An allele ((UK), /əˈliːl/ (US)) (from the Greek αλληλος allelos, meaning each other) is one member of a pair or series of different forms of a gene. Usually alleles are coding sequences, but sometimes the term is used to refer to a non-coding sequence. An individual's genotype for that gene is the set of alleles it happens to possess. In a diploid organism, one that has two copies of each chromosome, two alleles make up the individual's genotype. Alleles are prominently represented in a Punnett square.
An example is the gene for blossom colour in many species of flower — a single gene controls the colour of the petals, but there may be several different versions (or alleles) of the gene. One version might result in red petals, while another might result in white petals. The resulting colour of an individual flower will depend on which two alleles it possesses for the gene and how the two interact.
Diploid organisms (e.g. humans) have paired homologous chromosomes in their somatic cells, and these contain two copies of each gene. An organism in which the two copies of the gene are identical — that is, have the same allele — is called homozygous for that gene. An organism which has two different alleles of the gene is called heterozygous. Phenotypes (the expressed characteristics) associated with a certain allele can sometimes be dominant or recessive, but often they are neither. A dominant phenotype will be expressed when at least one allele of its associated type is present, whereas a recessive phenotype will only be expressed when both alleles are of its associated type.
However, there are exceptions to the way heterozygotes express themselves in the phenotype. One exception is incomplete dominance (sometimes called blending inheritance) when alleles blend their traits in the phenotype. An example of this would be seen if, when crossing Antirrhinums — flowers with incompletely dominant "red" and "white" alleles for petal color — the resulting offspring had pink petals. Another exception is co-dominance, where both alleles are active and both traits are expressed at the same time; for example, both red and white petals in the same bloom or red and white flowers on the same plant. Codominance is also apparent in human blood types. A person with one "A" blood type allele and one "B" blood type allele would have a blood type of "AB".
(Note that with the advent of neutral genetic markers, the term 'allele' is now often used to refer to DNA sequence variants in non-functional, or junk DNA. For example, allele frequency tables are often presented for genetic markers, such as the DYS markers.) Also there are many different types of alleles.
There are two equations for the frequency of two alleles of a given gene (see Hardy-Weinberg principle).
Equation 1: ,
where is the frequency of one allele and is the frequency of the other allele. Under appropriate conditions, subject to numerous limitations regarding the applicability of the Hardy-Weinberg principle, is the population fraction that is homozygous for the allele, is the frequency of heterozygotes and is the population fraction that is homozygous for the allele.
Natural selection can act on and in Equation 1, and obviously affect the frequency of genotypes seen in Equation 2.
Equation 2 is a consequence of Equation 1, obtained by squaring both sides and applying the binomial theorem to the left-hand side. Conversely, implies since and are positive numbers.
The following equation (commonly termed the Lee equation) can be used to calculate the number of possible genotypes in a diploid organism for a specific gene with a given number of alleles.
where is the number of different alleles for the gene being dealt with and is the number of possible genotypes. For example, the human ABO blood group gene has three alleles; A (for blood group A), B (for blood group B) and O (for blood group O). As such, (using the equation) the number of possible genotypes a human may have with respect to the ABO gene are 6 (AA, AO, AB, BB, BO, OO). The equation does not specify the number of possible phenotypes, however. Such an equation would be quite impossible as the number of possible phenotypes varies amongst different genes and their alleles. For example, in a diploid heterozygote some traits may show complete dominance, incomplete dominance etc., depending of the gene involved.
Genetic disorders are normally caused if an individual carries two alleles associated with a recessive, single-gene trait. Genetic disorders such as these include Albinism, Cystic Fibrosis, Galactosemia, Phenylketonuria (PKU), and Tay-Sachs Disease. In these cases the two alleles are autosomal (not sex chromosomes). Other disorders are also recessive, but because they are located on the X chromosomes (of which men have only one copy), they are much more frequent in men than in women. One example of such a disorder is the Fragile X syndrome.
Some other disorders, such as Huntington's disease, are dominant and it is sufficient to carry only one allele associated with the disorder to be affected.