Dominance in genetics is a non-linear relationship between different forms (alleles) of a gene and the resultant phenotype. A canonical example in a diploid species like humans is the simple 2-allele model of eye-color, where the brown (B) allele is dominant over the blue (b) allele. Both BB homozygotes and Bb heterozygotes express the brown-eye phenotype, with only bb homozygotes expressing blue eye phenotype. In practice many allele relationships are more complex, reflecting the varied molecular basis of these allelic effects.
 Background: Pairs of genes
 Diploid / haploid
Most familiar plants, like pea plants and apples, and familiar animals, like tigers, dogs, fruit flies and humans, have paired chromosomes. Organisms with paired chromosomes are considered diploid. In paired chromosomes, one chromosome of each pair is donated by a unique parent. For example, in humans, the mother gives one "chromosome #7" in her ova and the father adds another "chromosome #7" when his sperm donated the rest of the chromosomes. For all 23 pairs of chromosomes, one chromosome of each pair came from the mother and the other chromosome from each pair came from the father. Making organisms from two "half" (haploid) cells requires a special cell division process called (meiosis). Meiosis produces egg/ova and sperm in preparation for fertilization (ie. joining of haploid cells). This careful orchestration makes sure that each daughter cell gets exactly one of each matching pair of chromosomes. The other kind of nucleus replication, (mitosis), is simply making two identical copies of nuclei - with the same number of chromosomes - as the starting cell.
 Pairs of genes: Homologues
Each chromosome of a matching pair are called "homologues"; they are not quite identical. Each chromosome of a homologous pair has the same genes in the same location as the corresponding homologue. However, the genes on homologues, may be different alleles or the same alleles. In Mendel's pea plants, for example, on the homologous chromosomes containing the gene for pea plant height, each homologue may have a gene identical to the other (like "tall gene" and "tall gene") or it may have the "same" gene but a different version of the gene (like "tall gene" and "short gene"). The "same gene but different version" are called alleles. Both alleles affect the height, but one version of the gene makes pea plants short and the other makes pea plants tall.
 Homozygous, heterozygous
If two alleles are identical, the organism is called a homozygote and is said to be homozygous; if instead the two alleles are different, the organism is a heterozygote and is heterozygous. The genetic makeup of an organism, either at a single locus or over all its genes collectively, is called the genotype. The genotype of an organism directly or indirectly affects its molecular, physical, behavioral, and other traits, which individually or collectively are called the phenotype. At heterozygous gene loci, the two alleles interact to produce the phenotype. The simplest form of allele interaction is the one described by Mendel, now called Mendelian, in which the appearance/phenotype caused by one allele is apparent, called dominant, and the appearance/phenotype caused by the other allele is not apparent, called recessive.
In the simplest case, the phenotypic effect of one allele completely masks the other in heterozygous combination; that is, the phenotype produced by the two alleles in heterozygous combination is identical to that produced by one of the two homozygous genotypes. The allele that masks the other is said to be dominant to the latter, and the alternative allele is said to be recessive to the former.
The concept of dominance was first explained by the "father of genetics," Moravian monk Gregor Mendel, who recognized the principle based on his work with the common garden pea Pisum sativum. For example, the edible pea seeds occur in two distinct phenotypes, 'round' and 'wrinkled.' The shape phenotype is known to be influenced by a single gene that occurs in two allelic forms, A and B. Pea plants that are homozygous AA have round seeds, and those that are homozygous BB have wrinkled seeds. Plants that are heterozygous AB have round seeds that are indistinguishable in shape from AA seeds: the A allele "dominates" the B allele to produce the round phenotype. That is, the A allele is said to be dominant to the B allele, and the B allele is recessive to the A allele. The principle of dominance is known as Mendel's First Law.
 Which one is dominant?
A dominant trait does not mean "more potent," and recessive does not mean "weaker." Rather, the terms simply refer to the visible trait, the phenotype, seen in a heterozygote. If only two phenotypes are possible, and a heterozygote exhibits one phenotype, by definition the phenotype exhibited by the heterozygote is called "dominant" and the "hidden" phenotype is considered recessive. The key concept of dominance is that the heterozygote is phenotypically identical to one of the two homozygotes. The homozygous trait seen also in the heterozygous individual is called the 'dominant' trait.
It is critical to understand that dominance is a genotypic relationship between alleles, as manifested in the phenotype. It is unrelated to the nature of the phenotype itself, e.g., whether it is regarded as 'normal or abnormal,' 'standard or nonstandard,' 'healthy or diseased,' 'stronger or weaker,' or 'more or less' extreme. It is also important to distinguish between the 'round' gene locus, the 'round' allele at that locus, and the 'round' phenotype it produces. It is inaccurate to say that 'the round gene dominates the wrinkled gene' or that 'round peas dominate wrinkled peas.'
In genetics, the common convention is that dominant alleles are written as capital letters and recessive alleles as lower-case letters. In the pea example, once the dominance relationships of the two alleles are known, it is possible to designate the dominant allele that produces a round shape by a capital-letter symbol R, and the alternative recessive allele that produces a wrinkled shape by a lower-case symbol r. The homozygous dominant, heterozygous, and homozygous recessive genotypes are then written RR, Rr, and rr, respectively. It is also possible to designate the two alleles as W and w, and three genotypes WW, Ww, and ww, the first two of which produced round peas and the third wrinkled peas. Note that the choice or 'R' or 'W' as the symbol for the dominant allele does not pre-judge whether the allele causing the 'round' or 'wrinkled' phenotype when homozygous is the dominant one.
Another system of notation designates the gene involved in seed shape as the 'Shp' gene, which exists in two allelic forms, ShpR and Shpw, the dominance relationships of the two being indicated by the case of the superscripts. This system is the standard system in Drosophila genetics.
 Relationship to other genetic concepts
The concept of dominance is involved with a number of other genetic concepts.
 Multiple alleles
Although any individual has at most two different alleles, most genes exist in a large number of allelic forms in the population as a whole. In some cases, the alleles have different effects on the phenotype, and their dominance interactions with each other can be described as a series. For example, the best known human blood groups, the ABO system, comprises three sets of alleles at the I locus, IA, IB, and IO. The first two are dominant to the latter: that is, the AA and AO genotypes produce indistinguishable blood group phenotypes, called 'Type A', as do BB and BO, which produce 'Type B' blood. In another example, coat colour in siamese cats. and related breeds is determined by a series of alleles at the albino gene locus (c) that produce different levels of pigment and hence different levels of colour dilution. Four of these are c+, cb, cs, and ca (standard, Burmese, siamese, and albino, respectively), where the first allele is completely dominant to the last three, and the last is completely recessive to the first three.
 Incomplete and semi-dominance
Complete dominance occurs when the phenotype of the heterozygote is completely indistinguishable from that of the dominant homozygote. This is frequently not the case. In cases where the heterozygote differs from but more closely resembles one of the two homozygotes, that allele is described as an incomplete dominant. In the case of cats described above, the cb and cs alleles are incompletely dominant to each other, and the cb / cs heterozygote shows an intermediate coloration called tonkinese. If the heterozygote is precisely intermediate between the two homozygotes, the alleles are described as semi-dominant to each other.
Co-dominance occurs when the contributions of both alleles are visible in the phenotype. In the ABO example, the IA and IB alleles are co-dominant in producing the AB blood group phenotype, in which both A- and B-type antigens are made. Another example occurs at the locus for the Beta-globin component of hemoglobin, where the three molecular phenotypes of HbA/HbA, HbA/HbS, and HbS/HbS are all equally detectable by protein electrophoresis. (The medical condition produced by the heterozygous genotype is called an incomplete dominant, see above). For most gene loci at the molecular level, both alleles are expressed co-dominantly, because both are transcribed into RNA.
Co-dominance and incomplete or semi-dominance are not the same thing. For example, in some plant species, pink flowers may be the product of a mixture of red and white pigments (co-dominance on the pigment level, no dominance on the color level), or the result of one allele that produces the usual amount of red pigment and another non-functional allele that produces no pigment, so as to produce a dilute, intermediate pink color (no dominance at either level).
 Autosomal versus sex-linked dominance
In humans and many other species, sex is determined by two sex chromosomes called the X chromosome and the Y chromosome. Human females are typically XX, males are typically XY. The remaining pairs of chromosome are found in both sexes and are called autosomes; genetic traits due to loci on these chromosomes are described as autosomal, and may be dominant or recessive. Genetic traits on the X and Y chromosomes are called sex linked, because they tend to be characteristic of one sex or the other. Females have two copies of every gene locus found on the X chromosome, just as for the autosomes, and the same dominance relationships apply. Males however have only one copy of each X-chromosome gene locus, and are described as hemizygous for these genes. Dominance rules for sex-linked gene loci are determined by their behavior in the female: because the male has only one allele, that allele is always expressed regardless of whether it is dominant or recessive.
Epistasis ["epi + stasis = to sit on top"] is an interaction between genotypes at two different gene loci, which sometimes resembles a dominance interaction at a single locus. For example, in the determination of flower color, one gene locus may determine whether the pigment is red (AA or Aa) or white (aa), while another locus determines whether the pigment is produced (BB or Bb) or not (bb). In a bb plant, the flowers will be white, irrespective of the genotype of the other locus as AA, Aa, or aa. It is not the case that the b allele is dominant to the A allele: the B locus is said to show recessive epistasis to the A locus, because the B locus when homozygous for the recessive allele overrides the phenotypic expression of the A locus.
A second type of epistasis occurs when two loci affect the same phenotype. For example, if pigment color is produced by CC or Cc but not cc, and by DD or Dd but not dd, then pigment is produced only in C-D- genotypes, but not in any genotype combination with cc or dd. That is, both loci must be functional to produce the phenotype, and only 7 of 9 two-locus combinations produce pigment in supplementary epistasis. For two loci, 14 classes of epistatic interactions are recognized. Most genetic systems involve complex epistatic interactions among multiple gene loci.
 Molecular mechanisms
The molecular basis of dominance was unknown to Mendel. It is now understood that a gene locus includes a long series (hundreds to thousands) of bases or nucleotides of deoxyribonucleic acid (DNA) at a particular point on a chromosome. The central dogma of molecular biology states that 'DNA makes RNA makes protein', that is, that DNA is transcribed to make an RNA copy, and RNA is translated to make a protein. In this process, different alleles at a locus may or may not be transcribed, and if transcribed may be translated to slightly different forms of the same protein (called isoforms). Proteins often function as enzymes that catalyze chemical reactions in the cell, which directly or indirectly produce phenotypes. In any diploid organism, the DNA sequences of the two alleles present at any gene locus may be identical (homozygous) or different (heterozygous). Even if the gene locus is heterozygous at the level of the DNA sequence, the proteins made by each allele may be identical. In the absence of any difference between the protein products, neither allele can be said to be dominant (see co-dominance, below). Even if the two protein products are slightly different (allozymes), it is likely that they produce the same phenotype with respect to enzyme action, and again neither allele can be said to be dominant.
Dominance typically occurs when one of the two alleles is non-functional at the molecular level, that is, it is not transcribed or else does not produce a protein product. This can be the result of a mutation that alters the DNA sequence of the allele. An organism homozygous for the non-functional allele will generally show a distinctive phenotype, due to the absence of the protein product. For example, in humans and other organisms, the unpigmented skin of the albino phenotype  results when an individual is homozygous for an allele that prevents synthesis of the skin pigment protein melanin. It is important to understand that it is not the lack of function that allows the allele to be described as recessive: this is the interaction with the alternative allele in the heterozygote. Three general types of interaction are possible:
In some cases, dominance of a non-standard allele results when that allele produces a defective protein that interferes with the proper function of the protein produced by the standard allele. The presence of the defective protein 'dominates' the standard protein, and the disease phenotype of the heterozygote more closely resembles that of the homozygote for two variant alleles. This phenomenon occurs in a number of trinucleotide repeat diseases: for an example and more details see Huntington Disease.
 Dominant and recessive genetic diseases in humans
In humans, many genetic traits or diseases are classified simply as 'dominant' or 'recessive.' Especially with respect to so-called recessive diseases, this can oversimplify the underlying molecular basis and lead to misunderstanding of the nature of dominance. For example, the genetic disease phenylketonuria (PKU) results from any of a large number (>60) of alleles at the gene locus for the enzyme phenylalanine hydroxylase (PAH). Many of these alleles produce little or no PAH, as a result of which the substrate phenylalanine and its metabolic byproducts accumulate in the central nervous system and can cause severe mental retardation if untreated.
The genotypes and phenotypic consequences of three alleles are shown in the following table.
In unaffected persons homozygous for a standard functional allele (AA), PAH activity is standard (100%), and the concentration of phenylalanine in the blood [phe] is about 60 uM. In untreated persons homozygous for one of the PKU alleles (BB), PAH activity is close to zero, [phe] ten to forty times standard, and the individual manifests PKU.
In the AB heterozygote, PAH activity is only 30% (not 50%) of standard, blood [phe] is elevated two-fold, and the person does not manifest PKU. Thus, the A allele is dominant to the B allele with respect to PKU, but the B allele is incompletely dominant to the A allele with respect to its molecular effect, determination of PAH activity level (0.3% < 30% << 100%). Finally, the A allele is an incomplete dominant to B with respect to [phe], as 60 uM < 120 uM << 600 uM. Note once more that it is irrelevant to the question of dominance that the recessive allele produces a more extreme [phe] phenotype.
For a third allele C, a CC homozygote produces a very small amount of PAH enzyme, which results in a somewhat elevated level of [phe] in the blood, a condition called hyperphenylalanemia, which does not result in mental retardation.
That is, the dominance relationships of any two alleles may vary according to which aspect of phenotype is under discussion. It is typically more useful to talk about the phenotypic consequences of the alleles involved in any genotype, rather than to try to force them into dominant and recessive categories.
The concept of dominance was first described by the 'Father of Genetics,' Gregor Mendel, in the 1860s. Mendel observed that, for a variety of traits of garden peas having to do with the appearance of seeds, seed pods, and plant appearance, there occurred two discrete phenotypes: round vs wrinkled, or yellow vs green seeds, red vs white flowers, tall vs short plants, and so on. When bred separately, the plants always produced the same phenotypes, generation after generation. However, when lines with different phenotypes were crossed (interbred), one and only one of the parental phenotypes showed up in the offspring: green, or round, or red, or tall, and so on. However, when these hybrid plants were crossed, the offspring plants showed the two original phenotypes, in a characteristic 3:1 ratio, with the more common type having the phenotype of the parental hybrid plants. Mendel reasoned that each of the parents in the first cross were homozygotes for different alleles (AA and aa), that each contributed one allele to the offspring, such that all of these hybrids were heterozygotes (Aa), and that one of the two alleles in the hybrid cross masked (dominated) expression of the other. The final cross between two heterozygotes (Aa X Aa) would produce AA, Aa, aA, and aa offspring in equal proportions, with the first three classes showing the 'A' phenotype, and the last showing the 'a' phenotype, thereby producing the 3:1 ratio.
Mendel did not use the terms gene, allele, phenotype, genotype, homozygote, and heterozygote, all of which were introduced afterward. He did introduce the notation of capital and lowercase letters for dominant and recessive alleles, respectively, still in use today.
 See also
1. On-line notes for Biology 2250 - Principles of Genetics (Memorial University of Newfoundland) 
2. Phenylketonuria 
3. Sickle-Cell Anemia 
4. ABO blood groups 
5. Tri-nucleotide repeat: Huntington disease 
6. Albinism 
 External links
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