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Allele

January 26, 2023

An allele (UK: /ˈæliːl/, /əˈliːl/; US: /əˈliːl/; modern formation from Greek ἄλλος állos, "other") is a variation of the same sequence of nucleotides 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."[1]

The simplest alleles are single nucleotide polymorphisms (SNP),[2] but they can also be insertions and deletions of up to several thousand base pairs.[3]

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, nearly every living human's phenotype for the ABO gene is some combination of just these six alleles.[4][5]

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 traits, such as different pigmentation. A notable example of this is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of a single gene with two alleles.

Nearly all multicellular organisms have two sets of chromosomes at some point in their biological life cycle; that is, they are diploid. 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 with respect to that gene. If the alleles are different, they, and the organism, are heterozygous 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 and Edith Rebecca Saunders),[6][7] which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes. It derives from the Greek prefix ἀλληλο-, allelo-, meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, allos (cognate with Latin alius), meaning "other".

Alleles that lead to dominant or recessive phenotypes

Main article: Dominance (genetics)

In many cases, genotypic interactions between the two alleles at a locus can be described as dominant or recessive, according to which of the two homozygous phenotypes the heterozygote most resembles. Where the heterozygote is indistinguishable from one of the homozygotes, the allele expressed is the one that leads to the "dominant" phenotype,[8][9] 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. However, many traits defy this simple categorization and the phenotypes are modeled by co-dominance and polygenic inheritance[10]

The term "wild type" 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). Such a "wild type" allele was historically regarded as leading to a dominant (overpowering – always expressed), common, and normal phenotype, in contrast to "mutant" 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, 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

 
 
 
 
Eye color is an inherited trait influenced by more than one gene, including OCA2 and HERC2. The interaction of multiple genes—and the variation in these genes ("alleles") between individuals—help to determine a person's eye color phenotype. Eye color is influenced by pigmentation of the iris and the frequency-dependence of the light scattering by the turbid medium within the stroma of the iris.
 
In the ABO blood group system, a person with Type A blood displays A-antigens and may have a genotype IAIA or IAi. A person with Type B blood displays B-antigens and may have the genotype IBIB or IBi. A person with Type AB blood displays both A- and B-antigens and has the genotype IAIB and a person with Type O blood, displaying neither antigen, has the genotype ii.

A population or species 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 carbohydrate antigens in humans,[11] classical genetics recognizes three alleles, IA, IB, and i, which determine compatibility of blood transfusions. Any individual has one of six possible genotypes (IAIA, IAi, IBIB, IBi, IAIB, and ii) which produce one of four possible phenotypes: "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.[12] 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

Main article: Allele frequency

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;

 
 

where p is the frequency of one allele and q is the frequency of the alternative allele, which necessarily sum to unity. Then, p2 is the fraction of the population homozygous for the first allele, 2pq is the fraction of heterozygotes, and q2 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 p2 + 2pq, and the fraction with the recessive phenotype is q2.

With three alleles:

  and
 

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:

 

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, cystic fibrosis, galactosemia, phenylketonuria (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), they are more frequent in males than in females. Examples include red-green color blindness and fragile X syndrome.

Other disorders, such as Huntington's disease, occur when an individual inherits only one dominant allele.

Epialleles

While heritable traits are typically studied in terms of genetic alleles, epigenetic marks such as DNA methylation 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.[13] 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.[14][15]

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.[16][17]

See also

References and notes

  1. ^ Graur, D (2016). Molecular and Genome Evolution. Sunderland MA (USA): Sinauer Associates, Inc.
  2. ^ Smigielski, Elizabeth M.; Sirotkin, Karl; Ward, Minghong; Sherry, Stephen T. (1 January 2000). "dbSNP: a database of single nucleotide polymorphisms". Nucleic Acids Research. 28 (1): 352–355. doi:10.1093/nar/28.1.352. ISSN 0305-1048. PMC 102496. PMID 10592272.
  3. ^ Elston, Robert; Satagopan, Jaya; Sun, Shuying (2012). "Genetic Terminology". Statistical Human Genetics. Methods in Molecular Biology (Clifton, N.J.). Vol. 850. pp. 1–9. doi:10.1007/978-1-61779-555-8_1. ISBN 978-1-61779-554-1. ISSN 1064-3745. PMC 4450815. PMID 22307690.
  4. ^ Seltsam A, Hallensleben M, Kollmann A, Blasczyk R (October 2003). "The nature of diversity and diversification at the ABO locus". Blood. 102 (8): 3035–42. doi:10.1182/blood-2003-03-0955. PMID 12829588.
  5. ^ Ogasawara K, Bannai M, Saitou N, Yabe R, Nakata K, Takenaka M, Fujisawa K, Uchikawa M, Ishikawa Y, Juji T, Tokunaga K (June 1996). "Extensive polymorphism of ABO blood group gene: three major lineages of the alleles for the common ABO phenotypes". Human Genetics. 97 (6): 777–83. doi:10.1007/BF02346189. PMID 8641696. S2CID 12076999.
  6. ^ Craft, Jude (2013). "Genes and genetics: the language of scientific discovery". Genes and genetics. Oxford English Dictionary. from the original on 29 January 2018. Retrieved 14 January 2016.
  7. ^ Bateson, W. and Saunders, E. R. (1902) "The facts of heredity in the light of Mendel’s discovery." Reports to the Evolution Committee of the Royal Society, I. pp. 125–160
  8. ^ Hartl, Daniel L.; Elizabeth W. Jones (2005). Essential genetics: A genomics perspective (4th ed.). Jones & Bartlett Publishers. p. 600. ISBN 978-0-7637-3527-2.
  9. ^ "ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy". G3. 7 (9): 2931–2943. September 2017. doi:10.1534/g3.117.044024. PMID 28696921.
  10. ^ "Allele". Genome.gov. from the original on 28 June 2021. Retrieved 3 July 2021.
  11. ^ Victor A. McKusick; Cassandra L. Kniffin; Paul J. Converse; Ada Hamosh (10 November 2009). "ABO Glycosyltransferase; ABO". Online Mendelian Inheritance in Man. National Library of Medicine. from the original on 24 September 2008. Retrieved 24 March 2010.
  12. ^ Yip SP (January 2002). "Sequence variation at the human ABO locus". Annals of Human Genetics. 66 (1): 1–27. doi:10.1017/S0003480001008995. PMID 12014997.
  13. ^ Daxinger, Lucia; Whitelaw, Emma (31 January 2012). "Understanding transgenerational epigenetic inheritance via the gametes in mammals". Nature Reviews Genetics. 13 (3): 153–62. doi:10.1038/nrg3188. PMID 22290458. S2CID 8654616.
  14. ^ Rakyan, Vardhman K; Blewitt, Marnie E; Druker, Riki; Preis, Jost I; Whitelaw, Emma (July 2002). "Metastable epialleles in mammals". Trends in Genetics. 18 (7): 348–351. doi:10.1016/S0168-9525(02)02709-9. PMID 12127774.
  15. ^ Waterland, RA; Dolinoy, DC; Lin, JR; Smith, CA; Shi, X; Tahiliani, KG (September 2006). "Maternal methyl supplements increase offspring DNA methylation at Axin Fused". Genesis. 44 (9): 401–6. doi:10.1002/dvg.20230. PMID 16868943. S2CID 36938621.
  16. ^ Glass, N. L.; Lee, L. (1992). "Isolation of Neurospora crassa a mating type mutants by repeat induced point (RIP) mutation". Genetics. 132: 125–133. doi:10.1093/genetics/132.1.125. PMC 1205111. PMID 1398049.
  17. ^ Metzenberg, Robert L.; Glass, N. Louise (1990). "Mating type and mating strategies in Neurospora". BioEssays. 12 (2): 53–59. doi:10.1002/bies.950120202. PMID 2140508. S2CID 10818930.

External links

 
Look up allele in Wiktionary, the free dictionary.
  • ALFRED: The ALlele FREquency Database

January 26, 2023
allele, allele, modern, formation, from, greek, ἄλλος, állos, other, variation, same, sequence, nucleotides, same, place, long, molecule, described, leading, textbooks, genetics, evolution, chromosomal, genomic, location, gene, other, genetic, element, called,. An allele UK ˈ ae l iː l e ˈ l iː l US e ˈ l iː l modern formation from Greek ἄllos allos other is a variation of the same sequence of nucleotides 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 1 dd The simplest alleles are single nucleotide polymorphisms SNP 2 but they can also be insertions and deletions of up to several thousand base pairs 3 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 nearly every living human s phenotype for the ABO gene is some combination of just these six alleles 4 5 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 traits such as different pigmentation A notable example of this is Gregor Mendel s discovery that the white and purple flower colors in pea plants were the result of a single gene with two alleles Nearly all multicellular organisms have two sets of chromosomes at some point in their biological life cycle that is they are diploid 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 with respect to that gene If the alleles are different they and the organism are heterozygous with respect to that gene Contents 1 Etymology 2 Alleles that lead to dominant or recessive phenotypes 3 Multiple alleles 4 Genotype frequencies 5 Allelic dominance in genetic disorders 6 Epialleles 7 Idiomorph 8 See also 9 References and notes 10 External linksEtymology EditThe word allele is a short form of allelomorph other form a word coined by British geneticists William Bateson and Edith Rebecca Saunders 6 7 which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes It derives from the Greek prefix ἀllhlo allelo meaning mutual reciprocal or each other which itself is related to the Greek adjective ἄllos allos cognate with Latin alius meaning other Alleles that lead to dominant or recessive phenotypes EditMain article Dominance genetics In many cases genotypic interactions between the two alleles at a locus can be described as dominant or recessive according to which of the two homozygous phenotypes the heterozygote most resembles Where the heterozygote is indistinguishable from one of the homozygotes the allele expressed is the one that leads to the dominant phenotype 8 9 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 However many traits defy this simple categorization and the phenotypes are modeled by co dominance and polygenic inheritance 10 The term wild type 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 Such a wild type allele was historically regarded as leading to a dominant overpowering always expressed common and normal phenotype in contrast to mutant 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 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 Edit Eye color is an inherited trait influenced by more than one gene including OCA2 and HERC2 The interaction of multiple genes and the variation in these genes alleles between individuals help to determine a person s eye color phenotype Eye color is influenced by pigmentation of the iris and the frequency dependence of the light scattering by the turbid medium within the stroma of the iris In the ABO blood group system a person with Type A blood displays A antigens and may have a genotype IAIA or IAi A person with Type B blood displays B antigens and may have the genotype IBIB or IBi A person with Type AB blood displays both A and B antigens and has the genotype IAIB and a person with Type O blood displaying neither antigen has the genotype ii A population or species 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 carbohydrate antigens in humans 11 classical genetics recognizes three alleles IA IB and i which determine compatibility of blood transfusions Any individual has one of six possible genotypes IAIA IAi IBIB IBi IAIB and ii which produce one of four possible phenotypes 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 12 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 EditMain article Allele frequency 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 displaystyle p q 1 p 2 2 p q q 2 1 displaystyle 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 p2 is the fraction of the population homozygous for the first allele 2pq is the fraction of heterozygotes and q2 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 p2 2pq and the fraction with the recessive phenotype is q2 With three alleles p q r 1 displaystyle p q r 1 andp 2 q 2 r 2 2 p q 2 p r 2 q r 1 displaystyle 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 a a 1 2 displaystyle G frac a a 1 2 Allelic dominance in genetic disorders EditA number of genetic disorders are caused when an individual inherits two recessive alleles for a single gene trait Recessive genetic disorders include albinism cystic fibrosis galactosemia phenylketonuria 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 they are more frequent in males than in females Examples include red green color blindness and fragile X syndrome Other disorders such as Huntington s disease occur when an individual inherits only one dominant allele Epialleles EditWhile heritable traits are typically studied in terms of genetic alleles epigenetic marks such as DNA methylation 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 13 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 14 15 Idiomorph EditThe 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 16 17 See also Edit Evolutionary biology portalAllozyme Evolution Genealogical DNA test Haploinsufficiency Meiosis Mendelian error Mendelian inheritance Mitosis Penetrance Polymorphism Punnett square Single nucleotide polymorphismReferences and notes Edit Graur D 2016 Molecular and Genome Evolution Sunderland MA USA Sinauer Associates Inc Smigielski Elizabeth M Sirotkin Karl Ward Minghong Sherry Stephen T 1 January 2000 dbSNP a database of single nucleotide polymorphisms Nucleic Acids Research 28 1 352 355 doi 10 1093 nar 28 1 352 ISSN 0305 1048 PMC 102496 PMID 10592272 Elston Robert Satagopan Jaya Sun Shuying 2012 Genetic Terminology Statistical Human Genetics Methods in Molecular Biology Clifton N J Vol 850 pp 1 9 doi 10 1007 978 1 61779 555 8 1 ISBN 978 1 61779 554 1 ISSN 1064 3745 PMC 4450815 PMID 22307690 Seltsam A Hallensleben M Kollmann A Blasczyk R October 2003 The nature of diversity and diversification at the ABO locus Blood 102 8 3035 42 doi 10 1182 blood 2003 03 0955 PMID 12829588 Ogasawara K Bannai M Saitou N Yabe R Nakata K Takenaka M Fujisawa K Uchikawa M Ishikawa Y Juji T Tokunaga K June 1996 Extensive polymorphism of ABO blood group gene three major lineages of the alleles for the common ABO phenotypes Human Genetics 97 6 777 83 doi 10 1007 BF02346189 PMID 8641696 S2CID 12076999 Craft Jude 2013 Genes and genetics the language of scientific discovery Genes and genetics Oxford English Dictionary Archived from the original on 29 January 2018 Retrieved 14 January 2016 Bateson W and Saunders E R 1902 The facts of heredity in the light of Mendel s discovery Reports to the Evolution Committee of the Royal Society I pp 125 160 Hartl Daniel L Elizabeth W Jones 2005 Essential genetics A genomics perspective 4th ed Jones amp Bartlett Publishers p 600 ISBN 978 0 7637 3527 2 ASPsiRNA A Resource of ASP siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy G3 7 9 2931 2943 September 2017 doi 10 1534 g3 117 044024 PMID 28696921 Allele Genome gov Archived from the original on 28 June 2021 Retrieved 3 July 2021 Victor A McKusick Cassandra L Kniffin Paul J Converse Ada Hamosh 10 November 2009 ABO Glycosyltransferase ABO Online Mendelian Inheritance in Man National Library of Medicine Archived from the original on 24 September 2008 Retrieved 24 March 2010 Yip SP January 2002 Sequence variation at the human ABO locus Annals of Human Genetics 66 1 1 27 doi 10 1017 S0003480001008995 PMID 12014997 Daxinger Lucia Whitelaw Emma 31 January 2012 Understanding transgenerational epigenetic inheritance via the gametes in mammals Nature Reviews Genetics 13 3 153 62 doi 10 1038 nrg3188 PMID 22290458 S2CID 8654616 Rakyan Vardhman K Blewitt Marnie E Druker Riki Preis Jost I Whitelaw Emma July 2002 Metastable epialleles in mammals Trends in Genetics 18 7 348 351 doi 10 1016 S0168 9525 02 02709 9 PMID 12127774 Waterland RA Dolinoy DC Lin JR Smith CA Shi X Tahiliani KG September 2006 Maternal methyl supplements increase offspring DNA methylation at Axin Fused Genesis 44 9 401 6 doi 10 1002 dvg 20230 PMID 16868943 S2CID 36938621 Glass N L Lee L 1992 Isolation of Neurospora crassa a mating type mutants by repeat induced point RIP mutation Genetics 132 125 133 doi 10 1093 genetics 132 1 125 PMC 1205111 PMID 1398049 Metzenberg Robert L Glass N Louise 1990 Mating type and mating strategies in Neurospora BioEssays 12 2 53 59 doi 10 1002 bies 950120202 PMID 2140508 S2CID 10818930 External links Edit Look up allele in Wiktionary the free dictionary ALFRED The ALlele FREquency Database Retrieved from https en wikipedia org w index php title Allele amp oldid 1134520770, wikipedia, wiki, book, books, library,

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