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The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the
alleles An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is one of two, or more, forms of a given gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance ...
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 genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and ...

chromosome
found in that species, also referred to as
ploidy Ploidy () is the number of complete sets of chromosome A chromosome is a long DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, wh ...
. 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 A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγοῦν ''zygoun'' "to join" or "to yoke") is a eukaryotic cell formed by a fertilization event between two gamete A gamete ( /ˈ ...
. If the alleles are different, the genotype is referred to as heterozygous. Genotype contributes to
phenotype In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular inter ...

phenotype
, 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 in a pea plant 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 Mendelian inheritance is a type of biological Biology is the natural science Natural science is a branch o ...
because they are influenced by additional factors, such as environmental and
epigenetic In biology, epigenetics is the study of heritability, heritable phenotype changes that do not involve alterations in the DNA sequence. The Ancient Greek, Greek prefix ''wikt:epi-, epi-'' ( "over, outside of, around") in ''epigenetics'' implies f ...
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 * A national or citizen of Denmark, also called a "Dane", see Demographics of Denmark * Danish people or Danes, people with a Danish ancestral or ethnic identity * Danis ...

Danish
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 ...

botanist
Wilhelm Johannsen Wilhelm Johannsen (3 February 1857 – 11 November 1927) was a Danish pharmacist, 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 i ...
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 (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a meteorologist, mathematician, biologist, AugustinianAugustinian may refer to: *Augustinians Augustinians are members of Christian religious orders th ...

Gregor Mendel
). There are three available genotypes, PP (
homozygous dominant In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactio ...
), 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 Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interacti ...
or SNP. A SNP occurs when corresponding sequences of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

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 In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ''generation'' or ''birth ...
, 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 is a type of biological inheritance Inheritance is the practice of passing on private property, titles A title is one or more words used before or after a person's name, in certain contexts. It may signify either ...

Mendelian
pattern. These laws of inheritance were described extensively by
Gregor Mendel Gregor Johann Mendel (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a meteorologist, mathematician, biologist, AugustinianAugustinian may refer to: *Augustinians Augustinians are members of Christian religious orders th ...

Gregor Mendel
, 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 Domination or dominant may refer to: Society * World domination, which is mainly a conspiracy theory * Colonialism in which one group (usually a nation) invades another region for material gain or to eliminate competition * Chauvinism in which a p ...
, 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. 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 In the fields of molecular biology and genetics, a genome is all genetic information of an organism. It consists of nucleotide sequences of DNA ( ...
or conditions in humans or animals. Some conditions are inherited in an
autosomal An autosome is any chromosome that is not a sex chromosome (an allosome). The members of an autosome pair in a diploid Ploidy () is the number of complete sets of chromosome A chromosome is a long DNA molecule with part or all of the ...
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. 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 chromosomes The X chromosome is one of the two sex-determining chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aid ...

X chromosomes
, 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. Mendelian patterns of inheritance can be complicated by additional factors. Some diseases show incomplete
penetrancePenetrance in genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian sc ...
, 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 A neurodegenerative disease is caused by the progressive loss of structure or function of neuron A neuron or nerve cell is an membrane potentia ...
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 body part, supernumerary fingers and/or toes. Polydactyly is the opposite of oligodactyly (fewer fingers or toes). Signs ...

polydactyly
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 Plants are mainly multicellular organisms, predominantly photosynthetic Photosynthesis is a process ...

Mirabilis jalapa
'' 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 Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete copies or partial copies) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a pa ...

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 oligonucleotideAn 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 A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic ...

DNA sequencing
. Tools such as multiplex ligation-dependent probe amplification 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 arrays. This type of technology is commonly used for
genome-wide association studies In genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian scientist a ...
. Large-scale techniques to assess the entire genome are also available. This includes
karyotyping Karyotyping is the process by which photographs of chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided ...

karyotyping
to determine the number of chromosomes an individual has and 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 Genomics is an interdisciplinary field of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structur ...
, 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 The structure of part of a DNA do ...
, which sequences the entire genome including non-coding regions.


See also

* Endophenotype *
Genotype–phenotype distinction The genotype–phenotype distinction is drawn in genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical proce ...
*
Nucleic acid sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, ...
*
Phenotype In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular inter ...

Phenotype
*
Sequence (biology) A sequence in biology is the one-dimensional ordering of monomers, covalently linked within a biopolymer Biopolymers are natural polymers produced by the cells of Organism, living organisms. Biopolymers consist of monomeric units that are Covale ...


References


External links


Genetic nomenclature
{{Authority control Genetics Polymorphism (biology) Biology DNA sequencing