vegetal axis and the dorsal-ventral axis.  Along the animal-vegetal axis, the cells at the equator (margin) contribute to endoderm (primarily gut) and mesoderm (primarily muscle), whereas cells more distant from the equator contribute to mesoderm only.  Cells in the upper part of the animal hemisphere contribute to ectoderm (skin and nervous system).

Orthogonal to the animal-vegetal axis is the dorsal-ventral axis. At the dorsal margin, where the shield forms, are the cells that will form the head mesoderm and notochord.  This region is also called the Organizer since it secretes many signaling factors, particularly inhibitors of the Bmp and Wnt signaling pathways. The dorsal side of the embryo contributes to much of the nervous system of the embryo, with the most anterior aspects of the nervous system towards the animal pole.  The ventral side will produce the most posterior (P) aspects of the muscle and spinal cord, whereas more anterior (A) aspects of these tissues form toward the dorsal side.

The midline sagittal section shows the components along the middle of the embryo including the spinal cord, notochord and the aorta (A) and vein (V), as shown in the transverse section.  In the more lateral regions are the muscles, which form into chevron-shaped somites of approximately 100 cells each.  The main component of the somites is the fast muscle (red), whereas the less abundant slow muscle (dark blue) covers the lateral surface of the somites, as shown in the transverse section (the epidermis has been omitted for clarity).  In the transverse section, below the somites is the pronephros (P).


Kimelman, D. and Martin, B.L. Anterior–posterior patterning in early development: three strategies. WIREs Dev Biol, 2012, 1:253-266.

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