Different alleles of the same gene can have different levels of phenotypic expression (outward appearance). Because genes are usually present in two copies (sex chromosomes being the exception in diploid organisms like humans), this difference in expression can be important to the phenotype of the organism. Some alleles mask the effect of all other forms of the gene present. These alleles are said to be dominant. A dominant gene has the same effect when it is present as a single copy (heterozygous) as when it is present as two copies (homozygous). The allele not expressed in the heterozygous form is said to be recessive to the masking allele, the dominant allele.
In the pea plants studied by Austrian monk and botanist Gregor Johann Mendel, the allele for tall plants was dominant to the allele for dwarf plants. When a gene is said to be dominant or recessive without any qualification, then it is assumed that effect is with reference to the wild type allele. People often refer to the characteristic without acknowledging that it is caused by an allele; this is implied. For example, one may state that, in humans, blue eyes are recessive to all other eye colors when what is actually meant is that the allele for blue eyes is recessive to all other eye color alleles.
An effect called co-dominance can also occur where there is a blending of the effects of the two alleles. Many genes for characteristics that are not for discrete states (e.g. presence versus absence) can be co-dominant. Examples of this include such characteristics as blood types with the ABO blood system.
Alleles are not required (constrained) to act in an all or nothing manner. and degrees of blending may be possible. In certain instances, there is no dominance shown at all, and when two differing parental types cross there is simply an intermediate blending of the two forms. For example, snap dragons with white flowers when mated with those with red flowers give progeny with pink flowers. There are also situations between dominance and no dominance, which are known as partial dominance. With these situations there is an intermediate form produced in the first generation, but it is markedly more similar to one of the parents than the other.
For the effects of a recessive allele to be observable it has to be present in the homozygous form. In other words, there must be two copies of the same allele present. Recessive alleles can be hidden in one generation but they may reappear in the next depending upon the breeding that has occurred. Just because the allele cannot be directly observed does not mean it is not present. Punnet squares can be used to calculate the frequency of different phenotypes and genotypes (genetic constitution) in particular breeding experiments, and from observing the results of these the genetic makeup of the parental types can be inferred. It is also possible to perform crosses with a known genotype and then infer the unknown genotype from the resulting progeny.
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