Introduction to Color Genetics

Introduction:
      Many animal breeders shy away from the word genetics. Some think it's not necessary to know how the physical appearances of their animals happen, while others just think that genetics are too complicated to be worth while. I believe in the importance of knowing the genetics of the animals you breed. Even if it is something as seemingly trivial as color genetics, it will pave the way to helping you understand the inheritance of other traits so that you can do your part for improving the health, appearance, and overall quality of the species.
      The purpose of this page is to explain some of the basics of genetics: including basic concepts, and vocabulary. If you are already familiar with the basics of genetics (especially those pertaining to mammal coat color) then there is no need to read this page-- unless you would like to touch up on the subject.

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Introduction to Color Genetics:
What are Genes:
      A gene is a small piece of a big molecule called DNA; a 'wound-up' DNA molecule is called a chromatid— two identical chromatids (called sister chromatids) join together to form the structure known as a chromosome. DNA is a code that can be compared to an instruction manual. Mechanisms in a cell read the DNA, which instructs the cell to make a product or perform a task.
      Letters are used as symbols to refer to a gene's location within the DNA molecule, these locations are called loci (singular: locus). For example, the A locus of mammal colors, which is the location of the Agouti gene. Most genes have multiple variations that cause different things to happen to the process that it's involved in; these variant forms of a gene are called alleles. The alleles of the Agouti gene that will be discussed here are A (agouti), and a (not agouti).

     As most people know, an individual inherits its genes directly from both of its parents, because of this it will have two alleles for each locus. The combination of these two alleles is known as the genotype. If an individual inherits an A allele from its mother and an a allele from its father then its genotype for the A locus is Aa.

Dominant and Recessive:
     When there are two different alleles at a locus, such as with the genotype Aa, it is often the case that only one of the alleles will show a noticeable result in the individual's physical appearance. This is because of the phenomenon known as dominant and recessive expression. If an allele expresses when there is only one copy of it in the genotype then it is classed as a dominant gene. While an allele that only expresses when it has two copies in the genotype is classed as a recessive gene.
     For the Agouti locus the A allele is dominant, while the a allele is recessive. So an individual with the genotype AA or Aa will be agouti colored, while an individual with the genotype aa will be non agouti, i.e. solid colored.

Some Useful Terms:
     The genetic term for the physical appearance of an individual (such as color) is phenotype. An individual with the genotype Aa is said to have an Agouti phenotype. And an individual with the genotype aa is said to have a non-agouti phenotype.
     There are also terms used to describe whether or not a genotype is composed of like alleles. If a genotype is composed of like alleles (such as AA or aa) it's said to be homozygous. If a genotype is composed of different alleles (such as Aa) it is said to be heterozygous. It is quite common in the world of color breeding to hear people use the abbreviation 'het' in reference to an animal with a heterozygous genotype for a desired recessive trait.

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Color Inheritance:
     Color inheritance is often a fairly simple mechanism. When two individuals are crossed, half of each of their genotypes goes to their offspring. This means that if an individual has the genotype Aa, it will pass either an A or an a to each offspring; while the offspring would get the second half of its genotype from the other parent. Where the process starts to get complicated is when considering more than one locus.
      The B locus is the location of the Brown gene, of which two alleles will be discussed for this tutorial: the B allele (black) and the b allele (reduced to brown). The agouti locus is epistatic to the B locus, which means it changes the normal expressions of the B locus.
     The genotype AABB will produce a black agouti (sometimes called golden agouti) colored individual (hairs are banded by black and tan/orange), while the genotype AAbb will produce a color most commonly known as cinnamon (hairs are banded by brown and tan/orange). However, without the dominant agouti gene the banding affect goes away; the genotype aaBB will produce a solid black colored individual, while the genotype aabb will produce a solid brown colored individual.
     Many more traits can be taken into consideration to get an even larger and more complex genotype. The main color loci in most mammals are A (agouti), B (brown), C (albinism), D (dilution), and E (color extension).

Punnett Squares:
     The chance that an offspring has of inheriting certain allele combinations from its parents are frequently determined using a tool called a Punnett Square. This simple tool shows which allele combinations are possible in a particular cross.
     For an example, say two individuals are crossed. One black with the genotype BB, and the other brown with the genotype bb. The Punnett square would be set up as is shown below-- with the genotype of one parent written along the top, and the genotype of the other written along one side.

     Then in each box within the square combine the allele above it with the one to its left. The results can be seen in the square below. Each box represents the genotype of a potential offspring.

     There is a 100% chance of getting black offspring. Each of the parents had only one allele of the B locus to give, the one whose genotype is written across the top of the square could only give a B allele, while the other parent, whose genotype is written on the left side of the square could only give a b allele.

     If you were to cross two individuals who both had the genotype Bb, then the results would be as follows.

     Each baby born from this cross would have a 50% chance of being heterozygous black, a 25% chance of being homozygous black, and a 25% chance of being brown (overall, an offspring of this cross would have a 75% chance of being black colored, and a 25% chance of being brown colored; i.e. the cross yields a 1/4 chance of producing brown).

Multiple Traits:
     When tracking more than one trait you can either set up multiple Punnett squares and divide the percentages down to the final statistics, or you can combine the genotypes into a single large square.
     For this example, I will use genes found in domestic hedgehogs: the square below shows the cross of a heterozygous black hedgehog to a brown hedgehog (Chestnut x Cinnamon), where both carry a recessive gene for the snowflake pattern (sn) [Snowflake: this term is exclusive to hedgehogs and refers a pattern of white spines mixed into the coat over the back (comparable to roaning)].

B/b ; Sn/sn (Chestnut) x b/b ; Sn/sn (Cinnamon)

For each individual combine the alleles of the different loci: e.g., for the first individual start with the B allele and combine it with each allele of the snowflake locus to get B ; Sn and B ; sn; then do the same with the b allele to get b ; Sn and b ; sn. Then repeat the method with the second individual's genotype.

     the results are as follows

     Due to the fact that the genes are combined randomly, the percentages that a Punnett square gives do not apply to each litter. In other words, one litter from the cross above could consist of all cinnamon colored offspring, but if the cross is repeated many times, then the percentages from all of the crosses will begin to converge on those of the Punnett square (in other words, the Punnett square determines the percentages produced from crosses within a population).
     The Punnett square is really a very simple tool, it is used to see which colors are possible and, of those, which are most likely to occur. It does not predict the actual percentages of each cross.

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Modes of Inheritance:
      A mode of inheritance is how an allele is expressed when present with others. Up to this point I have already covered two modes of inheritance: the dominant and recessive modes. These are the easiest to understand, and tend to be very common in genetics. The third mode that I will discuss now is semidominance, wherein two different alleles both express together, rather than one hiding the effects of the other. There are two main varieties of semidominance: incomplete dominance and codominance. In the former mode the two different traits blend together to form an intermediate (e.g. red gene x white gene = pink color), while in the latter mode they don't blend (e.g. red gene x white gene = red and white spots). It is this second variety of semidominance that will be the focus of this section, since it plays a central role in hedgehog colors.

CoDominance:
      The codominant mode of inheritance, as mentioned above, dictates that two different traits will coexist, but that they will segregate to form a new pattern. This mode is most notable in cinnicot colorations of hedgehogs (also in tawny colorations, but the contrast isn't as prominent as with cinnicots). The two different traits do not produce colors that blend into an intermediate in the coat (the spine bandings), but rather produce their own expression separately, creating a pattern of cinnamon and apricot expression (hence the name cinnicot). A cinnicot can have either the ruby-red eyes of an apricot hedgehog or the dark brown eyes of a cinnamon hedgehog, the pink skin of an apricot or the browned-grey skin of a cinnamon, and the coat will be a mixture of brown banded spines and orange banded spines.
      If an orange (genotype = b/b ; Ru/Ru) is crossed with a brown (genotype = b/b ; ru/ru) then a Punnett square will show that all offspring will also have the genotype b/b at their B-locus and that...

     ... they will have the genotype Ru/ru at their Ru-locus, making them all cinnicots.

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Gene Linkage:
      So far we have seen that multiple traits are assorted independently; where A/a ; B/b crossed with A/a ; B/B yields the product of two independent ratios 1AA:2Aa:1aa x 1BB:1Bb. However, if the A-locus and the B-locus were close to each other on the same chromosome, then the allele combinations between the two loci would remain the same from one generation to the next. They would not be independently assorted-- these are called linked genes.
      The genotype of linked traits is written differently; since the two alleles of different loci are linked together they must be written in a way that shows this linkage. For example, if one individual had inherited an A allele and a B allele next to each other on the same chromosome from one parent, and from the other parent they inherited a chromosome with an a allele next to a b allele then that individual's genotype for these two loci would be written as A B//a b. This shows that on one chromosome the dominant allele of the A-locus is linked to the dominant allele of the B-locus, while on the other chromosome the recessive alleles of the two loci are linked.
      If A and B were linked and the above cross were made, then the outcome would be very different. I will now set up the same cross again, this time showing that the two loci are linked.

      The expected ratio is 1 [A B//A B] : 1 [A B//a b] : 1 [a B//A B] : 1 [a B//a b]. This is greatly different from the expected results of two non-linked traits.
      Unfortunately there is no shortcut method of figuring out the allele combinations of linked traits, you will have to keep detailed color-pedigrees and track the genotypes of each generation. Fortunately, there is only one set of loci known in hedgehogs at this time that could potentially be linked: the roan locus (Rn) and the dilution locus (D).

Conclusion:
     As can be seen, there are many loci and alleles that control the coat color of mammals, and many more ways for those colors to express. Hopefully after reading this page you will have no problems understanding color genetics, or any other kind of simple genetics.
     Although, if you are still feeling that genetics might be a little over your head, then feel free to e-mail me with any questions that you may have; my e-mail address is atlantishedgehogs@yahoo.com, and I am always glad to help.