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Angelfish Genetics

This section will give you a basic overview of angelfish genetics and how it applies to the different color varieties. Much of the information on angelfish genetics contained here, has come from Dr. Joanne Norton's research on angelfish genetics and from the practical knowledge obtained by Steve Rybicki, with the hundreds of crosses he has made over the last 50 years. Dr. Norton's information on angelfish genetics was first published in FAMA Magazines articles starting in the early '80s. A majority were published by the end of 1992. Dr. Norton's angelfish genetics research was later published in a couple of books, one put out by Tetra in 1992 called Aquariology. Steve personally confirmed all these crosses in his hatchery before 1990 except for Albino and Streaked, which came out later.

The angelfish gene names used here are those that were originally used by Dr. Norton or the person first researching the new angelfish gene mutation. Many different phenotype names names are used for angelfish, so it is important to also attach universally used angelfish gene names for the alleles that are proven in any particular angelfish strain.

Did you Know... that angelfish have more chromosomes than humans? It's true, angelfish (Pterophyllum scalare) have one more pair of homologous chromosomes than do humans. While human somatic cells (body cells) contain 23 homologous pairs for a total of 46 chromosomes, angelfish have 24 pairs of homologous chromosomes in their somatic cells giving them a total of 48 chromosomes.

In genetics, there are specific terms used to refer to the number of chromosomes in a cell. Gametic cells (gametes, or sperm and egg) contain half of an organism's genetic information so that when combined, two gametes will produce one zygote with the proper number of chromosomes. The haploid number of an organism refers to the number of chromosomes contained in each of its gametes. With angelfish, 24 is the haploid number and is represented by the letter n. After fertilization of an angelfish egg, the resulting zygote contains a full set of chromosomes and is known as a diploid cell. The diploid number of an organism refers to the number of chromosomes contained in its somatic cells. The diploid number, for angelfish 48, is represented by the symbol 2n.

Genetic Terms

Understanding the terms in this section can help you better track the results of your angelfish crosses and to predict the expected results of future angelfish pairings. Gene: Genes contain the genetic material by which hereditary characteristics are transmitted. Each gene occurs at a specific location (called locus) on each chromosome, whose existence can be confirmed by allelic variants (mutations). Chromosomes occur in pairs, one coming from each parent. Therefore, each gene has an opposing gene on the other chromosome.

Allele: Alleles are the mutational variations of a gene that can occur at each locus. Each is distinguished from other alleles by the effect it has on phenotype. There may be several alleles possible at any given location, though no more than two can occur at the same time in any individual.

Locus: The place on the chromosome where a particular gene resides. This location is like an address and is what is used in gene mapping.

Dose: A term commonly used to designate the allele donated by a parent. For example, a Double-Dose Black means that each angelfish parent transmitted one allele of Dark to the offspring.

Hybrid: An angelfish trait that was derived from two different alleles. The angelfish hybrid will not breed true, however, a percentage of the hybrid's offspring will be true-breeding.

Mutation: The process of mutation is the source of new alleles. It is an abrupt and permanent change in the genetic material. Minor mutations are relatively common and somewhat insignificant. They are either slight or have no desirable quality. Since mutations are random in the genetic code and the proper code is very specific, useful mutations of a major proportion are rather unlikely. Truly valuable or significant mutations are quite rare. In angelfish, there have been no more than 2 to 3 dozen major mutations that were perpetuated in the last 50 years. The gradual change in the looks of a fish, over many generations, is also caused by mutations. The result is simply the accumulation of less significant, minor mutations.

Homozygous: A trait determined by two identical alleles at the same locus, resulting in a true-breeding strain for that trait. i.e. a true-breeding Double Dose Black is homozygous for Dark.

Heterozygous: A trait determined by two different alleles at the same locus, resulting in a hybrid angelfish that will not breed true for that trait. i.e. a single dose of Dark and a single dose of its allele, Gold, will produce 25% homozygous Blacks, 25% Gold and 50% single dose Blacks that have a single-dose of Gold, thus the single-dose Black is heterozygous for Dark and Gold.

Recessive: When different alleles occur at the same locus and one of the alleles is not expressed in the presence of the other, the non-expressed trait is considered recessive.

Dominant: When different alleles occur at the same locus and one of the alleles is not expressed in the presence of the other, the expressed trait is considered dominant.

Intermediate Inheritance: When different alleles occur at the same locus and there is a blending of traits, each trait is an incomplete-dominant (or Co-dominant). In Black Lace Angelfish is there is a blending of traits, therefore Dark and Silver (wild type) act as incomplete dominants to each other.

Phenotype: The physical appearance of a trait. To be considered a distinct phenotype the trait should be uniquely identifiable.

Genotype: The written expression of the genetic makeup of the trait in question. With angelfish we use one or two-letter notation to represent this. There are two notations for each gene location. For example, Gm/g represents two possible alleles that could be found at this location - Gold Marble (Gm) and Gold (g).

Penetrance: Expressed as a percentage. It is the frequency with which a given genotype expresses its mutant phenotype to at least some degree. A good example is Halfblack angelfish, which is influenced by the environment. 100% penetrance occurs under ideal tank conditions with some lines. If at least a partial pattern develops on all the angelfish, then 100% penetrance has occurred. Some Halfblack angelfish lines appear to contain modifiers that inhibit the expression of Halfblack. In these lines, penetrance will be less than 100%, even under ideal conditions.

Expressivity: The degree or range in which a phenotype for a given trait is expressed. Once again, Halfblack is a good example. This mutation can exhibit a wide range of expressivity. Halfblack angelfish patterns are seldom complete on every fish in a spawn. Various degrees of partial patterns are somewhat normal. This range can be due to incomplete penetrance and well as adverse environmental conditions.

Epigenetics:  This has to due with changes in phenotype that do not involve any changes in DNA sequences. There appear to be "markers" that turn genes on or off. These markers can persist for a few generations. Environmental differences are one of the ways these markers are set.


Punnett Square

Punnett Square: This is particularly useful when first learning about angelfish genetics and how to identify the outcome of a monohybrid cross. It is recommended that you use this until you are very comfortable with how alleles are donated by each angelfish parent. Place the alleles of one parent across the top and the alleles of the other parent on the side. Then bring each allele down or across to the box in its row or column. Each box represents the possible outcome of each cross. This represents the genotype of each angelfish. The phenotype (how it looks) is determined by the dominant and recessive characteristics of each allele in its respective box. In the example below, each box represents 25% of the total spawn. Therefore, 25% of the spawn will be true breeding Double Dark Black angelfish (DD), 50% will be hybrid Black angelfish (Dg or gD) and 25% will be true-breeding Gold angelfish (gg).

Branch Diagram: When dealing with multiple traits, it is much less complex to consider the genetic interaction of these traits separately, and then combine the results using a branch-diagram.

Test Cross: There is a simple method used to distinguish the genotype of an angelfish with an unknown genetic inheritance. The angelfish of unknown genotype is crossed to a homozygous recessive individual. For example, you have a dark angelfish that shows streaking in the fins and you want to determine its genotype.

Test cross: Cross this dark angelfish into a homozygous recessive gold angelfish (gg) that is proven to have no other hidden mutations. Let's say the resulting (F1) shows 50% gold (gg) and 50% dark angelfish. Of the dark angelfish, 50% are streaked, like the one parent. The other dark angelfish appear as normal blacks.

Analysis: All of the F1s received a Gold allele from the Gold parent. The 50% gold fry means that the dark parent also contained the allele for Gold. The dark F1s without streaking proves that a Dark allele (D) was donated by the dark adult angelfish. This means the dark parent has two identified alleles at this point - (D and g). Since Dark and Gold are alleles, we now know that the gene that causes streaking is not an allele of Dark. The dark angelfish parent could not have 3 alleles on one locus. Because the original gold did not contain the allele that causes streaking (came from dark parents that showed no streaking), we know that the streaking in the F1s came from the dark parent. 50% streaked dark F1s is consistent with a dominant allele that causes streaking and shows that the original dark parent was heterozygous for this trait. The original angelfish parent is proven to be heterozygous for Dark, Gold and Streaked (D/g-St/+).

Variety: Any of a group of widely separated variants within a single interbreeding population. As used within the hobby, varieties of angelfish include all of the different color types, i.e., Black, Gold, Marble, etc.. Each variety is also its own separate phenotype

Strain: The descendants of a common group within a variety. I may be working on a strain of Koi angelfish that exhibits bright orange on most of the body and a yellow eye. Another breeder may have a different strain of Koi angelfish that exhibits yellow on the body and a red eye. They are both the same variety, but a different strain of that variety.

Line: The descendants of a common ancestor within a strain. For example, I decide to set up four separate lines within my strain of orange bodied, yellow eyed Koi angelfish. Each line is kept separate and periodically out-crossed to another of the four lines to create a new line. The use of lines helps to keep the immune system strong, while maintaining the same strain within the same variety.

Inbreeding: A breeding technique to fix traits known to a particular line of angelfish. This involves the mating of closely related angelfish, i.e. brother to sister, father to daughter. A strain's immune system is deteriorated using this method. With this technique you can also more easily identify recessive traits, both good and bad.

Line-breeding: A breeding technique for developing the positive attributes of a strain. This involves the mating of angelfish that are related, i.e. brother to grandmother, father to cousin, etc.. Separate lines are kept that are crossed to each other every 3rd or 4th generation. This is a more forgiving system then inbreeding, but care must be taken, because the immune system is still compromised, though to a lesser degree.

Out-crossing: A breeding technique of using unrelated parents. It can strengthen the immune system and it can be used to bring in desirable traits the current line does not have. Out-crossing can make it difficult to "fix" a characteristic and can also introduce hidden undesirable recessive traits to the line.

F1 Generation: F1 is the symbol given to the first filial generation of progeny from a cross of non-siblings. This cross is represented by (P1 x P2 = F1). When representing a cross, you use parent (P) to indicate the original breeders. You can only get to an F2 by breeding siblings (F1 x F1 = F2). If you cross back to a grandparent, the resulting fry are also F1's, because it would be represented the same way as the first example (P1 xP2 = F1).

The reason you want to track it in this manner is so you will know whenever a different gene pool has been added to the line. When trying to fix certain traits, rather than strict inbreeding, you may want to start different lines that will be inbred and then crossed to each other every 3rd or 4th generation. You would then probably want to change to a different labeling scheme. I would suggest lowercase letters to represent each line, to avoid confusion with the generation numbers. Adult angelfish would be labeled as follows: Line (a) = (aP), line (b) = (bP), line (c) = (cP), etc. This way, you can track this modified form of inbreeding. (aP1 x aP1 = aF2), (aP3 x bP3 = aF1). Let's say you linebreed for another 10 generations and then decide to bring in other unrelated stock and cross it into Line 1. You will want to label the new line so you know it's unrelated. (aP3 x eP1(new) = aF1), or if you decide to keep line (a) and create a new line (e), it would be (aP3 x eP1 = eF1).

Angelfish Color Mutations:  There are hundreds of mutations of little importance by themselves, that occur in angelfish. The following are the new angelfish gene mutations that have had a major effect on the appearance of angelfish and whose inheritance characteristics have been discovered. The letter in parenthesis is the gene notation (shorthand used to track the genotype). These are the only mutations whose allelic inheritance characteristics are demonstrated with documented spawnings. 

  • Albino(a)  A recessive mutation that removes the pterin and melanin pigments leaving the carotenoid pigment layer exposed.
  • Dark(D)  A incomplete dominant that is present in our Blacks and many other dark angelfish. Commonly referred to as the Black gene, in error. An allele of Gold Marble, New Gold and Marble.
  • Gold Marble(Gm)  A lightly marked marble that acts similar to the Gold allele in crosses. An allele of Dark, Marble and Gold.
  • Bulgarian Green (bg) A recessive gene that interferes with the expression of pigments in the body. Newly discovered and still being explored.
  • Halfblack(h)  Recessive mutation whose penetrance  may be influenced by modifiers. The environment will influence the expression of this gene.
  • Marble(M)  An incomplete dominant that is an allele of Dark, New Gold and Gold Marble.
  • Gold(g)  A recessive mutation that can be hidden in many strains. Originally referred to as New Gold. It is only one of a few gold mutations. Naja Gold and Hong Kong Gold (which are probably both lost to the hobby) are the other two. New Gold is an allele of Dark, Gold Marble and Marble.
  • Pearl(p)  Not a color mutation, but a recessive scale mutation that reflects light in a sparkling manner. Expressivity is environmentally influenced. The phenotype is commonly referred to as pearlscale.
  • Blue(b)  This recessive mutation is a relatively new one that most likely arose in Thailand. When homozygous, it increases iridescence in all strains and it greatly inhibits the storage of carotenoid pigments in those that are normally orange or gold in color. For example, Golds become white. With strains like Wild-type, since there is no orange to remove, it simply adds iridescence to the adults. Iridescence in the juveniles is very subtle and increases as the fish ages. It also appears to be somewhat deleterious, causing lower fertility, weaker, smaller fry and more deformities to occur in many spawns.  Our opinion of this gene is somewhat tainted.
  • Smokey(Sm)  A dominant mutation. The phenotype of an angel that is homozygous for Smokey is known as a Chocolate.
  • Streaked(St)  A dominant mutation that acts as a modifier of the Dark gene. It causes white or clear streaks in the fins and iridescent patches on the body in Blacks and other varieties containing the Dark gene. It exhibits variable expression. The streaks can be one or two fine lines or a bold white stripe. An underlying mottling can also be seen in (DD) and (Dg) that contain the gene for Streaked. There is some evidence that it is now expressing in some fish without the Dark gene present.
  • Stripeless(S)  An incomplete dominant that exhibits variable expressivity. It is not a color mutation, but a modifier that affects the expression of other color genes. More complete explanation below.
  • Zebra(Z)  A dominant mutation that is an allele of Stripeless, therefore you cannot have a Blushing Zebra - Wild-type(+)The gene that occurs most frequently in a population at any given gene location. The one that is designated as normal, is called wild-type.

Symbols for Alleles: The initial letter of the name of the mutant trait is selected, if not already in use. If the trait is recessive to wild-type, the lowercase letter is used. If it is dominant, the uppercase is used. The contrasting wild-type gene is denoted by (+). If the first letter is in use, then we use the first two letters, the second one, always being lower case. 

For information purposes we will list Dr. Norton's angelfish gene notation. This is a more descriptive angelfish notation that is more useful once learned. Each gene is named by location. The location name is determined by the first mutation discovered there. If the gene being discussed is not the original, it is superscripted. The first letter is uppercase if the allele is dominant over wild-type and it is lowercase if it is recessive to wild-type.

Locus #1 - Hong Kong Gold (hg), recessive to wild-type. Probably lost to the hobby.

Locus #2 - Smokey (Sm), dominant to wild-type.

Locus #3 - Stripeless (S), dominant to wild-type; Zebra (Sze), dominant to wild-type.

Locus #4 - Dark (D), dominant to wild-type; Marble (Dm), dominant to wild-type; New Gold (dng), recessive to wild-type; Gold Marble (Dgm), dominant to wild-type.

Locus #5 - Halfblack (h), recessive to wild-type.

Locus #6 - Pearl (p), recessive to wild-type.

Locus #7 - Streaked (St), dominant modifier of Dark.

Locus #8 - Blue (b), recessive modifier of all tested color mutations.

Using the above notation, the genotypes for the following strains are:

  • Smokey - Sm/Sm +
  • Chocolate - Sm/Sm
  • Ghost - S/s+
  • Blushing -  S/S
  • DD Black - D/D
  • Black Lace - D/d+
  • Zebra (one dose) - Sze/s+
  • Zebra Lace  - Sze/s+ - D/d+


Stripeless:  The most misunderstood angelfish gene, so it will be mentioned here. Many angelfish breeders do not even know of the existence of the gene Stripeless. In error, they commonly call this, Blushing. Stripeless is the gene, Blushing is the phenotype(trait). An angelfish that is homozygous for Stripeless will be a Blushing angelfish, but an angelfish that is heterozygous for Stripeless does not show the blushing trait. These are commonly referred to as Ghost angelfish. Fish with Stripeless in one dose exhibit intermediate inheritance resulting in an angelfish with incomplete bars and greater amounts of blue/green iridescence as an adult. It also appears to inhibit the expression of pigment on striped angelfish, such as Halfblack patterns and the orange coloration on any angelfish. Homozygous Stripeless also inhibits red eye color.


At this point it appears that Koi angelfish are the only blushing angelfish capable of having red eye color. It took many generations of selective breeding to accomplish this. Stripeless also causes iridophores to form as the angelfish matures. The amount of iridophores is variable in expression and may be due to modifiers that accompany the Stripeless allele.


Stripeless and Zebra act as alleles, therefore you can not have a double dose Stripeless Zebra angelfish (Zebra Blushing). All other angelfish strains can be homozygous for Stripeless and exhibit the blushing trait.

Environmental Influences
:  Many people assume angelfish genetics control the look of our angelfish almost exclusively, however, the appearance of our angelfish (the expressivity of the genes) is very much influenced by the environment. Most, if not all color types are influenced by the environment, some more than others. Mutations like Dark and Marble are not affected much. Those such as Gold, Smokey, Albino and Gold Marble are intermediate in their susceptibility to environmental conditions, whereas, genes like Halfblack, wild- type, Zebra and Pearlscale are highly affected by environment. Fish containing the Stripeless gene appear to be on the highest end of the spectrum of variability due to the environment. In other words, Stripeless and/or its modifiers appear to be very susceptible to the affects of the environment, especially in angelfish that normally exhibit the orange pigment layer, like Koi or Sunset Blushing angelfish.

Orange Pigment Genetics:  There is quite a bit of confusion about the inheritance of orange pigment that appears on some angelfish, particularly Koi angelfish. First, some basics about pigments.  There are four main groups of pigments that affect the color of our fish. There are the melanins, which provide the darker colors, and the pteridines, which are water-soluble pigments that result in bright colors. There doesn't appear to be many pteridines in freshwater angelfish. Then there are the purines, which consist largely of guanines. Guanines are not pigments, but waste products that accumulate and are stored in skin cells. They produce the silvery iridescence that occurs on many of our angelfish, especially blushing types. Combine these compounds with proteins and the result are structures that refract light into the blue, violets, and greens we see. The final group is the carotenoids. Carotenoids are lipid-soluble pigments ranging from yellow to red.

Carotenoids cannot be produced by angelfish and therefore must be added to their diet. Carotenoids have been shown to stimulate the immune system. They also assist in any detoxification process. It has been demonstrated that fish that are exposed to more stress, diseases and parasites, use carotenoids to defend themselves. Fish that use fewer carotenoids have the potential to retain the stored pigments, thus looking more orange. When a previously orange fish fades, it is an indication that the carotenoids were needed to help combat a stress situation. However, the genetics that produces the potential to store carotenoids remains the same.

Genetic factors - Some genes enable the storage of carotenoids. There is strong evidence that these genes are activated by the lack of stress factors and a healthy immune system. Therefore, the expression of carotenoids is environmentally influenced (epigenetics is a likely explanation). The degree of expression appears to vary according to the degree of stress, combined with a complex gene interaction. The maximum expression appears to be genetically determined. If adults have the genes needed to store excess carotenoids, then it appears that most of their offspring will also have the genes. Assuming the proper genes were inherited, the degree of expression and retention will be both diet and stress-related. It will be different in every situation. The one common denominator is the genetic makeup of the fish. Those who have the genes for the storage of carotenoids will pass them on to their young, regardless of whether they express the pigment or not. This is one reason why some Koi offspring will not express orange to the degree their parents do, or that they lose the pigment over time. We have shown time and time again, that very orange offspring can be produced by adults with little or no orange if the genes needed to store carotenoids are present.

In Conclusion:  When studying the angelfish genetics, one must first eliminate the effects of the environment before analyzing the allelic inheritance of the genes. Many people studying angelfish genetics are unable to provide a proper environment to prevent inhibiting the expression of all genes involved in the study. They also don't take into account that several environmental and genetic factors may be involved in combination, making analysis difficult if not impossible with some genes.

For those interested in mutation identification on the hobby level, the following guide as given by geneticist, Dr. Joanne Norton, should be used. "The studied trait should produce phenotypes that are statistically predictable and uniquely identifiable." If this holds true, then environmental influences were probably not much of a factor, and you should be able to determine the inheritance characteristics of the mutation.

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