Examine individual changes

'{{short description|One gene variant masking the effect of another in the other copy of the gene}} {{more citations needed|date=February 2018}} [[File:Autosomal dominant and recessive.svg|thumb|Autosomal dominant and autosomal recessive inheritance, the two most common [[Mendelian inheritance]] patterns. An [[autosome]] is any chromosome other than a [[sex chromosome]].|500px]] <!-- Note that "dominant x" and "recessive x" (for many values of x) redirect to this article so "dominant" and "recessive" are currently regarded as an important part of the _subject_ of this article. Therefore please ensure these words appear bolded and as early as possible in the lead. Similarly for "autosomal dominant" and "autosomal recessive". --> In [[genetics]], '''dominance''' is the phenomenon of one variant ([[allele]]) of a [[gene]] on a [[chromosome]] masking or overriding the [[Phenotype|effect]] of a different variant of the same gene on [[Homologous chromosome|the other copy of the chromosome]].<ref>{{cite web|title=dominance|url=http://www.oxforddictionaries.com/definition/english/dominance|work=Oxford Dictionaries Online|publisher=Oxford University Press|access-date=14 May 2014}}</ref><ref>{{cite web|title=express|url=http://www.oxforddictionaries.com/definition/english/express|work=Oxford Dictionaries Online|publisher=Oxford University Press|access-date=14 May 2014}}</ref> The first variant is termed '''dominant''' and the second '''recessive'''. This state of having [[Heterozygosity|two different variants]] of the same gene on each chromosome is originally caused by a [[mutation]] in one of the genes, either new (''de novo'') or [[Heredity|inherited]]. The terms '''autosomal dominant''' or '''autosomal recessive''' are used to describe gene variants on non-sex chromosomes ([[autosomes]]) and their associated traits, while those on [[sex chromosomes]] (allosomes) are termed [[X-linked dominant]], [[X-linked recessive]] or [[Y-linked]]; these have an inheritance and presentation pattern that depends on the sex of both the parent and the child (see [[Sex linkage]]). Since there is only one copy of the [[Y chromosome]], Y-linked traits cannot be dominant nor recessive. Additionally, there are other forms of dominance such as '''incomplete dominance''', in which a gene variant has a partial effect compared to when it is present on both chromosomes, and '''co-dominance''', in which different variants on each chromosome both show their associated traits. Dominance is not inherent to an allele or its traits ([[phenotype]]). It is a strictly relative effect between two alleles of a given gene of any function; one allele can be dominant over a second allele of the same gene, recessive to a third and [[Dominance (genetics)#Co-dominance|co-dominant]] with a fourth. Additionally, one allele may be dominant for one trait but not others. Dominance is a key concept in [[Mendelian inheritance]] and [[classical genetics]]. Letters and [[Punnett squares]] are used to demonstrate the principles of dominance in teaching, and the use of upper case letters for dominant alleles and lower case letters for recessive alleles is a widely followed convention. A classic example of dominance is the inheritance of [[seed]] shape in [[pea]]s. Peas may be round, associated with allele ''R'', or wrinkled, associated with allele ''r''. In this case, three combinations of alleles (genotypes) are possible: ''RR'', ''Rr'', and ''rr''. The ''RR'' ([[homozygous]]) individuals have round peas, and the ''rr'' (homozygous) individuals have wrinkled peas. In ''Rr'' ([[heterozygous]]) individuals, the ''R'' allele masks the presence of the ''r'' allele, so these individuals also have round peas. Thus, allele ''R'' is dominant over allele ''r'', and allele ''r'' is recessive to allele ''R''. Dominance differs from [[epistasis]], the phenomenon of an allele of one gene masking the effect of alleles of a ''different'' gene.<ref>{{cite book |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK21249/ |title=Modern Genetic Analysis |chapter=Gene Interaction Leads to Modified Dihybrid Ratios |date=1999 |author=Griffiths AJF |author2=Gelbart WM |author3=Miller JH |isbn=978-0-7167-3118-4 |publisher=W. H. Freeman & Company |place=New York |display-authors=etal |url-access=registration |url=https://archive.org/details/moderngeneticana0000unse }}</ref> ==Background== {{See also|Introduction to genetics}} [[File:Journal of Agricultural Research (1917) (14582377398).jpg|thumb|240px|Inheritance of dwarfing in maize. Demonstrating the heights of plants from the two parent variations and their F1 heterozygous hybrid (centre)]] The concept of dominance was introduced by ur mom [[Gregor Johann Mendel]]. Though Mendel, "The Father of Genetics", first used the term in the 1860s, it was not widely known until the early twentieth century. Mendel observed that, for a variety of traits of garden peas having to do with the appearance of seeds, seed pods, and plants, there were two discrete phenotypes, such as round versus wrinkled seeds, yellow versus green seeds, red versus white flowers or tall versus short plants. 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). However, when these [[Hybrid (biology)|hybrid]] plants were crossed, the offspring plants showed the two original phenotypes, in a characteristic 3:1 ratio, the more common phenotype being that of the parental hybrid plants. Mendel reasoned that each parent in the first cross was a homozygote for different alleles (one parent AA and the other parent aa), that each contributed one allele to the offspring, with the result that all of these hybrids were heterozygotes (Aa), and that one of the two alleles in the hybrid cross dominated expression of the other: A masked a. The final cross between two heterozygotes (Aa X Aa) would produce AA, Aa, and aa offspring in a 1:2:1 genotype ratio with the first two classes showing the (A) phenotype, and the last showing the (a) phenotype, thereby producing the 3:1 phenotype ratio. Mendel did not use the terms gene, allele, phenotype, genotype, homozygote, and heterozygote, all of which were introduced later. He did introduce the notation of capital and lowercase letters for dominant and recessive alleles, respectively, still in use today. In 1928, British population geneticist [[Ronald Fisher]] proposed that dominance acted based on natural selection through the contribution of [[modifier genes]].<!--[[natural selection]] was first proposed by the British population geneticist [[Ronald Fisher]] in 1928,<ref>Fisher, R.A. 1928. [http://digital.library.adelaide.edu.au/coll/special//fisher/68.pdf The possible modification of the response of the wild type to recurrent mutations] {{webarchive |url=https://web.archive.org/web/20090218135035/http://digital.library.adelaide.edu.au/coll/special/ |date=February 18, 2009 }}. Am. Nat., 62: 115–126.</ref> and expanded upon in his book ''[[The Genetical Theory of Natural Selection]]''.<ref>Fisher, R.A. 1930. ''The Genetical Theory of Natural Selection'', Clarendon Press, Oxford</ref> However, [[Sewall Wright]] and [[J.B.S. Haldane]] believed that the main explanation for dominance should be based on--> In 1929, American geneticist [[Sewall Wright]] responded by stating that dominance is simply a physiological consequence of metabolic pathways and the relative necessity of the gene involved. Wright's explanation became an established fact in genetics, and the debate was largely ended. Some traits may have their dominance influenced by evolutionary mechanisms, however.<ref>Mayo, O. and Bürger, R. 1997. [http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=637 The evolution of dominance: A theory whose time has passed?] "Biological Reviews", Volume 72, Issue 1, pp. 97–110</ref><ref>Bourguet, D. 1999. [http://www.nature.com/hdy/journal/v83/n1/full/6885600a.html The evolution of dominance] ''Heredity'', Volume 83, Number 1, pp. 1–4</ref><ref>Bagheri, H.C. 2006. [https://web.natur.cuni.cz/zoologie/biodiversity/prednasky/EvolucniGenetika/clanky_2017/Bagheri%202006%20allele%20dominance%20review.pdf Unresolved boundaries of evolutionary theory and the question of how inheritance systems evolve: 75 years of debate on the evolution of dominance] "Journal of Experimental Zoology Part B: Molecular and Developmental Evolution", Volume 306B, Issue 4, pp. 329–359</ref> ===Chromosomes, genes, and alleles=== {{see also|Ploidy|Zygosity}} Most animals and some plants have paired [[chromosome]]s, and are described as diploid. They have two versions of each chromosome, one contributed by the mother's [[ovum]], and the other by the father's [[sperm]], known as [[gamete]]s, described as haploid, and created through [[meiosis]]. These gametes then fuse during [[fertilization]] during [[sexual reproduction]], into a new single cell [[zygote]], which divides multiple times, resulting in a new organism with the same number of pairs of chromosomes in each (non-gamete) cell as its parents. Each chromosome of a matching (homologous) pair is structurally similar to the other, and has a very similar [[DNA]] [[sequencing|sequence]] ([[Locus (genetics)|loci]], singular locus). The DNA in each chromosome functions as a series of discrete [[genes]] that influence various traits. Thus, each gene also has a corresponding homologue, which may exist in different versions called [[allele]]s. The alleles at the same locus on the two homologous chromosomes may be identical or different. The [[blood type]] of a human is determined by a gene that creates an [[ABO blood group system|A, B, AB or O]] blood type and is located in the long arm of chromosome nine. There are three different alleles that could be present at this locus, but only two can be present in any individual, one inherited from their mother and one from their father.<ref>{{cite book |last=Ridley |first=Matt |title=Genome: The Autobiography of a Species in 23 Chapters |date=1999 |publisher=Harper Collins |pages=136–146 |chapter=Disease |isbn=978-0-06-089408-5 |chapter-url=https://books.google.com/books?id=h2zcDWshkEkC&pg=PA136}}</ref> If two alleles of a given gene are identical, the organism is called a homozygote and is said to be homozygous with respect to that gene; 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 its [[genotype]]. The genotype of an organism, directly and indirectly, affects its molecular, physical, and other traits, which individually or collectively are called its [[phenotype]]. At heterozygous gene loci, the two alleles interact to produce the phenotype.{{Citation needed|date=July 2021}} ==Dominance== ===Complete dominance=== In complete dominance, the effect of one allele in a heterozygous genotype completely masks the effect of the other. The allele that masks the other is said to be ''dominant'' to the latter, and the allele that is masked is said to be ''recessive'' to the former.<ref>{{cite book|first=RC |last=King |date=2006 |title=A Dictionary of Genetics |edition=7th|page=129 |publisher=Oxford University Press |isbn=978-0-19-530761-0 |url=https://books.google.com/books?id=ykp-7oJ5pREC&pg=PA129|quote=Dominance [refers] to alleles that fully manifest their phenotype when present in the [[zygosity|heterozygous]] ... state.|display-authors=etal}}</ref> Complete dominance, therefore, means that the phenotype of the heterozygote is indistinguishable from that of the dominant homozygote. <!--Yes, I know this pea example duplicates the lead. I believe this is entirely normal, as the lead should be an accessible summary of the article rather than contain truly unique content--> A classic example of dominance is the inheritance of seed shape (pea shape) in peas. Peas may be round (associated with allele ''R'') or wrinkled (associated with allele ''r''). In this case, three combinations of alleles ([[genotypes]]) are possible: ''RR'' and ''rr'' are homozygous and ''Rr'' is heterozygous. The ''RR'' individuals have round peas and the ''rr'' individuals have wrinkled peas. In ''Rr'' individuals the ''R'' allele masks the presence of the ''r'' allele, so these individuals also have round peas. Thus, allele ''R'' is completely dominant to allele ''r'', and allele ''r'' is recessive to allele ''R''. ===Incomplete dominance=== [[File:Incomplete dominance.svg|thumb|This [[Punnett square]] illustrates incomplete dominance. In this example, the red petal trait associated with the R [[allele]] recombines with the white petal trait of the r allele. The plant incompletely expresses the dominant trait (R) causing plants with the Rr genotype to express flowers with less red pigment resulting in pink flowers. The colors are not blended together, the dominant trait is just expressed less strongly.]] Incomplete dominance (also called ''partial dominance'', ''semi-dominance'' or ''intermediate inheritance'') occurs when the phenotype of the heterozygous genotype is distinct from and often intermediate (results from blending of characteristics in heterozygous state) to the phenotypes of the homozygous genotypes. For example, the [[Antirrhinum majus|snapdragon]] flower color is homozygous for either red or white. When the red homozygous flower is paired with the white homozygous flower, the result yields a pink snapdragon flower. The pink snapdragon is the result of incomplete dominance. A similar type of incomplete dominance is found in the [[four o'clock flower|four o'clock plant]] wherein pink color is produced when true-bred parents of white and red flowers are crossed. In [[quantitative genetics]], where phenotypes are measured and treated numerically, if a heterozygote's phenotype is exactly between (numerically) that of the two homozygotes, the phenotype is said to exhibit ''no dominance'' at all, i.e. dominance exists only when the heterozygote's phenotype measure lies closer to one homozygote than the other. When plants of the F₁ generation are self-pollinated, the phenotypic and genotypic ratio of the F₂ generation will be 1:2:1 (Red:Pink:White).<ref>{{cite book |first=Sandra |last=Pennington |title=11th Hour: Introduction to Genetics |url=https://books.google.com/books?id=RgsKUnM1IZoC&pg=PA43 |date=1999 |publisher=Wiley |isbn=978-0-632-04438-2 |page=43}}</ref> See [[partial dominance hypothesis]]. ===Co-dominance=== [[File:Co-dominance Rhododendron.jpg|thumb|left|Co-dominance in a [[Camellia]] cultivar]] [[File:ABO system codominance.svg|thumb|[[ABO blood group system|A and B blood types]] in humans show co-dominance, but the O type is recessive to A and B.]] [[File:Co-dominance in Roan Cattle.svg|thumb|This Punnett square shows co-dominance. In this example a white bull (WW) mates with a red cow (RR), and their offspring exhibit co-dominance expressing both white and red hairs.]] '''Co-dominance''' occurs when the contributions of both alleles are visible in the phenotype. For example, in the [[ABO blood group system]], chemical modifications to a [[glycoprotein]] (the H antigen) on the surfaces of blood cells are controlled by three alleles, two of which are co-dominant to each other (''I^A'', ''I^B'') and dominant over the recessive ''i'' at the [[ABO (gene)|ABO locus]]. The ''I^A'' and ''I^B'' alleles produce different modifications. The enzyme coded for by ''I^A'' adds an N-acetylgalactosamine to a membrane-bound H antigen. The ''I^B'' enzyme adds a galactose. The ''i'' allele produces no modification. Thus the ''I^A'' and ''I^B'' alleles are each dominant to ''i'' (''I^AI^A'' and ''I^Ai'' individuals both have type A blood, and ''I^BI^B'' and ''I^Bi'' individuals both have type B blood), but ''I^AI^B'' individuals have both modifications on their blood cells and thus have type AB blood, so the ''I^A'' and ''I^B'' alleles are said to be co-dominant. Another example occurs at the locus for the [[beta-globin]] component of [[hemoglobin]], where the three molecular phenotypes of ''Hb^A/Hb^A'', ''Hb^A/Hb^S'', and ''Hb^S/Hb^S'' are all distinguishable by [[protein electrophoresis]]. (The medical condition produced by the heterozygous genotype is called ''[[sickle-cell trait]]'' and is a milder condition distinguishable from ''[[sickle-cell anemia]]'', thus the alleles show ''incomplete dominance'' with respect to anemia, see above). For most gene loci at the molecular level, both alleles are expressed co-dominantly, because both are [[Transcription (genetics)|transcribed]] into [[RNA]]. Co-dominance, where allelic products co-exist in the phenotype, is different from incomplete dominance, where the quantitative interaction of allele products produces an intermediate phenotype. For example, in co-dominance, a red homozygous flower and a white homozygous flower will produce offspring that have red and white spots. When plants of the F1 generation are self-pollinated, the phenotypic and genotypic ratio of the F2 generation will be 1:2:1 (Red:Spotted:White). These ratios are the same as those for incomplete dominance. Again, this classical terminology is inappropriate – in reality such cases should not be said to exhibit dominance at all. ==={{anchor|Which trait is dominant?}}Addressing common misconceptions=== <!--Which trait is dominant? anchor above is to preserve any links to that section now it has been merged into here--> {{Unreferenced|section|date=January 2020}} While it is often convenient to talk about a ''recessive allele'' or a ''dominant trait'', dominance is not inherent to either an allele or its phenotype. Dominance is a relationship between two alleles of a gene and their associated phenotypes. A "dominant" allele is dominant to a particular allele of the same gene that can be inferred from the context, but it may be recessive to a third allele, and codominant to a fourth. Similarly, a "recessive" trait is a trait associated with a particular recessive allele implied by the context, but that same trait may occur in a different context where it is due to some other gene and a dominant allele. Dominance is unrelated to the nature of the phenotype itself, that is, whether it is regarded as "normal" or "abnormal," "standard" or "nonstandard," "healthy" or "diseased," "stronger" or "weaker," or more or less extreme. A dominant or recessive allele may account for any of these trait types. Dominance does not determine whether an allele is deleterious, neutral or advantageous. However, [[Natural selection|selection]] must operate on genes indirectly through phenotypes, and dominance affects the exposure of alleles in phenotypes, and hence the rate of change in allele frequencies under selection. Deleterious recessive alleles may persist in a population at low frequencies, with most copies carried in heterozygotes, at no cost to those individuals. These rare recessives are the basis for many hereditary [[genetic disorder]]s. Dominance is also unrelated to the distribution of alleles in the population. Both dominant and recessive alleles can be extremely common or extremely rare. ==Nomenclature== {{About|gene notations that identify dominance|modern formal nomenclature|Gene nomenclature|section=yes}} In genetics, symbols began as algebraic placeholders. When one allele is dominant to another, the oldest convention is to symbolize the dominant allele with a capital letter. The recessive allele is assigned the same letter in lower case. In the pea example, once the dominance relationship between the two alleles is known, it is possible to designate the dominant allele that produces a round shape by a capital-letter symbol '''R''', and the 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 would also be possible to designate the two alleles as '''W''' and '''w''', and the three genotypes '''WW''', '''Ww''', and '''ww''', the first two of which produced round peas and the third wrinkled peas. The choice of "'''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. A gene may have several alleles. Each allele is symbolized by the locus symbol followed by a unique superscript. In many species, the most common allele in the wild population is designated the wild type allele. It is symbolized with a + character as a superscript. Other alleles are dominant or recessive to the wild type allele. For recessive alleles, the locus symbol is in lower case letters. For alleles with any degree of dominance to the wild type allele, the first letter of the locus symbol is in upper case. For example, here are some of the alleles at the ''a'' locus of the laboratory mouse, ''Mus musculus'': ''A^y'', dominant yellow; ''a⁺'', wild type; and ''a^bt'', black and tan. The ''a^bt'' allele is recessive to the wild type allele, and the ''A^y'' allele is codominant to the wild type allele. The ''A^y'' allele is also codominant to the ''a^bt'' allele, but showing that relationship is beyond the limits of the rules for mouse genetic nomenclature. Rules of genetic nomenclature have evolved as genetics has become more complex. Committees have standardized the rules for some species, but not for all. Rules for one species may differ somewhat from the rules for a different species.<ref>[http://www.informatics.jax.org/mgihome/nomen/gene.shtml], Online 'Guidelines for nomenclature of genes, genetic markers, alleles, and mutations in mouse and rat'</ref><ref>[http://www.maizegdb.org/maize_nomenclature.php], Online 'A standard for maize genetic nomenclature'</ref> ==Relationship to other genetic concepts== ===Multiple alleles=== {{Main|Allele#Multiple alleles}} Although any individual of a diploid organism has at most two different alleles at any one locus (barring [[Aneuploidy|aneuploidies]]), most genes exist in a large number of allelic versions in the population as a whole. If the alleles have different effects on the phenotype, sometimes their dominance relationships can be described as a series. For example, coat color in domestic cats is affected by a series of alleles of the ''TYR'' gene (which encodes the enzyme [[tyrosinase]]). The alleles ''C'', ''c^b'', ''c^s'', and ''c^a'' (full colour, [[Burmese (cat)#Genetics|Burmese]], [[Siamese (cat)|Siamese]], and [[albino]], respectively) produce different levels of pigment and hence different levels of colour dilution. The ''C'' allele (full colour) is completely dominant over the last three and the ''c^a'' allele (albino) is completely recessive to the first three.<ref>{{cite web |url=http://www.vgl.ucdavis.edu/service/cat/coatcolor.html |title=Cat Coat Color |publisher=Veterinary Genetics Laboratory, University of California |access-date=2011-11-02}}</ref><ref>{{cite journal | first1 = D. L. | last1 = Imes | first2 = L. A. | last2 = Geary | first3 = R. A. | last3 = Grahn | first4 = L. A. | last4 = Lyons | date=April 2006 | title = Albinism in the domestic cat (''Felis catus'') is associated with a ''tyrosinase'' (''TYR'') mutation | journal = Animal Genetics | volume = 37 | issue = 2 | doi = 10.1111/j.1365-2052.2005.01409.x | pmid = 16573534 | pmc = 1464423 | pages = 175–8 }}</ref><ref>{{cite journal | first1 = A. | last1 = Schmidt-Küntzel | first2 = E. | last2 = Eizirik | first3 = S. J. | last3 = O'Brien | first4 = M. | last4 = Menotti-Raymond | date=April 2005 | title = Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of the albino and brown loci | journal = Journal of Heredity | volume = 96 | issue = 4 | pmid = 15858157 | doi = 10.1093/jhered/esi066 | pages = 289–301 | doi-access = free}}</ref> ===Autosomal ''versus'' sex-linked dominance=== {{Main|Sex linkage}} {{Unreferenced|section|date=January 2020}} In humans and other [[mammal]] species, [[sex-determination system|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 [[autosome]]s; 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 are linked to sex chromosomes, not because they are characteristic of one sex or the other. In practice, the term almost always refers to '''X'''-linked traits and a great many such traits (such as red-green colour vision deficiency) are not affected by sex. 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 [[zygosity|hemizygous]] for these genes. The Y chromosome is much smaller than the '''X''', and contains a much smaller set of genes, including, but not limited to, those that influence 'maleness', such as the [[SRY gene]] for [[testis determining factor]]. Dominance rules for sex-linked gene loci are determined by their behavior in the female: because the male has only one allele (except in the case of certain types of Y chromosome [[aneuploidy]]), that allele is always expressed regardless of whether it is dominant or recessive. Birds have opposite sex chromosomes: male birds have ZZ and female birds ZW chromosomes. However, inheritance of traits reminds XY-system otherwise; male zebra finches may carry white colouring gene in their one of two Z chromosome, but females develop white colouring always. Grasshoppers have XO-system. Females have XX, but males only X. There is no Y chromosome at all. ===Epistasis=== {{Main|Epistasis}} [[Epistasis]] ["''epi'' + ''stasis'' = to sit on top"] is an interaction between alleles at two ''different'' gene loci that affect a single trait, which may sometimes resemble a dominance interaction between two ''different'' alleles at the ''same'' locus. Epistasis modifies the characteristic [[Dihybrid cross|9:3:3:1]] ratio expected for two non-epistatic genes. For two loci, 14 classes of epistatic interactions are recognized. As an example of '''''recessive epistasis''''', one gene locus may determine whether a flower pigment is yellow ('''AA''' or '''Aa''') or green ('''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'''. The '''bb''' combination is ''not'' dominant to the '''A''' allele: rather, the '''B''' gene shows '''''recessive epistasis''''' to the '''A''' gene, because the '''B''' locus when homozygous for the ''recessive'' allele ('''bb''') suppresses phenotypic expression of the '''A''' locus. In a cross between two '''AaBb''' plants, this produces a characteristic '''9:3:4''' ratio, in this case of yellow : green : white flowers. In '''''dominant epistasis''''', one gene locus may determine yellow or green pigment as in the previous example: '''AA''' and '''Aa''' are yellow, and '''aa''' are green. A second locus determines whether a pigment precursor is produced ('''dd''') or not ('''DD''' or '''Dd'''). Here, in a '''DD''' or '''Dd''' plant, the flowers will be colorless irrespective of the genotype at the '''''A''''' locus, because of the epistatic effect of the dominant '''D''' allele. Thus, in a cross between two '''AaDd''' plants, 3/4 of the plants will be colorless, and the yellow and green phenotypes are expressed only in '''dd''' plants. This produces a characteristic '''12:3:1''' ratio of white : yellow : green plants. '''''Supplementary 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 not produced in any genotypic combination with either '''cc''' ''or'' '''dd'''. That is, ''both'' loci must have at least one dominant allele to produce the phenotype. This produces a characteristic '''9:7''' ratio of pigmented to unpigmented plants. '''''Complementary epistasis''''' in contrast produces an unpigmented plant if and only if the genotype is '''cc''' ''and'' '''dd''', and the characteristic ratio is '''15:1''' between pigmented and unpigmented plants.<ref name="CarrExt">{{cite web |last=Carr |first=Steven M |url=https://www.mun.ca/biology/scarr/2250_Extensions_to_Mendelian_Analysis.html |title=Extensions to Mendelian Analysis |publisher=Memorial University of Newfoundland }}</ref> Classical genetics considered epistatic interactions between two genes at a time. It is now evident from molecular genetics that all gene loci are involved in complex interactions with many other genes (e.g., metabolic pathways may involve scores of genes), and that this creates epistatic interactions that are much more complex than the classic two-locus models. ===Hardy–Weinberg principle (estimation of carrier frequency)=== {{Main|Hardy–Weinberg principle}} {{Unreferenced|section|date=January 2020}} The frequency of the heterozygous state (which is the carrier state for a recessive trait) can be estimated using the [[Hardy–Weinberg formula]]: <math> p^2+2pq+q^2=1 </math> This formula applies to a gene with exactly two alleles and relates the frequencies of those alleles in a large population to the frequencies of their three genotypes in that population. For example, if ''p'' is the frequency of allele '''A''', and ''q'' is the frequency of allele '''a''' then the terms ''p''², 2''pq'', and ''q''² are the frequencies of the genotypes '''AA''', '''Aa''' and '''aa''' respectively. Since the gene has only two alleles, all alleles must be either '''A''' or '''a''' and {{math|''p'' + ''q'' {{=}} 1}}. Now, if '''A''' is completely dominant to '''a''' then the frequency of the carrier genotype '''Aa''' cannot be directly observed (since it has the same traits as the homozygous genotype '''AA'''), however it can be estimated from the frequency of the recessive trait in the population, since this is the same as that of the homozygous genotype '''aa'''. i.e. the individual allele frequencies can be estimated: {{math|''q'' {{=}} {{radical|<var>f</var>(aa)}}}}, {{math|''p'' {{=}} 1 − ''q''}}, and from those the frequency of the carrier genotype can be derived: {{math|<var>f</var>(Aa) {{=}} 2''pq''}}.<!-- FIXME – switch to a more concrete example? peas again?--> This formula relies on a number of [[Hardy–Weinberg formula#Deviations from Hardy–Weinberg equilibrium|assumptions]] and an accurate estimate of the frequency of the recessive trait. In general, any real-world situation will deviate from these assumptions to some degree, introducing corresponding inaccuracies into the estimate. If the recessive trait is rare, then it will be hard to estimate its frequency accurately, as a very large sample size will be needed. ===Dominant versus advantageous=== {{Unreferenced|section|date=January 2020}} The property of "dominant" is sometimes confused with the concept of advantageous and the property of "recessive" is sometimes confused with the concept of deleterious, but the phenomena are distinct. Dominance describes the phenotype of heterozygotes with regard to the phenotypes of the homozygotes and without respect to the degree to which different phenotypes may be beneficial or deleterious. Since many genetic disease alleles are recessive and because the word dominance has a positive connotation, the assumption that the dominant phenotype is superior with respect to fitness is often made. This is not assured however; as discussed below while most genetic disease alleles are deleterious and recessive, not all genetic diseases are recessive. Nevertheless, this confusion has been pervasive throughout the history of genetics and persists to this day. Addressing this confusion was one of the prime motivations for the publication of the [[Hardy–Weinberg principle#History|Hardy–Weinberg principle]]. ==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 [[nucleobase|bases]] or [[nucleotide]]s of [[dNA|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 [[Transcription (genetics)|transcribed]] to make an RNA copy, and RNA is [[translation|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 versions of the same protein (called [[protein isoform|isoform]]s). Proteins often function as [[enzyme]]s 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'', above). Even if the two protein products are slightly different ([[allozyme]]s), it is likely that they produce the same phenotype with respect to enzyme action, and again neither allele can be said to be dominant. ===Loss of function and haplosufficiency=== 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 functional protein product. This can be the result of a [[mutation]] that alters the DNA sequence of the allele.{{citation needed|date=October 2016}} 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 [[albinism|albino]] phenotype<ref name="OMIM203100">{{OMIM|203100|Albinism, oculocutaneous, type IA}}</ref> results when an individual is homozygous for an allele that encodes a non-functional version of an enzyme needed to produce the skin pigment [[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 the typical case, the single functional allele makes sufficient protein to produce a phenotype identical to that of the homozygote: this is called ''[[haplo-sufficiency|haplosufficiency]]''. For example, suppose the standard amount of enzyme produced in the functional homozygote is 100%, with the two functional alleles contributing 50% each. The single functional allele in the heterozygote produces 50% of the standard amount of enzyme, which is sufficient to produce the standard phenotype. If the heterozygote and the functional-allele homozygote have identical phenotypes, the functional allele is dominant to the non-functional allele. This occurs at the albino gene locus: the heterozygote produces sufficient enzyme to convert the pigment precursor to melanin, and the individual has standard pigmentation. # Less commonly, the presence of a single functional allele gives a phenotype that is not normal but less severe than that of the non-functional homozygote. This occurs when the functional allele is not haplo-sufficient. The terms haplo-insufficiency and incomplete dominance are typically applied to these cases. The intermediate interaction occurs where the heterozygous genotype produces a phenotype intermediate between the two homozygotes. Depending on which of the two homozygotes the heterozygote most resembles, one allele is said to show ''incomplete dominance'' over the other. For example, in humans the ''Hb'' gene locus is responsible for the Beta-chain protein ([[HBB]]) that is one of the two [[globin]] proteins that make up the blood pigment [[hemoglobin]].<ref name="OMIM203100"/> Many people are homozygous for an allele called ''Hb^A''; some persons carry an alternative allele called ''Hb^S'', either as homozygotes or heterozygotes. The hemoglobin molecules of ''Hb^S''/''Hb^S'' homozygotes undergo a change in shape that distorts the morphology of the [[red blood cells]], and causes a severe, life-threatening form of [[anemia]] called [[sickle-cell anemia]]. Persons heterozygous ''Hb^A''/''Hb^S'' for this allele have a much less severe form of anemia called [[sickle-cell trait]]. Because the disease phenotype of ''Hb^A''/''Hb^S'' heterozygotes is more similar to but not identical to the ''Hb^A''/''Hb^A'' homozygote, the ''Hb^A'' allele is said to be ''incompletely dominant'' to the ''Hb^S'' allele. # Rarely, a single functional allele in the heterozygote may produce insufficient gene product for any function of the gene, and the phenotype resembles that of the homozygote for the non-functional allele. This complete ''[[haploinsufficiency]]'' is very unusual. In these cases, the non-functional allele would be said to be dominant to the functional allele. This situation may occur when the non-functional 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 defective alleles. The term "dominant" is often incorrectly applied to defective alleles whose homozygous phenotype has not been examined, but which cause a distinct phenotype when heterozygous with the normal allele. This phenomenon occurs in a number of [[trinucleotide repeat]] diseases, one example being [[Huntington's disease]].<ref>{{OMIM|143100|Huntington disease}}</ref> ===Dominant-negative mutations=== Many proteins are normally active in the form of a multimer, an aggregate of multiple copies of the same protein, otherwise known as a [[Multiprotein complex#Homomultimeric and heteromultimeric proteins|homomultimeric protein or homooligomeric protein]]. In fact, a majority of the 83,000 different enzymes from 9800 different organisms in the BRENDA Enzyme Database<ref>{{cite journal |author=Schomburg I|author2=Chang A|author3=Ebeling C|title=BRENDA, the enzyme database: updates and major new developments |journal=Nucleic Acids Res. |volume=32 |issue=Database issue |pages=D431–3 |date=January 2004 |pmid=14681450 |pmc=308815 |doi=10.1093/nar/gkh081 |url=|display-authors=etal}}</ref> represent homooligomers.<ref>{{cite journal |author=Hashimoto K|author2=Nishi H|author3=Bryant S|author4=Panchenko AR |title=Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization |journal=Phys Biol |volume=8 |issue=3 |page=035007 |date=June 2011 |pmid=21572178 |pmc=3148176 |doi=10.1088/1478-3975/8/3/035007 |bibcode=2011PhBio...8c5007H}}</ref> When the wild-type version of the protein is present along with a mutant version, a mixed multimer can be formed. A mutation that leads to a mutant protein that disrupts the activity of the wild-type protein in the multimer is a dominant-negative mutation. A dominant-negative mutation may arise in a human somatic cell and provide a proliferative advantage to the mutant cell, leading to its clonal expansion. For instance, a dominant-negative mutation in a gene necessary for the normal process of programmed cell death ([[Apoptosis]]) in response to DNA damage can make the cell resistant to apoptosis. This will allow proliferation of the clone even when excessive DNA damage is present. Such dominant-negative mutations occur in the tumor suppressor gene ''[[p53]]''.<ref name=Marutani>{{cite journal |author=Marutani M|author2=Tonoki H|author3=Tada M|title=Dominant-negative mutations of the tumor suppressor p53 relating to early onset of glioblastoma multiforme |journal=Cancer Res. |volume=59 |issue=19 |pages=4765–9 |date=October 1999 |pmid=10519380 |url=http://cancerres.aacrjournals.org/cgi/pmidlookup?view=long&pmid=10519380|display-authors=etal}}</ref><ref>{{cite journal |author=Goh AM|author2=Coffill CR|author3=Lane DP |title=The role of mutant p53 in human cancer |journal=J. Pathol. |volume=223 |issue=2 |pages=116–26 |date=January 2011 |pmid=21125670 |doi=10.1002/path.2784 |s2cid=23998813|doi-access=free }}</ref> The P53 wild-type protein is normally present as a four-protein multimer (oligotetramer). Dominant-negative ''p53'' mutations occur in a number of different types of cancer and pre-cancerous lesions (e.g. brain tumors, breast cancer, oral pre-cancerous lesions and oral cancer).<ref name=Marutani /> Dominant-negative mutations also occur in other tumor suppressor genes. For instance two dominant-negative germ line mutations were identified in the [[Ataxia telangiectasia mutated]] (ATM) gene which increases susceptibility to breast cancer.<ref>{{cite journal |author=Chenevix-Trench G|author2=Spurdle AB|author3=Gatei M|title=Dominant negative ATM mutations in breast cancer families |journal=J. Natl. Cancer Inst. |volume=94 |issue=3 |pages=205–15 |date=February 2002 |pmid=11830610 |doi=10.1093/jnci/94.3.205|display-authors=etal|doi-access=free }}</ref> Dominant negative mutations of the transcription factor [[CEBPA|C/EBPα]] can cause acute myeloid leukemia.<ref>{{cite journal |author=Pabst T|author2=Mueller BU|author3=Zhang P|title=Dominant-negative mutations of CEBPA, encoding CCAAT/enhancer binding protein-alpha (C/EBPalpha), in acute myeloid leukemia |journal=Nat. Genet. |volume=27 |issue=3 |pages=263–70 |date=March 2001 |pmid=11242107 |doi=10.1038/85820 |s2cid=33788907|display-authors=etal}}</ref> Inherited dominant negative mutations can also increase the risk of diseases other than cancer. Dominant-negative mutations in [[Peroxisome proliferator-activated receptor gamma]] (PPARγ) are associated with severe insulin resistance, diabetes mellitus and hypertension.<ref>{{cite journal |author=Barroso I|author2=Gurnell M|author3=Crowley VE|title=Dominant negative mutations in human PPARgamma associated with severe insulin resistance, diabetes mellitus and hypertension |journal=Nature |volume=402 |issue=6764 |pages=880–3 |date=1999 |pmid=10622252 |doi=10.1038/47254 |display-authors=etal|bibcode=1999Natur.402..880B|s2cid=4423555}}</ref> Dominant-negative mutations have also been described in organisms other than humans. In fact, the first study reporting a '''mutant protein''' inhibiting the normal function of a wild-type protein in a mixed multimer was with the bacteriophage T4 tail fiber protein GP37.<ref>{{cite journal |author=Bernstein H|author2=Fisher KM |title=Dominance in bacteriophage T4D |journal=Genetics |volume=58 |issue=3 |pages=307–18 |date=March 1968 |doi=10.1093/genetics/58.3.307 |pmid=5662621 |pmc=1211863 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=5662621}}</ref> Mutations that produce a truncated protein rather than a full-length mutant protein seem to have the strongest dominant-negative effect in the studies of P53, ATM, C/EBPα, and bacteriophage T4 GP37. ==Dominant and recessive genetic diseases in humans== In humans, many genetic traits or diseases are classified simply as "dominant" or "recessive". Especially with so-called recessive diseases, which are indeed a factor of recessive genes, but can oversimplify the underlying molecular basis and lead to misunderstanding of the nature of dominance. For example, the recessive genetic disease [[phenylketonuria]] (PKU)<ref>{{OMIM|261600|Hyperphenylalaninemia, non-PKU mild}}</ref> results from any of a large number (>60) of alleles at the gene locus for the enzyme [[phenylalanine hydroxylase]] ('''PAH''').<ref name="OMIM612349">{{OMIM|612349|Phenylalanine Hydroxylase; PAH}}</ref> Many of these alleles produce little or no '''PAH''', as a result of which the substrate [[phenylalanine]] (Phe) and its metabolic byproducts accumulate in the [[central nervous system]] and can cause severe [[intellectual disability]] if untreated. To illustrate these nuances, the genotypes and phenotypic consequences of interactions among three hypothetical PAH alleles are shown in the following table:<ref>{{cite web |last=Carr |first=Steven M. |url=https://www.mun.ca/biology/scarr/2250_One_Gene_One_Enzyme.html |title=One Gene, One Enzyme |publisher=Memorial University of Newfoundland }}</ref> {| class="wikitable" |- ! Genotype ! '''PAH''' activity ! ['''Phe'''] conc ! PKU ? |- | '''AA''' | 100% | 60 μM | No |- | '''AB''' | 30% | 120 μM | No |- | '''CC''' | 5% | 200 ~ 300 μM | Hyperphenylalaninemia |- | '''BB''' | 0.3% | 600 ~ 2400 μM | Yes |} 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 μM (= [[Molar concentration|μmol/L]]). 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 incompletely dominant to the '''B''' allele with respect to [Phe], as 60 μM < 120 μM << 600 μM. 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 [[hyperphenylalaninemia]], which does not result in intellectual disability. That is, the dominance relationships of any two alleles may vary according to which aspect of the phenotype is under consideration. It is typically more useful to talk about the phenotypic consequences of the allelic interactions involved in any genotype, rather than to try to force them into dominant and recessive categories. ==See also== *[[List of Mendelian traits in humans]] * [[Mitochondrial DNA]] * [[Punnett square]] ==References== {{Reflist|30em}} * [https://www.mun.ca/biology/scarr/Bio2250.html "On-line notes for Biology 2250 – Principles of Genetics"]. Memorial University of Newfoundland. * {{OMIM|141900|Hemoglobin—Beta Locus; HBB}} — Sickle-Cell Anemia * {{OMIM|110300|ABO Glycosyltransferase}} — ABO blood groups ==External links== * [https://web.archive.org/web/20111026062710/http://www.omim.org/ "Online Mendelian Inheritance in Man"] (OMIM) * [https://web.archive.org/web/20090414125159/http://hopes.stanford.edu/causes/inherit/c0.html "Autosomal dominance of Huntington's Disease"]. [[Huntington's Disease Outreach Project for Education at Stanford]] {{DEFAULTSORT:Dominance (Genetics)}} [[Category:Classical genetics]] [[Category:Genetics concepts]] [[Category:Autosomal dominant disorders|*]]'