Theshells of individuals within thebivalvemollusk speciesDonax variabilis show diversecoloration andpatterning in their phenotypes.Here the relation betweengenotype and phenotype is illustrated, using aPunnett square, for the character of petal color in pea plants. The letters B and b representgenes for color, and the pictures show the resultant phenotypes. This shows how multiple genotypes (BB and Bb) may yield the same phenotype (purple petals).
Ingenetics, thephenotype (from Ancient Greekφαίνω (phaínō)'to appear, show' and τύπος (túpos)'mark, type') is the set of observable characteristics ortraits of anorganism.[1][2] The term covers all traits of an organism other than itsgenome, however transitory: the organism'smorphology (physical form and structure), itsdevelopmental processes, its biochemical and physiological properties whether reversible or irreversible, and all itsbehavior, from a peacock's display to the phone number you half remember.[3] An organism's phenotype results from two basic factors: theexpression of an organism's unique profile of genes (itsgenotype) and the influence of environmental factors experienced by that same organism which influence the variable expression of said genes, and thereby shape the resulting profile of defining traits. Since the developmental process is a complex interplay of gene-environment, gene-gene interactions, there is a high degree of phenotypic variation in a given population that extends beyond mere genotypic variation.
A well-documented example of polymorphism isLabrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown.Richard Dawkins in 1978[4] and again in his 1982 bookThe Extended Phenotype suggested that one can regardbird nests and other built structures such ascaddisfly larva cases andbeaver dams as "extended phenotypes".
Wilhelm Johannsen proposed thegenotype–phenotype distinction in 1911 to make clear the difference between an organism'shereditary material and 'all the typical phenomena of the organic world', the description of which, with regard 'to forms, structures, sizes, colors and other characters of the living organisms has been the chief aim of natural history'.[5][6] The distinction somewhat resembles that proposed byAugust Weismann (1834–1914), who distinguished betweengerm plasm (heredity) andsomatic cells (the body). More recently inThe Selfish Gene (1976), Dawkins redescribed these concepts as replicators and vehicles.
"Phenome" redirects here. For the speech unit, seePhoneme.
Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on thegenotype is a phenotype, includingmolecules such asRNA andproteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example byWestern blotting) and are thus part of the phenotype; humanblood 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.[citation needed]
ABO blood groups determined through a Punnett square and displaying phenotypes and genotypes
The term "phenotype" has sometimes been incorrectly used as a shorthand for the phenotypic difference between a mutant and itswild type, which would lead to the false statement that a"mutation has no phenotype".[7]
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[8] or syndromes.[9][10]
Aphenome is the set of all traits expressed by acell,tissue,organ,organism, orspecies. The term was first used by Davis in 1949, "We here propose the namephenome for the sum total of extragenic, non-autoreproductive portions of the cell, whether cytoplasmic or nuclear. The phenome would be the material basis of the phenotype, just as the genome is the material basis of thegenotype."[11] 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.[12]
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".[13] 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."[14] Plant biologists have begun to explore the phenome in the study of plant physiology.[15] In 2009, a research team demonstrated the feasibility of identifying genotype–phenotype associations usingelectronic health records (EHRs) linked to DNAbiobanks. They called this methodphenome-wide association study (PheWAS).[16]
Exploring relationships among phenotype, genotype and environment at different levels[17]
Inspired by the evolution from genotype to genome topan-genome, a concept of eventually exploring the relationship among pan-phenome,pan-genome, and pan-envirome was proposed in 2023.[17]
Biston betularia morphatypica, the standard light-colored peppered mothB.betularia morphacarbonaria, the melanic form, illustrating discontinuous variation
Phenotypic variation is a fundamental prerequisite forevolution bynatural selection. Not all phenotypic variation is caused by underlying heritablegenetic variation. This is because the organization of living things is 'plastic', as Darwin emphasized, or 'readily capable of change.'[18] It is the living organism as a whole that interacts with the environment and so contributes (or not) to the next generation. Thus, natural selection affects the genetic structure of a populationindirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.[19]
The interaction between genotype and phenotype has often been conceptualized without reference to living organisms, as in the following relationship:
genotype (G) + environment (E) → phenotype (P)
But a genotype can only be affected by or affect the environment insofar as it is embodied in a living organism. Hence, a more nuanced version of the relationship is:
Phenotypes often show much flexibility orphenotypic plasticity in the expression of genotypes; in many organisms the phenotypes which 'express' a given genotype are very different under varying environmental conditions. The plantHieracium umbellatum is found growing in two differenthabitats inSweden. One habitat is rocky, sea-sidecliffs, where the plants develop to be bushy with broad leaves and expandedinflorescences; the other is amongsand dunes where the plants develop to lie prostrate with narrow leaves and compact inflorescences. The habitats alternate along the coast of Sweden and the habitat that seeds containing the identical genotype ofHieracium umbellatum land in, determines the phenotype which develops.[20]
An example of random variation inDrosophila flies is the number ofommatidia, which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or betweenclones raised in different environments.[citation needed]
The concept of phenotype can be extended to variations below the level of thegene which 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 ofguanine-cytosine base pairs (GC content). The base pairs have a higher thermal stability (melting point) thanadenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.[citation needed]
Richard Dawkins described a phenotype that included all effects that a gene has on its surroundings, including other organisms, as an extended phenotype, arguing that "An animal's behavior tends to maximize the survival of the genes 'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it."[4] For instance, an organism such as abeaver modifies its environment by building abeaver dam; this can be considered anexpression of its genes, just as itsincisor teeth are—which it uses to modify its environment. Similarly, when a bird feeds abrood parasite such as acuckoo, it is unwittingly extending its phenotype; and when genes in anorchid affectorchid bee behavior to increase pollination, or when genes in apeacock affect the copulatory decisions of peahens, again, the phenotype is being extended. Genes are, in Dawkins's view, selected by their phenotypic effects.[21]
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.[22]
An organism's phenotype is determined by the sum of its genetic material along with the influence of its environment. This is mediated by a range of biological mechanisms: either the direct activities of gene products or their downstream effects.[23]
Phenotypes develop through an interaction of genes and their immediate cellular environment, the cellular environment being under the influence of the host-organism's interaction withits environment. Thus there is a multiplicity of ways that genes and phenotypes interact. Most simply, for example, we might say analbino phenotype develops as a consequence of a mutation in the gene encodingtyrosinase which is a key enzyme inmelanin formation. Even here, however, exposure toUV 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.[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 particularenzyme 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.[24] Gene expression is regulated at various levels and thus each level can affect certain phenotypes, includingtranscriptional and post-transcriptional regulation.[citation needed]
The patchy colors of a tortoiseshell cat are the result of different levels of expression of pigmentation genes in different areas of the skin.
Changes in the levels of gene expression can be influenced by a variety of factors, such as environmental conditions, genetic variations, andepigenetic 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 involvingmachine learning methods utilizing gene expressions measured from RNA sequencing found that they can contain enough signal to separate individuals in the context of phenotype prediction.[25]
Although a phenotype is the ensemble of observable characteristics displayed by an organism, the wordphenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to asphenomics.[26][27] Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness.[28] Phenomics forms a large part of theHuman Genome Project.[29]
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.[30][15] Phenomics may be a stepping stone towardspersonalized medicine, particularlydrug therapy.[31] Once the phenomic database has acquired enough data, a person's phenomic information can be used to select specific drugs tailored to the individual.[31]
Large-scale genetic screens can identify the genes ormutations that affect the phenotype of an organism. Analyzing the phenotypes of mutant genes can also aid in determining gene function.[32] Most genetic screens have used microorganisms, in which genes can be easily deleted. For instance, nearly all genes have been deleted inE. coli[33] and many otherbacteria, but also in several eukaryotic model organisms such asbaker's yeast[34] andfission yeast.[35] Among other discoveries, such studies have revealed lists of essential genes.[citation needed]
This experiment involves the progeny of mice treated withENU, or N-ethyl-N-nitrosourea, which is a potent mutagen that causespoint 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.[citation needed]
These experiments show that mutations in therhodopsin gene affected vision and can even cause retinal degeneration in mice.[36] The sameamino acid change causeshuman familial blindness, showing how phenotyping in animals can inform medical diagnostics and possibly therapy.
TheRNA world is the hypothesized pre-cellular stage in the evolutionary history of life on earth, in which self-replicating RNA molecules proliferated prior to the evolution ofDNA and proteins.[37] The foldedthree-dimensional physical structure of the first RNA molecule that possessed ribozyme activity promoting replication while avoiding destruction would have been the first phenotype, and thenucleotide sequence of the first self-replicating RNA molecule would have been the original genotype.[37]
^"Genotype versus phenotype".Understanding Evolution. Retrieved2020-04-29.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.
^West-Eberhard, Mary Jane.Developmental Plasticity and Evolution. Oxford: Oxford University Press, 2003, Oxford University Press, p.31ISBN978-0-19-512234-3
^Cassidy SB, Morris CA (2002-01-01). "Behavioral phenotypes in genetic syndromes: genetic clues to human behavior".Advances in Pediatrics.49:59–86.PMID12214780.
^O'Brien G, Yule W, eds. (1995).Behavioural Phenotype. Clinics in Developmental Medicine No.138. London: Mac Keith Press.ISBN978-1-898683-06-3.
^Rahman H, Ramanathan V, Jagadeeshselvam N, Ramasamy S, Rajendran S, Ramachandran M, et al. (2015-01-01). "Phenomics: Technologies and Applications in Plant and Agriculture". In Barh D, Khan MS, Davies E (eds.).PlantOmics: The Omics of Plant Science. New Delhi: Springer. pp. 385–411.doi:10.1007/978-81-322-2172-2_13.ISBN978-81-322-2171-5.
^Nislow C, Wong LH, Lee AH, Giaever G (September 2016). "Functional genomics using theSaccharomyces cerevisiae yeast deletion collections".Cold Spring Harbor Protocols.2016 (9) pdb.top080945.doi:10.1101/pdb.top080945.PMID27587784.
