27th October 2020
What is an Allele

Concept of Gene: Allele, Multiple Alleles, Pseudoallele, Complementation Tests

Physiological, Psychological, and even behavioral characteristics are amazingly controlled by genes. Genes are contained in chromosomes and are segments of DNA that code for specific proteins responsible for specific functions. These specific functions can be of variable nature which arises due to alleles of a specific gene.

What is an Allele?

The term ‘allele’ is used for describing a variety of genes. Commonly allele is a gene’s variant (1). The definition of an allele is the one version of two or more varieties of a gene mutation at the same position as a chromosome.

Mostly in multicellular organisms, two sets of chromosomes are present (diploid). In the diploid individual, for a single gene, two alleles are inherited, one from the mother and another from the father. Chromosomes are paired; each pair contributes a set of homologous chromosomes. If both alleles of a single gene present on the same locus of a homologous chromosome, the organism is known as homozygous for that particular gene, if they are different then heterozygous.

Different alleles of a gene are responsible for providing different varieties of a single trait such as different eye color, different skin color, different colors of the flower, etc. Some alleles also show little or no observable phenotypic differences.

In a locus, allelic interaction can be seen as either dominant or recessive. When phenotypic expression of heterozygote allele does not show any difference from homozygote, in that condition expressed alleles leads to produce dominant character (2) and which is not expressed is recessive.

Allele Vs Gene

Genes are basically a part of DNA that is responsible for determining certain characteristics. Different types of proteins are encoded by a gene that influences different traits like the pigmentation of the skin, eye color, and hormone production, etc. From parent to offspring, genetic materials are inherited by the help of a gene. An available entire set of genes are denoted as an organism’s genotype. For example, every person has a unique genotype, as a result, vast distinguishable traits are observed.

Gene Vs Allele
Fig: Gene Vs Allele

When mutation takes place in a gene, it can provide multiple varieties of a single gene which causes slight differences in DNA base sequence. These varieties of a gene encode the identical trait but they differ in the expression pattern of the trait. These different varieties of a gene are known as alleles. A gene may have two or more alleles. A greater the allele number represents more diversity in a characteristic given by a gene.

Gene is a portion of DNA that contributes genotype of an individual trait. Allele contributes to diversity in phenotype.

Example of Alleles

Example of Alleles
Fig: Example of allele, Source: Wikipedia Common

As plants reproduce sexually, so two alleles are available for a particular trait such as the flower color of a green pea that may occur between purple and white. A gene is responsible for this flower color which produces the enzyme for generating such type of color. Whether one functional allele is present, it gives purple color but when both are nonfunctional alleles then the white color is observed. The previous allele is termed as dominant as it is present only one still it can mask the effect of another allele. Both nonfunctional alleles are known as recessive.

How to Calculation Allele Frequency

Allele frequency is expressed in percentage or infraction which describes as the relative frequency in a population; at a particular locus (3). Allele frequency can be changed within a population over time by microevolution. Allele frequency can be calculated from genotype frequency (3). Calculation of allele frequency is utilized for assessing the genetic diversity at a particular locus or multiple loci in the field of population genetics.

How to Calculation Allele Frequency
Fig: Calculation Allele Frequency

What are Multiple Alleles

Many alleles of a gene are produced by a genetic mutation. If at least two alleles are present in a gene then it is recognized as polymorphic. If more than two alleles may exist, this is known as multiple allele conditions. These three or more variations of a gene (allele) have the ability to occupy the same locus but among all only two alleles can be present in an organism.

A classic example of multiple alleles is ABO blood group system in humans. It is controlled by three alleles. Among them, only two are present in an individual. In the human ABO system 3 alleles are – IA, IB, I0 (I=isohaemagglutinin). IA and IB allele can act codominant by producing A type and B type antigen which are present on RBC’s surface whereas I0 does not produce any antigen, it is a recessive allele. For the presence of these 3 alleles, different possible genotypes can be achieved by combining them in different ways. As an outcome blood groups A, B, AB, and O are found.

In the case of multiple alleles, possible genotypes can be calculated by a formula – n (n+1) /2. Here ‘n’ denotes the number of alleles of a gene.

Suppose 3 alleles of a gene P, Q, R are present. Then what is the possible number of genotypes?

  • Formula is n (n+1)/2 = 3*4/2 =6. So the possible genotype number is six and these are PP, QQ, RR, PQ, PR, QR.

Another example is the HLA (Human Leukocyte Associated Gene) gene. HLA genes encode antigen which is present in the cell of humans responsible for generating immune responses. These are also known as the MHC gene (major histocompatibility genes) which play an important role in transplanted organ rejection. A higher degree of polymorphism is observed in these HLA genes. There may be almost 100 different alleles are present in a locus. That’s the reason for the mismatching possibility of donor and recipient MHC during transplantation. So rejection is mostly found (4).

Traits with Multiple Alleles

  • The best example of it is ABO blood group system. Other traits that are controlled by multiple alleles – hair texture, eye color, hair color, physical structure, etc.
  • Multiple allele study is mainly done in a population.
  • These alleles are located in a single locus of a chromosome.
  • No crossing over occurs between these multiple alleles because crossing over takes place in two different genes, not in a single gene. As multiple alleles are present in the same gene so no crossing over.
  • Only a single trait is influenced by multiple alleles.
  • Multiple alleles do not show complementation to each other. So by using the complementation test allelic and non-allelic genes can be differentiated.
  • The wild type alleles are almost always dominant whereas mutant alleles may show dominance as well as an intermediate phenotypic pattern.
  • When any two of the multiple alleles are crossed then found phenotype is mutant type. In the F2 generation, the cross shows a typical monohybrid ratio for the specific character.


A state in which two genes having similar functions are so closely situated to eat other that it seems like both are genetically linked – this is called pseudoallelism (5,6) and the genes are termed as pseudoallele.

Due to their close location they always inherited together and do the same function so mistakenly they are recognized as a single gene. These two genes can be recombined and can be separated also but in rare cases. There is a hypothetical explanation regarding pseudoalle formation – which is gene duplication and farther evolution.

Features of Pseudoallele

  • Very closely linked allele.
  • Unction on the same character.
  • They show a lower frequency of genetic recombination by crossover.
  • They have the capability for displaying cis- Trans effect where trans heterozygote exhibits a mutant phenotype but heterozygote in cis form exhibits a wild-type phenotype.

For Example

Drosophila’s red eye has different variants like white, apricot by different pigmentation. They affect the same character which is eye color so they are allele but recombination can occur in between them, so non-allelic.

Another common example is the Lozenge eye in Drosophila.

What is Complementation Test

It was developed by Edward B Lewis, an American geneticist. Complementation test genetics is also known as the Cis-trans test.

Mutation in many genes can provide a similar phenotypic pattern. Cis-trans test is mainly used to test whether the mutation is present in two different genes or in the same gene. If the mutation occurs in the same gene, complementation will not found. If a mutation occurs in different genes then only complementation occurs. This test is used to find out how many genes are defined by a test of mutations that can express the same mutant phenotype.

What is Cis –Heterozygote?

It is the condition when mutant alleles are present on the same chromosome and wild type alleles are present on the homologous chromosomes.

What is Trans-Heterozygote?

It is a condition when one of the two mutant alleles are present on one chromosome and another present on its homologous chromosome.

Fig: Heterozygote



 Two mutant strains of Drosophila melanogaster display black and grey-yellow (wild type) body color. When both strains were crossed all F1 progeny showed wild type grey-yellow body color as the complementation was occurred in between two genes responsible for body color determination.

Recessive autosomal gene, ebony (e) if present as homozygous then it produces black body color. In another autosome, a different recessive gene, black (b) also produces black body color when homozygous. This is found when parents are homozygous. Their genotype is e/e b+/b+ & e+/e+ b/b which is in trans configuration.

Complementation of Two Mutant Genes
Fig: Complementation of Two Mutant Genes


If wild type phenotype is found then it is concluded that two mutations are complementing each other. If the mutant phenotype is observed then it can be said that mutations are not showing complementation and must be in the same unit of function.

Genetic Complementation

When different gene mutation gives similar phenotypic features is known as genetic heterogeneity and by the mating of two organisms having similar mutant phenotype can form wild type offspring is called genetic complementation.

Complementation Genetics Example

White eye color due to autosomal recessive mutation which manifests interruption in the step of pigment production. But when mating is done between them, it produces a hybrid red-eye strain.


Genetic Complementation
Fig: Genetic Complementation
Genetic Complementation Group
Fig: Genetic Complementation Group


  1. Wood EJ (1995). The encyclopedia of molecular biology. Biochemical education. 23(3).
  2. Hartl, Daniel L; Elizabeth W. Jones (2005). Essential genetics: Agenomics perspective (4th ed). Jones & Bartlett Publishers, p-600. ISBN- 978-0-7637-3527-2.
  3. Gilliespic, John H. (2004). Population Genetics: a concise guide (2nd ed) Baltimore, Md: The Johns Hopkins University Press.
  4. Alberts. Bruce et al. Molecular Biology of the Cell, 4th ed. New York, Garland, 2002.
  5. Morange M (2015).Pseudoallele & Gene Complexes. The search for the elusive link between genome structure and gene function. Perspective in Biology and Medicine. 58(2):196-204.
  6. Welshons WJ, Von Halle ES (1962). Pseudoallelism at the notch locus in Drosophila. Genetics. 47:743-59.

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