Phenotype
In
Wilhelm Johannsen proposed the genotype–phenotype distinction in 1911 to make clear the difference between an organism's hereditary material and what that hereditary material produces.[4][5] The distinction resembles that proposed by August Weismann (1834–1914), who distinguished between germ plasm (heredity) and somatic cells (the body). More recently, in The Selfish Gene (1976), Dawkins distinguished these concepts as replicators and vehicles.
Definition
Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by Western blotting) and are thus part of the phenotype; human blood groups are an example. It may seem that this goes beyond the original intentions of the concept with its focus on the (living) organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits that can be made visible by some technical procedure.
The term "phenotype" has sometimes been incorrectly used as a shorthand for the phenotypic difference between a mutant and its wild type, which would lead to the false statement that a "mutation has no phenotype".[6]
Behaviors and their consequences are also phenotypes, since behaviors are observable characteristics. Behavioral phenotypes include cognitive, personality, and behavioral patterns. Some behavioral phenotypes may characterize psychiatric disorders[7] or syndromes.[8][9]
A phenome is the set of all traits expressed by a
Although phenome has been in use for many years, the distinction between the use of phenome and phenotype is problematic. A proposed definition for both terms as the "physical totality of all traits of an organism or of one of its subsystems" was put forth by Mahner and Kary in 1997, who argue that although scientists tend to intuitively use these and related terms in a manner that does not impede research, the terms are not well defined and usage of the terms is not consistent.[11]
Some usages of the term suggest that the phenome of a given organism is best understood as a kind of matrix of data representing physical manifestation of phenotype. For example, discussions led by A. Varki among those who had used the term up to 2003 suggested the following definition: "The body of information describing an organism's phenotypes, under the influences of genetic and environmental factors".[12] Another team of researchers characterize "the human phenome [as] a multidimensional search space with several neurobiological levels, spanning the proteome, cellular systems (e.g., signaling pathways), neural systems and cognitive and behavioural phenotypes."[13]
Plant biologists have started to explore the phenome in the study of plant physiology.[14]
In 2009, a research team demonstrated the feasibility of identifying genotype–phenotype associations using
Inspired by the evolution from genotype to genome to pan-genome, a concept of exploring the relationship ultimately among pan-phenome, pan-genome, and pan-envirome was proposed in 2023.[16]
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.[17]
The interaction between genotype and phenotype has often been conceptualized by the following relationship:
- genotype (G) + environment (E) → phenotype (P)
A more nuanced version of the relationship is:
- genotype (G) + environment (E) + genotype & environment interactions (GE) → phenotype (P)
Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions. The plant Hieracium umbellatum is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy with broad leaves and expanded inflorescences; the other is among sand dunes where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine the phenotype that grows.[18]
An example of random variation in
The concept of phenotype can be extended to variations below the level of the
The extended phenotype
Other biologists broadly agree that the extended phenotype concept is relevant, but consider that its role is largely explanatory, rather than assisting in the design of experimental tests.[20]
Genes and phenotypes
Phenotypes are determined by an interaction of genes and the environment, but the mechanism for each gene and phenotype is different. For instance, an albino phenotype may be caused by a mutation in the gene encoding tyrosinase which is a key enzyme in melanin formation. However, exposure to UV radiation can increase melanin production, hence the environment plays a role in this phenotype as well. For most complex phenotypes the precise genetic mechanism remains unknown. For instance, it is largely unclear how genes determine the shape of bones or the human ear.[citation needed]
Gene expression plays a crucial role in determining the phenotypes of organisms. The level of gene expression can affect the phenotype of an organism. For example, if a gene that codes for a particular enzyme is expressed at high levels, the organism may produce more of that enzyme and exhibit a particular trait as a result. On the other hand, if the gene is expressed at low levels, the organism may produce less of the enzyme and exhibit a different trait.[22]
Gene expression is regulated at various levels and thus each level can affect certain phenotypes, including transcriptional and post-transcriptional regulation.
Changes in the levels of gene expression can be influenced by a variety of factors, such as environmental conditions, genetic variations, and epigenetic modifications. These modifications can be influenced by environmental factors such as diet, stress, and exposure to toxins, and can have a significant impact on an individual's phenotype. Some phenotypes may be the result of changes in gene expression due to these factors, rather than changes in genotype. An experiment involving machine learning methods utilizing gene expression measured from RNA sequencing can contain enough signal to separate individuals in the context of phenotype prediction.[23]
Phenome and phenomics
Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word
Phenomics has applications in agriculture. For instance, genomic variations such as drought and heat resistance can be identified through phenomics to create more durable GMOs.[28][29]
Phenomics may be a stepping stone towards
Large-scale phenotyping and genetic screens
Large-scale genetic screens can identify the genes or mutations that affect the phenotype of an organism. Analyzing the phenotypes of mutant genes can also aid in determining gene function.[31] Most genetic screens have used microorganisms, in which genes can be easily deleted. For instance, nearly all genes have been deleted in E. coli[32] and many other bacteria, but also in several eukaryotic model organisms such as baker's yeast[33] and fission yeast.[34] Among other discoveries, such studies have revealed lists of essential genes .
More recently, large-scale phenotypic screens have also been used in animals, e.g. to study lesser understood phenotypes such as behavior. In one screen, the role of mutations in mice were studied in areas such as learning and memory, circadian rhythmicity, vision, responses to stress and response to psychostimulants.
Phenotypic Domain | Assay | Notes | Software Package |
---|---|---|---|
Circadian Rhythm | Wheel running behavior | ClockLab | |
Learning and Memory | Fear conditioning | Video-image-based scoring of freezing | FreezeFrame |
Preliminary Assessment | Open field activity and elevated plus maze | Video-image-based scoring of exploration | LimeLight |
Psychostimulant response | Hyperlocomotion behavior | Video-image-based tracking of locomotion | BigBrother |
Vision | Electroretinogram and Fundus photography | L. Pinto and colleagues |
This experiment involved the progeny of mice treated with ENU, or N-ethyl-N-nitrosourea, which is a potent mutagen that causes point mutations. The mice were phenotypically screened for alterations in the different behavioral domains in order to find the number of putative mutants (see table for details). Putative mutants are then tested for heritability in order to help determine the inheritance pattern as well as map out the mutations. Once they have been mapped out, cloned, and identified, it can be determined whether a mutation represents a new gene or not.
Phenotypic domain | ENU Progeny screened | Putative mutants | Putative mutant lines with progeny | Confirmed mutants |
---|---|---|---|---|
General assessment | 29860 | 80 | 38 | 14 |
Learning and memory | 23123 | 165 | 106 | 19 |
Psychostimulant response | 20997 | 168 | 86 | 9 |
Neuroendocrine response to stress | 13118 | 126 | 54 | 2 |
Vision | 15582 | 108 | 60 | 6 |
These experiments showed that mutations in the
Evolutionary origin of phenotype
The
See also
- Bioinformatics
- Ecotype
- Endophenotype
- Genotype–phenotype distinction
- Molecular phenotyping
- Phenomics
- Physiome
- Physiomics
- Race and genetics
- Systems biology
- List of omics topics in biology
References
- ^ "Phenotype adjective – Definition, pictures, pronunciation and usage notes". Oxford Advanced Learner's Dictionary at OxfordLearnersDictionaries.com. Retrieved 2020-04-29.
the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.
- ^ "Genotype versus phenotype". Understanding Evolution. Retrieved 2020-04-29.
An organism's genotype is the set of genes that it carries. An organism's phenotype is all of its observable characteristics — which are influenced both by its genotype and by the environment.
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