Genotype
Phenotype
Genotype-Phenotype Distinction

In biology, the genotype is the genetic constitution of an individual organism, often contrasted with phenotype.

In biology, the phenotype is the observable characteristics of an individual resulting from the interaction of its genotype with the environment.

Here the relation between genotype and phenotype is illustrated for the character of petal colour in pea. The letters B and b represent genes for colour and the pictures show the resultant flowers.

The genotype is the genetic constitution of an individual, that is the specific allele makeup of the individual, usually with reference to a specific character under consideration ^[1]. For instance, the human albino gene has two allelic forms, dominant A and recessive a, and there are three possible genotypes- AA (homozygous dominant), Aa (heterozygous), and aa (homozygous recessive).

It is a generally accepted theory that inherited genotype, transmitted epigenetic factors, and non-hereditary environmental variation contribute to the phenotype of an individual.

Non-hereditary DNA mutations are not classically understood as representing the individuals' genotype. Hence, scientists and doctors sometimes talk for example about the (geno)type of a particular cancer, that is the genotype of the disease as distinct from the diseased.

Genotype and genomic sequence

Main article: Genome

One's genotype differs subtly from one's genomic sequence. A sequence is an absolute measure of base composition of an individual, or a representative of a species or group; a genotype typically implies a measurement of how an individual differs or is specialized within a group of individuals or a species. So typically, one refers to an individual's genotype with regard to a particular gene of interest and, in polyploid individuals, it refers to what combination of alleles the individual carries (see homozygous, heterozygous).

Genotype and phenotype

Main article: 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:

1. 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).
2. 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 colour, or various hereditary diseases).

A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see Gregor Mendel). There are three available genotypes, PP (homozygous dominant), 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 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, such as microsatellites, can have more than two alleles, and thus many different genotypes.

Genotype and Mendelian inheritance

Main article: Mendelian inheritance

The distinction between genotype and phenotype is commonly experienced when studying family patterns for certain hereditary diseases or conditions, for example, haemophilia. Due to the diploidy of humans (and most animals), there are two alleles for any given gene. These alleles can be the same (homozygous) or different(heterozygous), depending on the individual (see zygote). With a dominant allele, the offspring is guaranteed to inherit the trait in question irrespective of the second allele. With a recessive allele, the phenotype depends upon the other allele. In the case of haemophilia and similarly recessive diseases a heterozygous individual is a carrier. This person has a normal phenotype but runs a 50-50 risk of passing his or her abnormal gene on to offspring. A homozygous recessive individual has a normal phenotype and no risk of abnormal offspring. A homozygous dominant individual has an abnormal phenotype and is guaranteed to pass the abnormal gene onto offspring.

Genotype and genetics

Main article: Genetics

With careful experimental design, one can use statistical methods to correlate differences in the genotypes of populations with differences in their observed phenotype. These genetic association studies can be used to determine the genetic risk factors associated with a disease. They may even be able to differentiate between populations who may or may not respond favorably to a particular drug treatment. Such an approach is known as personalized medicine or pharmacogenetics.

Genotype and mathematics

Main articles: Genetic programming and evolutionary algorithm

Inspired by the biological concept and usefulness of genotypes, computer science employs simulated phenotypes in genetic programming and evolutionary algorithms. Such techniques can help evolve mathematical solutions to certain types of otherwise difficult problems.

Determining Genotype

Main article: Genotyping

Genotyping is the process of ellucidating the genotype of an individual with a biological assay. Also known as a genotypic assay, techniques include PCR, DNA fragment analysis, ASO probes, sequencing, and nucleic acid hybridization to microarrays or beads. Several common genotyping techniques include Restriction Fragment Length Polymorphism (RFLP), Terminal Restriction Fragment Length Polymorphism (t-RFLP)[1], Amplified Fragment Length Polymorphisms (AFLP)[2], and Multiplex Ligation-dependent Probe Amplification (MLPA)[3]. DNA fragment analysis can also be used to determine such disease causing genetics aberrations as Microsatellite Instability (MSI)[4], Trisomy [5] or Aneuploidy, and Loss of Heterozygosity (LOH)[6]. MSI and LOH in particular have been associated with cancer cell genotypes for colon, breast, and cervical cancer. The most common chromosomal aneuploidy is a trisomy of chromosome 21 which manifests itself as Down Syndrome. Current technological limitations typically allow only a fraction of an individual’s genotype to be determined efficiently. Typical results for PCR genotyping can be found at GeneTyper, a company that offers PCR genotyping service.

See also

• phenotype

References

1. ^ wiktionary:genotype retrieved 2007-Apr-22

Individuals in the mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes.

A phenotype is any observed quality of an organism, such as its morphology, development, or behavior, as opposed to its genotype - the inherited instructions it carries, which may or may not be expressed. This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces.^[1][2] The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). A more modern version is Francis Crick's Central dogma of molecular biology.

Despite its seemingly straightforward definition, the concept of the phenotype has some hidden subtleties. First, most of the molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet are part of the phenotype. Human blood groups are an example. So, by extension, the term phenotype must include characteristics that can be made visible by some technical procedure. A further, and more radical, extension would add inherited behaviour to the phenotype.

Biston betularia morpha typica, the standard light-coloured Peppered Moth.

Biston betularia morpha carbonaria, the melanic Peppered Moth, illustrating discontinuous variation.

Second, the phenotype is not simply a product of the genotype, but is influenced by the environment to a greater or lesser extent (see also phenotypic plasticity). And, further, if the genotype is defined narrowly, then it must be remembered that not all heredity is carried by the nucleus. For example, mitochondria transmit their own DNA directly, not via the nucleus, though they divide in unison with the nucleus.

The phenotype is composed of traits or characteristics ^[3]. Some phenotypes are controlled entirely by the individual's genes. Others are controlled by genes but are significantly affected by extragenetic or environmental factors. Almost all humans inherit the capacity to speak and understand language, but which language they learn is entirely an environmental matter.

Phenotypic variation

Phenotypic variation (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.

The interaction between genotype and phenotype has often been conceptualized by the following relationship:

genotype + environment → phenotype

A slightly more nuanced version of the relationships is:

genotype + environment + random-variation → phenotype

An example of random variation in Drosophila flies is the number of ommatidia, which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.

A phenotype is any detectable characteristic of an organism (i.e., structural, biochemical, physiological, and behavioral) determined by an interaction between its genotype and environment (of this distinction).

According to the autopoietic notion of living systems by Humberto Maturana, the phenotype is epigenetically being constructed throughout ontogeny, and we as observers make the distinctions that define any particular trait at any particular state of the organism's life cycle.

The idea of the phenotype has been generalized by Richard Dawkins in The Extended Phenotype to mean all the effects a gene has on the outside world that may influence its chances of being replicated. These can be effects on the organism in which the gene resides, the environment, or other organisms. For instance, a beaver dam might be considered a phenotype of beaver genes, the same way beaver's powerful incisor teeth are phenotype expressions of their genes.

The concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, silent mutations that do not change the corresponding amino acid sequence of a gene may change the frequency of guanine-cytosine base pairs (GC content). These base pairs have a higher thermal stability (melting point, see also DNA-DNA hybridization) than adenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.

References

1. ^ Churchill F.B. 1974. William Johannsen and the genotype concept. J History of Biology 7, 5-30.
2. ^ Johannsen W. 1911. The genotype conception of heredity. American Naturalist 45, 129-159
3. ^ Sydney Brenner and Jeffrey H. Miller. 2002. Encyclopedia of Genetics San Diego: Academic Press.

See also

• Phenome
• Genotype

The genotype-phenotype distinction is drawn in genetics. "Genotype" is an organism's full hereditary information, even if not expressed. "Phenotype" is an organism's actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution.

The genotype represents its exact genetic makeup — the particular set of genes it possesses. Two organisms whose genes differ at even one locus (position in their genome) are said to have different genotypes. The transmission of genes from parents to offspring is under the control of precise molecular mechanisms. The discovery of these mechanisms and their manifestations began with Mendel and comprises the field of genetics.

It is the organism's physical properties that directly determine its chances of survival and reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of the inheritance of genes Therefore, to properly understand the theory of evolution via natural selection, one must understand the genotype-phenotype distinction.

The mapping of a set of genotypes to a set of phenotypes is sometimes referred to as the genotype-phenotype map.

An organism's genotype is a major (the largest by far for morphology) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical.

The concept of phenotypic plasticity describes the degree to which an organism's phenotype is determined by its genotype. A high level of plasticity means that environmental factors have a strong influence on the particular phenotype that develops. If there is little plasticity, the phenotype of an organism can be reliably predicted from knowledge of the genotype, regardless of environmental peculiarities during development. An example of high plasticity can be observed in larval newts¹: when these larvae sense the presence of predators such as dragonflies, they develop larger heads and tails relative to their body size and display darker pigmentation. Larvae with these traits have a higher chance of survival when exposed to the predators, but grow more slowly than other phenotypes.

In contrast to phenotypic plasticity, the concept of genetic canalization addresses the extent to which an organism's phenotype allows conclusions about its genotype. A phenotype is said to be canalized if mutations (changes in the genome) do not noticeably affect the physical properties of the organism. This means that a canalized phenotype may form from a large variety of different genotypes, in which case it is not possible to exactly predict the genotype from knowledge of the phenotype (i.e. the genotype-phenotype map is not invertible). If canalization is not present, small changes in the genome have an immediate effect on the phenotype that develops.

The terms "genotype" and "phenotype" were created by Wilhelm Johannsen in 1911.

Bibliography

1. J. Van Buskirk and B. R. Schmidt, "Predator-induced Phenotypic Plasticity in Larval Newts: Trade-offs, Selection, and Variation in Nature," Ecology 81 (2000): 3009-3028.

External links

• Stanford Encyclopedia of Philosophy entry