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The eye color in humans is controlled by the amount and type of pigment that is deposited in the iris.Eyes of all color except the reddish or pinkish eye of people with albinism contain a dark-brown pigment in the iris epithelium that is called eumelanin.

How is eye color determined?

It is produced by the melanocytes in the iris and is the same substance that darkens our skin when it is exposed to sunlight. The red eye color in people with albinism is due to the absence of pigment in the iris. Light that enters the eyes get reflected by the retina in the back of the eye. Since the retina is well circulated, the reflected light sows the color of the blood in the back of the eye.

The amount of eumelanin in the iris epithelium, as well as the amount of it in the iris stroma determines how light or dark the eyes are. Another factor is also the density of the cells in the stroma, as fewer cells will let more light through and will let the iris appear lighter colored. The colors determined by this range of eumelanin content, mainly of the stroma, and cell density can range from dark brown to light blue.

Green, hazel and amber eyes additionally contain another pigment that is yellow in color and is called lipofuscin or lipochrome.

How do genes that we inherit from our parent control which color our eyes will have?

A gene is a relatively short stretch of DNA, which is our genetic material, that usually contains the building plan for a protein. Genes sit in on the DNA molecule like pearls on a strand with short stretches of control sequences between them. The entirety of genetic material of an organism is called the genome, and it contains all information necessary for this organism to develop and to function. Genomes of all organisms with a nucleus in their cells are divided in several smaller packages called chromosomes. Humans have 46 chromosomes. Gene that are located on the same chromosome are inherited together, while gene on different chromosomes are inherited independently from each other.

How does the inheritance of a trait work with one gene involved?

Many inherited traits are controlled by the action of a single gene. A famous example among geneticists is the color of peas that can be yellow or green.

In humans, the blood type system is such a system that is controlled by one single gene. However, unlike the example of the peas that have only two different phenotypes (yellow or green), there are several phenotypes possible with human blood types: A, B, AB, and 0. The reason for this is that the gene that controls the blood type can come in three different versions, A, B and 0.

The versions of a gene are called allele. We all have two copies of each gene, one from our father and the other one from our mother. If somebody has two A-alleles on the two copies of blood type gene (geneticists call this a genotype AA), the person has the blood type A. The same is true for genotypes BB, and 00, they lead to the blood type B and 0, respectively. But what happens, if somebody inherits an A-allele from one parent and a 0-allele from the other? In this case, the A-allele is dominant and the blood type will be A. Scientist call the fact that the 0-allele does not show up in the phenotype, recessive. 0 is also recessive when mixed with B, so that a person, who has 0B-genotype, has the blood type B. However, if somebody has an A- and a B-allele, they are both expressed and the blood type is AB. This is called co-dominant.

How do the genetics of the eye color work?

Scientist believed for a long time that the inheritance of the eye color is similarly controlled with a single gene having brown and blue alleles. Brown was considered dominant and blue recessive. However, it is not that easy. There are many different colors possible other than just different shades of brown and blue, such as green, amber, hazel, and very rarely even purple. Furthermore, blue-eyed parents can have brown eyed children, which would be impossible, if blue were the recessive trait in a simple one-gene inheritance.

Though the exact number of genes that contribute to the eye color in humans is still unknown, scientists believe that there are at least six genes, possibly more, which together control the color of the iris. Some of these genes, like e.g. a gene called OCA2, also contribute to the appearance of freckles, moles and to hair and skin color. Each of the genes in question can have several alleles, making the inheritance all the more complicated.

The OCA2 gene for example, can be completely without function. If two such defect OCA2 genes are inherited, this results in a form of albinism called oculocutanous albinism type II, which gave the gene its name. Other alleles of OCA2 are associated with blue and green eye colors.

The Herc2 gene is a gene that regulates how much of the product of the OCA2 gene is made. In a study done in 2008, scientists were able to find a mutation in the Herc2 gene that leads to blue eye color. Scientists believe that this mutation developed in a single individual in the Middle East or in the area around the Black Sea sometime 6000-10000 years ago. It spread from there throughout Europe with its highest prevalence being in Northern and Central Europe.

Other genes involved with the control of the appearance of blue of brown eye color are SLC24A4[13]and TYR. The product of the TYR is an enzyme called tyrosinase and it is involved in the final production steps of eumelanin. If somebody has two defect versions of the TYR gene, oculocutanous albinism Type I is the result.

Color variations like blue with brown spots, or the appearance of yellow color in the eye like in green, hazel, or amber eyes, are due to an additional pigment that is yellow in color. The production of this pigment called lipofuscin is controlled by an entirely different set of genes.