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 nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chro ...
s or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific gene depends on the number of copies of each
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 ...
found in that species, also referred to as
ploidy
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 diploid species like humans, two full sets of chromosomes are present, meaning each individual has two alleles for any given gene. If both alleles are the same, the genotype is referred to as
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 ...
. If the alleles are different, the genotype is referred to as heterozygous.
Genotype contributes to
phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...
, the observable traits and characteristics in an individual or organism. The degree to which genotype affects phenotype depends on the trait. For example, the
petal color
Biological pigments, also known simply as pigments or biochromes, are substances produced by living organisms that have a color resulting from selective color absorption. Biological pigments include plant pigments and flower pigments. Many biol ...
in a
pea plant
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 ...
is exclusively determined by genotype. The petals can be purple or white depending on the alleles present in the pea plant. However, other traits are only partially influenced by genotype. These traits are often called
complex traits
Complex traits, also known as quantitative traits, are traits that do not behave according to simple Mendelian inheritance laws. More specifically, their inheritance cannot be explained by the genetic segregation of a single gene. Such traits show ...
because they are influenced by additional factors, such as environmental and
epigenetic
In biology, epigenetics is the study of stable phenotypic changes (known as ''marks'') that do not involve alterations in the DNA sequence. The Greek prefix '' epi-'' ( "over, outside of, around") in ''epigenetics'' implies features that are "o ...
factors. Not all individuals with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have the same genotype.
The term ''genotype'' was coined by the
Danish
Danish may refer to:
* Something of, from, or related to the country of Denmark
People
* A national or citizen of Denmark, also called a "Dane," see Demographics of Denmark
* Culture of Denmark
* Danish people or Danes, people with a Danish a ...
botanist
Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek wo ...
Wilhelm Johannsen
Wilhelm Johannsen (3 February 1857 – 11 November 1927) was a Danish pharmacist, botanist, plant physiologist, and geneticist. He is best known for coining the terms gene, phenotype and genotype, and for his 1903 "pure line" experiments in gen ...
in 1903.
Phenotype
Any given gene will usually cause an observable change in an organism, known as the phenotype. The terms
genotype and phenotype are distinct for at least two reasons:
* To distinguish the source of an observer's knowledge (one can know about genotype by observing DNA; one can know about phenotype by observing outward appearance of an organism).
* Genotype and phenotype are not always directly correlated. Some genes only express a given phenotype in certain environmental conditions. Conversely, some phenotypes could be the result of multiple genotypes. The genotype is commonly mixed up with the phenotype which describes the end result of both the genetic and the environmental factors giving the observed expression (e.g. blue eyes, hair color, or various hereditary diseases).
A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see
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 Brà ...
). There are three available genotypes, PP (
homozygous dominant
In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and t ...
), Pp (heterozygous), and pp (homozygous recessive). All three have different genotypes but the first two have the same phenotype (purple) as distinct from the third (white).
A more technical example to illustrate genotype is the
single-nucleotide polymorphism
In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently lar ...
or SNP. A SNP occurs when corresponding sequences of
DNA from different individuals differ at one DNA base, for example where the sequence AAGCCTA changes to AAGCTTA. This contains two alleles : C and T. SNPs typically have three genotypes, denoted generically AA Aa and aa. In the example above, the three genotypes would be CC, CT and TT. Other types of
genetic marker A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be ...
, such as
microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
s, can have more than two alleles, and thus many different genotypes.
Penetrance is the proportion of individuals showing a specified genotype in their phenotype under a given set of environmental conditions.
Mendelian inheritance
Traits that are determined exclusively by genotype are typically inherited in a
Mendelian
Mendelian inheritance (also known as Mendelism) is a type of biology, biological Heredity, inheritance following the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 by Hugo de Vries and Carl Correns, an ...
pattern. These laws of inheritance were described extensively 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 Brà ...
, who performed experiments with pea plants to determine how traits were passed on from generation to generation.
He studied phenotypes that were easily observed, such as plant height, petal color, or seed shape.
He was able to observe that if he crossed two true-breeding plants with distinct phenotypes, all the offspring would have the same phenotype. For example, when he crossed a tall plant with a short plant, all the resulting plants would be tall. However, when he self-fertilized the plants that resulted, about 1/4 of the second generation would be short. He concluded that some traits were
dominant, such as tall height, and others were recessive, like short height. Though Mendel was not aware at the time, each phenotype he studied was controlled by a single gene with two alleles. In the case of plant height, one allele caused the plants to be tall, and the other caused plants to be short. When the tall allele was present, the plant would be tall, even if the plant was heterozygous. In order for the plant to be short, it had to be homozygous for the recessive allele.
One way this can be illustrated is using a
Punnett square
The Punnett square is a square diagram that is used to predict the genotypes of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach in 1905. The diagram is used by biologists to determine ...
. In a Punnett square, the genotypes of the parents are placed on the outside. An uppercase letter is typically used to represent the dominant allele, and a lowercase letter is used to represent the recessive allele. The possible genotypes of the offspring can then be determined by combining the parent genotypes. In the example on the right, both parents are heterozygous, with a genotype of Bb. The offspring can inherit a dominant allele from each parent, making them homozygous with a genotype of BB. The offspring can inherit a dominant allele from one parent and a recessive allele from the other parent, making them heterozygous with a genotype of Bb. Finally, the offspring could inherit a recessive allele from each parent, making them homozygous with a genotype of bb. Plants with the BB and Bb genotypes will look the same, since the B allele is dominant. The plant with the bb genotype will have the recessive trait.
These inheritance patterns can also be applied to
hereditary 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 ...
or conditions in humans or animals.
Some conditions are inherited in an
autosomal
An autosome is any chromosome that is not a sex chromosome. The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosome, allosomal (sex chromosome) pairs, which may have different structures. The DNA in au ...
dominant pattern, meaning individuals with the condition typically have an affected parent as well. A classic pedigree for an autosomal dominant condition shows affected individuals in every generation.
![Example autosomal dominant pedigree 01](https://upload.wikimedia.org/wikipedia/commons/9/9d/Example_autosomal_dominant_pedigree_01.png)
Other conditions are inherited in an autosomal recessive pattern, where affected individuals do not typically have an affected parent. Since each parent must have a copy of the recessive allele in order to have an affected offspring, the parents are referred to as carriers of the condition.
In autosomal conditions, the sex of the offspring does not play a role in their risk of being affected. In sex-linked conditions, the sex of the offspring affects their chances of having the condition. In humans, females inherit two
X chromosome
The X chromosome is one of the two sex-determining chromosomes (allosomes) in many organisms, including mammals (the other is the Y chromosome), and is found in both males and females. It is a part of the XY sex-determination system and XO sex-d ...
s, one from each parent, while males inherit an X chromosome from their mother and a Y chromosome from their father. X-linked dominant conditions can be distinguished from autosomal dominant conditions in pedigrees by the lack of transmission from fathers to sons, since affected fathers only pass their X chromosome to their daughters.
In X-linked recessive conditions, males are typically affected more commonly because they are hemizygous, with only one X chromosome. In females, the presence of a second X chromosome will prevent the condition from appearing. Females are therefore carriers of the condition and can pass the trait on to their sons.
![Example autosomal recessive pedigree](https://upload.wikimedia.org/wikipedia/commons/1/16/Example_autosomal_recessive_pedigree.png)
Mendelian patterns of inheritance can be complicated by additional factors. Some diseases show incomplete
penetrance
Penetrance in genetics is the proportion of individuals carrying a particular variant (or allele) of a gene (the genotype) that also express an associated trait (the phenotype). In medical genetics, the penetrance of a disease-causing mutation is t ...
, meaning not all individuals with the disease-causing allele develop signs or symptoms of the disease.
Penetrance can also be age-dependent, meaning signs or symptoms of disease are not visible until later in life. For example,
Huntington disease
Huntington's disease (HD), also known as Huntington's chorea, is a neurodegenerative disease that is mostly inherited. The earliest symptoms are often subtle problems with mood or mental abilities. A general lack of coordination and an unst ...
is an autosomal dominant condition, but up to 25% of individuals with the affected genotype will not develop symptoms until after age 50. Another factor that can complicate Mendelian inheritance patterns is variable
expressivity, in which individuals with the same genotype show different signs or symptoms of disease.
For example, individuals with
polydactyly
Polydactyly or polydactylism (), also known as hyperdactyly, is an anomaly in humans and animals resulting in supernumerary fingers and/or toes. Polydactyly is the opposite of oligodactyly (fewer fingers or toes).
Signs and symptoms
In humans ...
can have a variable number of extra digits.
Non-Mendelian inheritance
Many traits are not inherited in a Mendelian fashion, but have more complex patterns of inheritance.
Incomplete dominance
For some traits, neither allele is completely dominant. Heterozygotes often have an appearance somewhere in between those of homozygotes.
For example, a cross between true-breeding red and white ''
Mirabilis jalapa
''Mirabilis jalapa'', the marvel of Peru or four o'clock flower, is the most commonly grown ornamental species of ''Mirabilis'' plant, and is available in a range of colors. ''Mirabilis'' in Latin means wonderful and Jalapa (or Xalapa) is the st ...
'' results in pink flowers.
Codominance
Codominance refers to traits in which both alleles are expressed in the offspring in approximately equal amounts.
A classic example is the ABO blood group system in humans, where both the A and B alleles are expressed when they are present. Individuals with the AB genotype have both A and B proteins expressed on their red blood cells.
Epistasis
Epistasis is when the phenotype of one gene is affected by one or more other genes. This is often through some sort of masking effect of one gene on the other. For example, the "A" gene codes for hair color, a dominant "A" allele codes for brown hair, and a recessive "a" allele codes for blonde hair, but a separate "B" gene controls hair growth, and a recessive "b" allele causes baldness. If the individual has the BB or Bb genotype, then they produce hair and the hair color phenotype can be observed, but if the individual has a bb genotype, then the person is bald which masks the A gene entirely.
Polygenic traits
A polygenic trait is one whose phenotype is dependent on the additive effects of multiple genes. The contributions of each of these genes are typically small and add up to a final phenotype with a large amount of variation. A well studied example of this is the number of sensory bristles on a fly.
These types of additive effects is also the explanation for the amount of variation in human eye color.
Genotyping
Genotyping refers to the method used to determine an individual's genotype. There are a variety of techniques that can be used to assess genotype. The genotyping method typically depends on what information is being sought. Many techniques initially require amplification of the DNA sample, which is commonly done using
PCR.
Some techniques are designed to investigate specific SNPs or alleles in a particular gene or set of genes, such as whether an individual is a carrier for a particular condition. This can be done via a variety of techniques, including
allele specific oligonucleotide An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot bl ...
(ASO) probes or
DNA sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
.
Tools such as
multiplex ligation-dependent probe amplification
Multiplex ligation-dependent probe amplification (MLPA) is a variation of the multiplex polymerase chain reaction that permits amplification of multiple targets with only a single primer pair. It detects copy number changes at the molecular level, ...
can also be used to look for duplications or deletions of genes or gene sections.
Other techniques are meant to assess a large number of SNPs across the genome, such as
SNP array
In molecular biology, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the most frequent type of variation in the geno ...
s.
This type of technology is commonly used for
genome-wide association studies
In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any varia ...
.
Large-scale techniques to assess the entire genome are also available. This includes
karyotyping
A karyotype is the general appearance of the complete set of metaphase chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is disce ...
to determine the number of chromosomes an individual has and
chromosomal microarrays to assess for large duplications or deletions in the chromosome.
More detailed information can be determined using
exome sequencing
Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subse ...
, which provides the specific sequence of all DNA in the coding region of the genome, or
whole genome sequencing
Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a s ...
, which sequences the entire genome including non-coding regions.
See also
*
Endophenotype In genetic epidemiology, endophenotype (or intermediate phenotype) is a term used to separate behavioral symptoms into more stable phenotypes with a clear genetic connection. The concept was coined by Bernard John and Kenneth R. Lewis in a 1966 pap ...
*
Genotype–phenotype distinction
The genotype–phenotype distinction is drawn in genetics. " Genotype" is an organism's full hereditary information. "Phenotype" is an organism's actual observed properties, such as morphology, development, or behavior. This distinction is fund ...
*
Nucleic acid sequence
A nucleic acid sequence is a succession of Nucleobase, bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequence ...
*
Phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...
*
Sequence (biology)
A sequence in biology is the one-dimensional ordering of monomers, covalently linked within a biopolymer; it is also referred to as the primary structure of a biological macromolecule. While it can refer to many different molecules, the term seque ...
References
External links
Genetic nomenclature
{{Authority control
Genetics
Polymorphism (biology)
Biology
DNA sequencing