The zebrafish (
Danio rerio) is a freshwater fish belonging to the
minnow family (Cyprinidae) of the order Cypriniformes. Native to
the Himalayan region, it is a popular aquarium fish, frequently sold
under the trade name zebra danio (and thus often called a "tropical
fish" although not native to the tropics). The zebrafish is also an
important and widely used vertebrate model organism in scientific
research. It is particularly notable for its regenerative
abilities, and has been modified by researchers to produce many
6 In the aquarium
7.1 Wild-type strains
8 In scientific research
8.1 Model characteristics
8.3.3 Mitochondrial DNA
8.3.4 Pigmentation genes
8.3.6 Transparent adult bodies
8.3.7 Use in environmental monitoring
8.3.8 RNA splicing
8.4 Inbreeding depression
9 In medical research
9.2 Cardiovascular disease
9.3 Immune system
9.4 Infectious diseases
9.5 Repairing retinal damage
9.6 Drug discovery
9.7 Muscular dystrophies
10 See also
12 Further reading
13 External links
The zebrafish is a derived member of the genus Danio, of the family
Cyprinidae. It has a sister-group relationship with Danio
Zebrafish are also closely related to the genus
Devario, as demonstrated by a phylogenetic tree of close species.
The zebrafish was referred to in scientific literature as Brachydanio
rerio for many years until its reassignment to the genus Danio.
The zebrafish is native to the streams of the southeastern Himalayan
region, and is found in parts of India, Pakistan, Bangladesh,
Nepal, and Myanmar. The species arose in the
Ganges region in
eastern India, and commonly inhabits streams, canals, ditches, ponds,
and slow-moving or stagnant water bodies, including rice fields.
Zebrafish are most commonly found in low flow streams that has sandy
Zebrafish have been introduced to parts of the United
States, presumably by deliberate release or by escape from fish
The zebrafish is named for the five uniform, pigmented, horizontal,
blue stripes on the side of the body, which are reminiscent of a
zebra's stripes, and which extend to the end of the caudal fin. Its
shape is fusiform and laterally compressed, with its mouth directed
upwards. The male is torpedo-shaped, with gold stripes between the
blue stripes; the female has a larger, whitish belly and silver
stripes instead of gold. Adult females exhibit a small genital papilla
in front of the anal fin origin. The zebrafish can grow to 6.4 cm
(2.5 in) in length, although it seldom grows larger than
4 cm (1.6 in) in captivity. Its lifespan in captivity is
around two to three years, although in ideal conditions, this may be
extended to over five years.
Stages of zebrafish development. Photos to scale except adult, which
is ~2.5 cm (0.98 in) long.
The approximate generation time for
Danio rerio is three months. A
male must be present for ovulation and spawning to occur. Females are
able to spawn at intervals of two to three days, laying hundreds of
eggs in each clutch. Upon release, embryonic development begins;
absent sperm, growth stops after the first few cell divisions.
Fertilized eggs almost immediately become transparent, a
characteristic that makes D. rerio a convenient research model
The zebrafish embryo develops rapidly, with precursors to all major
organs appearing within 36 hours of fertilization. The embryo begins
as a yolk with a single enormous cell on top (see image, 0 h panel),
which divides into two (0.75 h panel) and continues dividing until
there are thousands of small cells (3.25 h panel). The cells then
migrate down the sides of the yolk (8 h panel) and begin forming a
head and tail (16 h panel). The tail then grows and separates from the
body (24 h panel). The yolk shrinks over time because the fish uses it
for food as it matures during the first few days (72 h panel). After a
few months, the adult fish reaches reproductive maturity (bottom
To encourage the fish to spawn, some researchers use a fish tank with
a sliding bottom insert, which reduces the depth of the pool to
simulate the shore of a river.
Zebrafish spawn best in the morning due
to their Circadian rhythms. Researchers have been able to collect
10,000 embryos in 10 minutes using this method. Male zebrafish are
furthermore known to respond to more pronounced markings on females,
i.e., "good stripes", but in a group, males will mate with whichever
females they can find. What attracts females is not currently
understood. The presence of plants, even plastic plants, also
apparently encourages spawning.
Zebrafish are omnivorous, primarily eating zooplankton, phytoplankton,
insects and insect larvae, although they can eat a variety of other
foods, such as worms and small crustaceans, if their preferred food
sources are not readily available.
In research, adult zebrafish are often fed with brine shrimp, or
In the aquarium
Zebrafish are hardy fish and considered good for beginner aquarists.
Their enduring popularity can be attributed to their playful
disposition, as well as their rapid breeding, aesthetics, cheap
price and broad availability. They also do well in schools or shoals
of six or more, and interact well with other fish species in the
aquarium. However, they are susceptible to
Oodinium or velvet disease,
microsporidia (Pseudoloma neurophilia), and
Given the opportunity, adults eat hatchlings, which may be protected
by separating the two groups with a net, breeding box or separate
tank. In captivity, zebrafish live approximately forty two months.
Some captive zebrafish can develop a curved spine.
Danio was also used to make genetically modified fish and
were the first species to be sold as
GloFish (fluorescent colored
In late 2003, transgenic zebrafish that express green, red, and yellow
fluorescent proteins became commercially available in the United
States. The fluorescent strains are tradenamed GloFish; other
cultivated varieties include "golden", "sandy", "longfin" and
The leopard danio, previously known as
Danio frankei, is a spotted
colour morph of the zebrafish which arose due to a pigment
mutation. Xanthistic forms of both the zebra and leopard pattern,
along with long-finned subspecies, have been obtained via selective
breeding programs for the aquarium trade.
Various transgenic and mutant strains of zebrafish were stored at the
China Zebrafish Resource Center (CZRC), a non-profit organization,
which was jointly supported by the Ministry of Science and Technology
of China and the Chinese Academy of Sciences.
Zebrafish Information Network (ZFIN) provides up-to-date
information about current known wild-type (WT) strains of D. rerio,
some of which are listed below.
Hong Kong (HK)
RIKEN WT (RW)
Tupfel long fin (TL)
Tupfel long fin nacre (TLN)
Hybrids between different
Danio species may be fertile: for example,
between D. rerio and D. nigrofasciatus.
In scientific research
Zebrafish chromatophores, shown here mediating background adaptation,
are widely studied by scientists.
A zebrafish pigment mutant (bottom) produced by insertional
mutagenesis. A wild-type embryo (top) is shown for comparison. The
mutant lacks black pigment in its melanocytes because it is unable to
synthesize melanin properly.
D. rerio is a common and useful scientific model organism for studies
of vertebrate development and gene function. Its use as a laboratory
animal was pioneered by the American molecular biologist George
Streisinger and his colleagues at the
University of Oregon
University of Oregon in the
1970s and 1980s; Streisinger's zebrafish clones were among the
earliest successful vertebrate clones created. Its importance has
been consolidated by successful large-scale forward genetic screens
(commonly referred to as the Tübingen/Boston screens). The fish has a
dedicated online database of genetic, genomic, and developmental
Zebrafish Information Network (ZFIN). The Zebrafish
International Resource Center (ZIRC) is a genetic resource repository
with 29,250 alleles available for distribution to the research
community. D. rerio is also one of the few fish species to have been
sent into space.
Research with D. rerio has yielded advances in the fields of
developmental biology, oncology, toxicology,
reproductive studies, teratology, genetics, neurobiology,
environmental sciences, stem cell research, regenerative
medicine, muscular dystrophies and evolutionary theory.
As a model biological system, the zebrafish possesses numerous
advantages for scientists. Its genome has been fully sequenced, and it
has well-understood, easily observable and testable developmental
behaviors. Its embryonic development is very rapid, and its embryos
are relatively large, robust, and transparent, and able to develop
outside their mother. Furthermore, well-characterized mutant
strains are readily available.
Other advantages include the species' nearly constant size during
early development, which enables simple staining techniques to be
used, and the fact that its two-celled embryo can be fused into a
single cell to create a homozygous embryo. The zebrafish is also
demonstrably similar to mammalian models and humans in toxicity
testing, and exhibits a diurnal sleep cycle with similarities to
mammalian sleep behavior. However, zebrafish are not a universally
ideal research model; there are a number of disadvantages to their
scientific use, such as the absence of a standard diet and the
presence of small but important differences between zebrafish and
mammals in the roles of some genes related to human disorders.
Zebrafish have the ability to regenerate their heart and lateral line
hair cells during their larval stages. In 2011, the British
Heart Foundation ran an advertising campaign publicising its intention
to study the applicability of this ability to humans, stating that it
aimed to raise £50 million in research funding.
Zebrafish have also been found to regenerate photoreceptor cells and
retinal neurons following injury, which has been shown to be mediated
by the dedifferentiation and proliferation of Müller glia.
Researchers frequently amputate the dorsal and ventral tail fins and
analyze their regrowth to test for mutations. It has been found that
histone demethylation occurs at the site of the amputation, switching
the zebrafish's cells to an "active", regenerative, stem cell-like
state. In 2012, Australian scientists published a study revealing
that zebrafish use a specialised protein, known as fibroblast growth
factor, to ensure their spinal cords heal without glial scarring after
injury. In addition, hair cells of the posterior lateral line have
also been found to regenerate following damage or developmental
disruption. Study of gene expression during regeneration has
allowed for the identification of several important signaling pathways
involved in the process, such as
Wnt signaling and Fibroblast growth
In probing disorders of the nervous system, including
neurodegenerative diseases, movement disorders, psychiatric disorders
and deafness, researchers are using the zebrafish to understand how
the genetic defects underlying these conditions cause functional
abnormalities in the human brain, spinal cord and sensory organs.
Researchers have also studied the zebrafish to gain new insights into
the complexities of human musculoskeletal diseases, such as muscular
dystrophy. Another focus of zebrafish research is to understand
how a gene called Hedgehog, a biological signal that underlies a
number of human cancers, controls cell growth.
Due to their short lifecycles and relatively large clutch sizes,
zebrafish are a useful model for genetic studies. A common reverse
genetics technique is to reduce gene expression or modify splicing
Morpholino antisense technology.
(MO) are stable, synthetic macromolecules that contain the same bases
as DNA or RNA; by binding to complementary RNA sequences, they can
reduce the expression of specific genes or block other processes from
occurring on RNA. MO can be injected into one cell of an embryo after
the 32-cell stage, reducing gene expression in only cells descended
from that cell. However, cells in the early embryo (less than 32
cells) are interpermeable to large molecules, allowing
diffusion between cells. Guidelines for using Morpholinos in zebrafish
describe appropriate control strategies. Morpholinos are commonly
microinjected in 500pL directly into 1-2 cell stage zebrafish embryos.
The morpholino is able to integrate into most cells of the embryo.
A known problem with gene knockdowns is that, because the genome
underwent a duplication after the divergence of ray-finned fishes and
lobe-finned fishes, it is not always easy to silence the activity one
of the two gene paralogs reliably due to complementation by the other
paralog. Despite the complications of the zebrafish genome, a
number of commercially available global platforms exist for analysis
of both gene expression by microarrays and promoter regulation using
Wellcome Trust Sanger Institute started the zebrafish genome
sequencing project in 2001, and the full genome sequence of the
Tuebingen reference strain is publicly available at the National
Center for Biotechnology Information (NCBI)'s
The zebrafish reference genome sequence is annotated as part of the
Ensembl project, and is maintained by the
In 2009, researchers at the Institute of Genomics and Integrative
Biology in Delhi, India, announced the sequencing of the genome of a
wild zebrafish strain, containing an estimated 1.7 billion genetic
letters. The genome of the wild zebrafish was sequenced at
39-fold coverage. Comparative analysis with the zebrafish reference
genome revealed over 5 million single nucleotide variations and over
1.6 million insertion deletion variations. The zebrafish reference
genome sequence of 1.4GB and over 26,000 protein coding genes was
published by Kerstin Howe et al. in 2013.
In October 2001, researchers from the
University of Oklahoma
University of Oklahoma published
D. rerio's complete mitochondrial DNA sequence. Its length is
16,596 base pairs. This is within 100 base pairs of other related
species of fish, and it is notably only 18 pairs longer than the
goldfish (Carassius auratus) and 21 longer than the carp (Cyprinus
carpio). Its gene order and content are identical to the common
vertebrate form of mitochondrial DNA. It contains 13 protein-coding
genes and a noncoding control region containing the origin of
replication for the heavy strand. In between a grouping of five tRNA
genes, a sequence resembling vertebrate origin of light strand
replication is found. It is difficult to draw evolutionary conclusions
because it is difficult to determine whether base pair changes have
adaptive significance via comparisons with other vertebrates'
In 1999, the nacre mutation was identified in the zebrafish ortholog
of the mammalian
MITF transcription factor. Mutations in human
MITF result in eye defects and loss of pigment, a type of Waardenburg
Syndrome. In December 2005, a study of the golden strain identified
the gene responsible for its unusual pigmentation as SLC24A5, a solute
carrier that appeared to be required for melanin production, and
confirmed its function with a
Morpholino knockdown. The orthologous
gene was then characterized in humans and a one base pair difference
was found to strongly segregate fair-skinned Europeans and
Zebrafish with the nacre mutation have
since been bred with fish with a roy orbison (roy) mutation to make
fish that have no melanophores or iridophores, and are transparent
into adulthood. These fish are characterized by uniformly pigmented
eyes and translucent skin.
Transgenesis is a popular approach to study the function of genes in
zebrafish. Construction of transgenic zebrafish is rather easy by a
method using the Tol2 transposon system.
Transparent adult bodies
In 2008, researchers at
Boston Children's Hospital
Boston Children's Hospital developed a new
strain of zebrafish, named Casper, whose adult bodies had transparent
skin. This allows for detailed visualization of cellular activity,
circulation, metastasis and many other phenomena. Because many gene
functions are shared between fish and humans, the Casper strain is
expected to yield insights into human diseases such as leukemia and
other cancers. In January 2013, Japanese scientists genetically
modified a transparent zebrafish specimen to produce a visible glow
during periods of intense brain activity, allowing the fish's
"thoughts" to be recorded as specific regions of its brain lit up in
response to external stimuli.
Use in environmental monitoring
In January 2007, Chinese researchers at
Fudan University genetically
modified zebrafish to detect oestrogen pollution in lakes and rivers,
which is linked to male infertility. The researchers cloned
oestrogen-sensitive genes and injected them into the fertile eggs of
zebrafish. The modified fish turned green if placed into water that
was polluted by oestrogen.
In 2015, researchers at
Brown University discovered that 10% of
zebrafish genes do not need to rely on the
U2AF2 protein to initiate
RNA splicing. These genes have the DNA base pairs AC and TG as
repeated sequences at the ends of each intron. On the 3'ss (3'
splicing site), the base pairs adenine and cytosine alternate and
repeat, and on the 5'ss (5' splicing site), their complements thymine
and guanine alternate and repeat as well. They found that there was
less reliance on
U2AF2 protein than in humans, in which the protein is
required for the splicing process to occur. The pattern of repeating
base pairs around introns that alters RNA secondary structure was
found in other teleosts, but not in tetrapods. This indicates that an
evolutionary change in tetrapods may have led to humans relying on the
U2AF2 protein for
RNA splicing while these genes in zebrafish undergo
splicing regardless of the presence of the protein.
When close relatives mate, progeny may exhibit the detrimental effects
of inbreeding depression.
Inbreeding depression is predominantly
caused by the homozygous expression of recessive deleterious
alleles. For zebra fish, inbreeding depression might be expected
to be more severe in stressful environments, including those caused by
anthropogenic pollution. Exposure of zebra fish to environmental
stress induced by the chemical clotrimazole, an imidazole fungicide
used in agriculture and in veterinary and human medicine, amplified
the effects of inbreeding on key reproductive traits. Embryo
viability was significantly reduced in inbred exposed fish and there
was a tendency for inbred males to sire fewer offspring.
In medical research
Zebrafish have been used to make several transgenic models of cancer,
including melanoma, leukemia, pancreatic cancer and hepatocellular
Zebrafish expressing mutated forms of either the
BRAF or NRAS oncogenes develop melanoma when placed onto a p53
deficient background. Histologically, these tumors strongly resemble
the human disease, are fully transplantable, and exhibit large-scale
genomic alterations. The BRAF melanoma model was utilized as a
platform for two screens published in March 2011 in the journal
Nature. In one study, by Ceol, Houvras and Zon, the model was used as
a tool to understand the functional importance of genes known to be
amplified and overexpressed in human melanoma. One gene, SETDB1,
markedly accelerated tumor formation in the zebrafish system,
demonstrating its importance as a new melanoma oncogene. This was
particularly significant because SETDB1 is known to be involved in the
epigenetic regulation that is increasingly appreciated to be central
to tumor cell biology.
In another study, by White and Zon, an effort was made to
therapeutically target the genetic program present in the tumor's
origin neural crest cell using a chemical screening approach. This
revealed that an inhibition of the DHODH protein (by a small molecule
called leflunomide) prevented development of the neural crest stem
cells which ultimately give rise to melanoma via interference with the
process of transcriptional elongation. Because this approach would aim
to target the "identity" of the melanoma cell rather than a single
genetic mutation, leflunomide may have utility in treating human
In cardiovascular research, the zebrafish has been used to model blood
clotting, blood vessel development, heart failure, and congenital
heart and kidney disease.
In programmes of research into acute inflammation, a major
underpinning process in many diseases, researchers have established a
zebrafish model of inflammation, and its resolution. This approach
allows detailed study of the genetic controls of inflammation and the
possibility of identifying potential new drugs.
Zebrafish has been extensively used as a model organism to study
vertebrate innate immunity. The innate immune system is capable of
phagocytic activity by 28 to 30 h postfertilization (hpf) while
adaptive immunity is not functionally mature until at least 4 weeks
As the immune system is relatively conserved between zebrafish and
humans, many human infectious diseases can be modeled in
zebrafish. The transparent early life stages are well
suited for in vivo imaging and genetic dissection of host-pathogen
Zebrafish models for a wide range of
bacterial, viral and parasitic pathogens have already been
established; for example, the zebrafish model for tuberculosis
provides fundamental insights into the mechanisms of pathogenesis of
mycobacteria. Furthermore, robotic technology has been
developed for high-throughput antimicrobial drug screening using
zebrafish infection models.
Repairing retinal damage
The development of a single zebrafish retina captured on a light sheet
microscope approx. every 12 hours from 1.5 days to 3.5 days after
birth of the embryo.
Another notable characteristic of the zebrafish is that it possesses
four types of cone cell, with ultraviolet-sensitive cells
supplementing the red, green and blue cone cell subtypes found in
Zebrafish can thus observe a very wide spectrum of colours.
The species is also studied to better understand the development of
the retina; in particular, how the cone cells of the retina become
arranged into the so-called 'cone mosaic'. Zebrafish, in addition to
certain other teleost fish, are particularly noted for having extreme
precision of cone cell arrangement.
This study of the zebrafish's retinal characteristics has also
extrapolated into medical enquiry. In 2007, researchers at University
College London grew a type of zebrafish adult stem cell found in the
eyes of fish and mammals that develops into neurons in the retina.
These could be injected into the eye to treat diseases that damage
retinal neurons—nearly every disease of the eye, including macular
degeneration, glaucoma, and diabetes-related blindness. The
researchers studied Müller glial cells in the eyes of humans aged
from 18 months to 91 years, and were able to develop them into all
types of retinal neurons. They were also able to grow them easily in
the lab. The stem cells successfully migrated into diseased rats'
retinas, and took on the characteristics of the surrounding neurons.
The team stated that they intended to develop the same approach in
As demonstrated through ongoing research programmes, the zebrafish
model enables researchers not only to identify genes that might
underlie human disease, but also to develop novel therapeutic agents
in drug discovery programmes.
Zebrafish embryos have proven to be
a rapid, cost-efficient, and reliable teratology assay model. Drug
screens in zebrafish can be used to identify novel classes of
compounds with biological effects, or to repurpose existing drugs for
novel uses; an example of the latter would be a screen which found
that a commonly used statin (rosuvastatin) can suppress the growth of
prostate cancer  To date, 65 small-molecule screens have been
carried out and at least one has led to clinical trials. Within
these screens, many technical challenges remain to be resolved,
including differing rates of drug absorption resulting in levels of
internal exposure that cannot be extrapolated from the water
concentration, and high levels of natural variation between individual
animals. To understand drug effects, the internal drug exposure is
essential, as this drives the pharmacological effect. Translating
experimental results from zebrafish to higher vertebrates (like
humans) requires concentration-effect relationships, which can be
derived from pharmacokinetic and pharmacodynamic analysis. To date,
only a pharmacokinetic model for paracetamol has been developed in
zebrafish larvae. The potential for pharmacological analyses in
this organism is however promising.
Muscular dystrophies (MD) are a heterogeneous group of genetic
disorders that cause muscle weakness, abnormal contractions and muscle
wasting, often leading to premature death.Zebraish is widely used
model to study muscular dystrophies. For example the sapje (sap)
mutant is the zebrafish orthologue of human Duchenne muscular
dystrophy (DMD). The Machuca-Tzili and co-workers applied
zebrafish to determine the role of alternative splicing factor, MBNL,
in myotonic dystrophy type 1 (DM1) pathogenesis. More recently,
Todd et al. described a new zebrafish model designed to explore the
impact of CUG repeat expression during early development in DM1
Zebrafish is also an excellent animal model to study
congenital muscular dystrophies including CMD Type 1 A (CMD 1A) caused
by mutation in the human laminin α2 (LAMA2) gene. The zebrafish,
because of its advantages discussed above, and in particular the
ability of zebrafish embryos to absorb chemicals, has become a model
of choice in screening and testing new drugs against muscular
Japanese brown frog, which has been modified to develop translucent
List of freshwater aquarium fish species
ZebraBox, a specialised container for the scientific study of
Drosophila melanogaster Fruit fly also used in research
Oryzias latipes medaka fish used for genetic, developmental, and
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