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An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of
nucleotide Nucleotides are Organic compound, organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential ...
s at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chromosomal or genomic location of a gene or any other genetic element is called a locus (plural: loci) and alternative DNA sequences at a locus are called alleles." The simplest alleles are
single nucleotide polymorphisms In genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians ...
(SNP). but they can also be insertions and deletions of up to several thousand
base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both ...
s. Popular definitions of 'allele' typically refer only to different alleles within genes. For example, the ABO blood grouping is controlled by the ABO gene, which has six common alleles (variants). In
population genetics Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, ...
, nearly every living human's
phenotype In genetics, the phenotype () is the set of observable characteristics or phenotypic trait, traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, dev ...
for the ABO gene is some combination of just these six alleles. Most alleles observed result in little or no change in the function of the gene product it codes for. However, sometimes, different alleles can result in different observable
phenotypic trait A phenotypic trait, simply trait, or character state is a distinct variant of a phenotype, phenotypic characteristic of an organism; it may be either heredity, inherited or determined environmentally, but typically occurs as a combination of the ...
s, such as different
pigmentation A pigment is a colored material that is completely or nearly Solubility, insoluble in water. In contrast, dyes are typically soluble, at least at some stage in their use. Generally dyes are often organic compounds whereas pigments are often inorg ...
. A notable example of this is
Gregor Mendel Gregor Johann Mendel, Augustinians, OSA (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a biologist, meteorologist, mathematician, Augustinians, Augustinian friar and abbot of St Thomas's Abbey, Brno, St. Thomas' Abbey in Br ...
's discovery that the white and purple flower colors in
pea The pea is most commonly the small spherical seed or the seed-pod of the flowering plant species ''Pisum sativum''. Each pod contains several peas, which can be green or yellow. Botanically, pea pods are fruit, since they contain seeds and d ...
plants were the result of a single gene with two alleles. Nearly all
multicellular organism A multicellular organism is an organism that consists of more than one cell (biology), cell, in contrast to unicellular organism. All species of animals, Embryophyte, land plants and most fungi are multicellular, as are many algae, whereas a few ...
s have two sets of
chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
s at some point in their
biological life cycle In biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of Cell (biology), cel ...
; that is, they are
diploid Ploidy () is the number of complete sets of chromosomes in a cell (biology), cell, and hence the number of possible alleles for Autosome, autosomal and Pseudoautosomal region, pseudoautosomal genes. Sets of chromosomes refer to the number of mat ...
. In this case, the chromosomes can be paired. Each chromosome in the pair contains the same genes in the same order, and place, along the length of the chromosome. For a given gene, if the two chromosomes contain the same allele, they, and the organism, are
homozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mo ...
with respect to that gene. If the alleles are different, they, and the organism, are
heterozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mo ...
with respect to that gene.


Etymology

The word "allele" is a short form of allelomorph ("other form", a word coined by British geneticists
William Bateson William Bateson (8 August 1861 – 8 February 1926) was an English biologist A biologist is a scientist who conducts research in biology. Biologists are interested in studying life on Earth, whether it is an individual Cell (biology), cell, ...
and Edith Rebecca Saunders), which was used in the early days of
genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian fr ...
to describe variant forms of a
gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian inheritance#History, Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanin ...
detected as different
phenotypes In genetics, the phenotype () is the set of observable characteristics or phenotypic trait, traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, dev ...
. It derives from the
Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
prefix ἀλληλο-, ''allelo-'', meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, ''allos'' (cognate with
Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally a dialect spoken in the lower Tiber area (then known as Latium) around present-day Rome, but through ...
''alius''), meaning "other".


Alleles that lead to dominant or recessive phenotypes

In many cases, genotypic interactions between the two alleles at a locus can be described as dominant or
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. The first ...
, according to which of the two homozygous phenotypes the
heterozygote Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mo ...
most resembles. Where the heterozygote is indistinguishable from one of the homozygotes, the allele expressed is the one that leads to the "dominant" phenotype, and the other allele is said to be "recessive". The degree and pattern of dominance varies among loci. This type of interaction was first formally-described by
Gregor Mendel Gregor Johann Mendel, Augustinians, OSA (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a biologist, meteorologist, mathematician, Augustinians, Augustinian friar and abbot of St Thomas's Abbey, Brno, St. Thomas' Abbey in Br ...
. However, many traits defy this simple categorization and the phenotypes are modeled by
co-dominance 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. The first ...
and
polygenic inheritance A quantitative trait locus (QTL) is a Locus (genetics), locus (section of DNA) that correlates with variation of a quantitative trait in the phenotype of a Population genetics, population of organisms. QTLs are mapped by identifying which molecula ...
The term "
wild type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "m ...
" allele is sometimes used to describe an allele that is thought to contribute to the typical phenotypic character as seen in "wild" populations of organisms, such as fruit flies (''
Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly" or "pomace fly". Starting with Ch ...
''). Such a "wild type" allele was historically regarded as leading to a dominant (overpowering – always expressed), common, and normal phenotype, in contrast to "
mutant In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It i ...
" alleles that lead to recessive, rare, and frequently deleterious phenotypes. It was formerly thought that most individuals were homozygous for the "wild type" allele at most gene loci, and that any alternative "mutant" allele was found in homozygous form in a small minority of "affected" individuals, often as
genetic diseases A genetic disorder is a health problem caused by one or more abnormalities in the genome. It can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosomal abnormality. Although polygenic disorders ...
, and more frequently in heterozygous form in " carriers" for the mutant allele. It is now appreciated that most or all gene loci are highly polymorphic, with multiple alleles, whose frequencies vary from population to population, and that a great deal of genetic variation is hidden in the form of alleles that do not produce obvious phenotypic differences.


Multiple alleles

A population or
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
of organisms typically includes multiple alleles at each locus among various individuals. Allelic variation at a locus is measurable as the number of alleles ( polymorphism) present, or the proportion of heterozygotes in the population. A null allele is a gene variant that lacks the gene's normal function because it either is not expressed, or the expressed protein is inactive. For example, at the gene locus for the ABO
blood type A blood type (also known as a blood group) is a classification of blood, based on the presence and absence of antibody, antibodies and Heredity, inherited antigenic substances on the surface of red blood cells (RBCs). These antigens may be prot ...
carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may or may ...
antigen In immunology, an antigen (Ag) is a molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. ...
s in humans, classical genetics recognizes three alleles, IA, IB, and i, which determine compatibility of
blood transfusion Blood transfusion is the process of transferring blood products into a person's Circulatory system, circulation intravenously. Transfusions are used for various medical conditions to replace lost components of the blood. Early transfusions used w ...
s. Any individual has one of six possible
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleot ...
s (IAIA, IAi, IBIB, IBi, IAIB, and ii) which produce one of four possible
phenotype In genetics, the phenotype () is the set of observable characteristics or phenotypic trait, traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, dev ...
s: "Type A" (produced by IAIA homozygous and IAi heterozygous genotypes), "Type B" (produced by IBIB homozygous and IBi heterozygous genotypes), "Type AB" produced by IAIB heterozygous genotype, and "Type O" produced by ii homozygous genotype. (It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus. Hence an individual with "Type A" blood may be an AO heterozygote, an AA homozygote, or an AA heterozygote with two different "A" alleles.)


Genotype frequencies

The frequency of alleles in a diploid population can be used to predict the frequencies of the corresponding genotypes (see Hardy–Weinberg principle). For a simple model, with two alleles; : p + q=1 \, : p^2 + 2pq + q^2=1 \, where ''p'' is the frequency of one allele and ''q'' is the frequency of the alternative allele, which necessarily sum to unity. Then, ''p''2 is the fraction of the population homozygous for the first allele, 2''pq'' is the fraction of heterozygotes, and ''q''2 is the fraction homozygous for the alternative allele. If the first allele is dominant to the second then the fraction of the population that will show the dominant phenotype is ''p''2 + 2''pq'', and the fraction with the recessive phenotype is ''q''2. With three alleles: : p + q + r = 1 \, and : p^2 + q^2 + r^2 + 2pq + 2pr + 2qr = 1. \, In the case of multiple alleles at a diploid locus, the number of possible genotypes (G) with a number of alleles (a) is given by the expression: : G= \frac.


Allelic dominance in genetic disorders

A number of genetic disorders are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include
albinism Albinism is the congenital absence of melanin in an animal or plant resulting in white hair, feathers, scales and skin and pink or blue eyes. Individuals with the condition are referred to as albino. Varied use and interpretation of the term ...
,
cystic fibrosis Cystic fibrosis (CF) is a rare genetic disorder that affects mostly the lungs, but also the pancreas, liver, kidneys, and intestine. Long-term issues include Shortness of breath, difficulty breathing and coughing up sputum, mucus as a result of ...
, galactosemia,
phenylketonuria Phenylketonuria (PKU) is an inborn error of metabolism that results in decreased metabolism of the amino acid phenylalanine. Untreated PKU can lead to intellectual disability, seizures, behavioral problems, and mental disorders. It may also resu ...
(PKU), and Tay–Sachs disease. Other disorders are also due to recessive alleles, but because the gene locus is located on the X chromosome, so that males have only one copy (that is, they are
hemizygous Zygosity (the noun, zygote A zygote (, ) is a eukaryote, eukaryotic cell (biology), cell formed by a fertilization event between two gametes. The zygote's genome is a combination of the DNA in each gamete, and contains all of the genetic in ...
), they are more frequent in males than in females. Examples include red-green
color blindness Color blindness or color vision deficiency (CVD) is the decreased ability to color vision, see color or differences in color. It can impair tasks such as selecting ripe fruit, choosing clothing, and reading traffic lights. Color blindness may ...
and
fragile X syndrome Fragile X syndrome (FXS) is a genetic disorder characterized by mild-to-moderate intellectual disability. The average Intelligence quotient, IQ in males with FXS is under 55, while about two thirds of affected females are intellectually disabled. ...
. Other disorders, such as
Huntington's disease Huntington's disease (HD), also known as Huntington's chorea, is a neurodegenerative disease that is mostly Genetic disorder#Autosomal dominant, inherited. The earliest symptoms are often subtle problems with mood or mental abilities. A gener ...
, occur when an individual inherits only one dominant allele.


Epialleles

While heritable traits are typically studied in terms of genetic alleles,
epigenetic In biology, epigenetics is the study of stable phenotypic changes (known as ''marks'') that do not involve alterations in the DNA sequence. The Ancient Greek, Greek prefix ''wikt:epi-, epi-'' ( "over, outside of, around") in ''epigenetics'' imp ...
marks such as
DNA methylation DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter (genetics), promoter, DNA methylati ...
can be inherited at specific genomic regions in certain species, a process termed transgenerational epigenetic inheritance. The term ''epiallele'' is used to distinguish these heritable marks from traditional alleles, which are defined by nucleotide sequence. A specific class of epiallele, the metastable epialleles, has been discovered in mice and in humans which is characterized by stochastic (probabilistic) establishment of epigenetic state that can be mitotically inherited.


Idiomorph

The term “idiomorph”, from Greek ‘morphos’ (form) and ‘idio’ (singular, unique), was introduced in 1990 in place of “allele” to denote sequences at the same locus in different strains that have no sequence similarity and probably do not share a common phylogenetic relationship. It is used mainly in the genetic research of mycology.


See also


References and notes


External links


ALFRED: The ALlele FREquency Database
{{Genetics Classical genetics Genetic genealogy