Genotype

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The genotype of an organism is its complete set of genetic material. [1] Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. [2] The number of alleles an individual can have in a specific gene depends on the number of copies of each chromosome found in that species, also referred to as ploidy. 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. If the alleles are different, the genotype is referred to as heterozygous.

Contents

Genotype contributes to phenotype, the observable traits and characteristics in an individual or organism. [3] 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. [4] However, other traits are only partially influenced by genotype. These traits are often called complex traits because they are influenced by additional factors, such as environmental and epigenetic 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 botanist Wilhelm Johannsen in 1903. [5]

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:

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. [6] 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.

Penetrance is the proportion of individuals showing a specified genotype in their phenotype under a given set of environmental conditions. [7]

Mendelian inheritance

Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal colour in a pea plant. The letters B and b represent alleles for colour and the pictures show the resultant flowers. The diagram shows the cross between two heterozygous parents where B represents the dominant allele (purple) and b represents the recessive allele (white). Punnett square mendel flowers.svg
Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal colour in a pea plant. The letters B and b represent alleles for colour and the pictures show the resultant flowers. The diagram shows the cross between two heterozygous parents where B represents the dominant allele (purple) and b represents the recessive allele (white).

Traits that are determined exclusively by genotype are typically inherited in a Mendelian pattern. These laws of inheritance were described extensively by Gregor Mendel, who performed experiments with pea plants to determine how traits were passed on from generation to generation. [8] He studied phenotypes that were easily observed, such as plant height, petal color, or seed shape. [8] 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. [8] [9]

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. [10] 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 or conditions in humans or animals. [11] [12] [13] Some conditions are inherited in an autosomal 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. [11] [12] [13]

An example of a pedigree for an autosomal dominant condition Example autosomal dominant pedigree 01.png
An example of a pedigree for an autosomal dominant condition

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. [11] [12] [13] 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, 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. [13] [14] [15] 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. [13] [14] [15]

An example of a pedigree for an autosomal recessive condition Example autosomal recessive pedigree.png
An example of a pedigree for an autosomal recessive condition

Mendelian patterns of inheritance can be complicated by additional factors. Some diseases show incomplete penetrance, meaning not all individuals with the disease-causing allele develop signs or symptoms of the disease. [13] [16] [17] Penetrance can also be age-dependent, meaning signs or symptoms of disease are not visible until later in life. For example, Huntington disease is an autosomal dominant condition, but up to 25% of individuals with the affected genotype will not develop symptoms until after age 50. [18] 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. [13] [16] [17] For example, individuals with polydactyly can have a variable number of extra digits. [16] [17]

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. [19] [20] For example, a cross between true-breeding red and white Mirabilis jalapa results in pink flowers. [20]

Codominance

Codominance refers to traits in which both alleles are expressed in the offspring in approximately equal amounts. [21] 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. [21] [22]

Epistasis

Epistasis is when the phenotype of one gene is affected by one or more other genes. [23] This is often through some sort of masking effect of one gene on the other. [24] 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. [25] 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 (ASO) probes or DNA sequencing. [26] [27] Tools such as multiplex ligation-dependent probe amplification can also be used to look for duplications or deletions of genes or gene sections. [27] Other techniques are meant to assess a large number of SNPs across the genome, such as SNP arrays. [26] [27] This type of technology is commonly used for genome-wide association studies.

Large-scale techniques to assess the entire genome are also available. This includes karyotyping to determine the number of chromosomes an individual has and chromosomal microarrays to assess for large duplications or deletions in the chromosome. [26] [27] More detailed information can be determined using exome sequencing, which provides the specific sequence of all DNA in the coding region of the genome, or whole genome sequencing, which sequences the entire genome including non-coding regions. [26] [27]

Genotype encoding

In linear models, the genotypes can be encoded in different manners. Let us consider a biallelic locus with two possible alleles, encoded by and . We consider to correspond to the dominant allele to the reference allele . The following table details the different encoding. [28]

Genotype
Additive encoding012
Dominant encoding011
Recessive encoding001
Codominant encoding0,00,11,0

See also

Related Research Articles

An allele, or allelomorph, is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule.

<span class="mw-page-title-main">Genetic disorder</span> Health problem caused by one or more abnormalities in the genome

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 are the most common, the term is mostly used when discussing disorders with a single genetic cause, either in a gene or chromosome. The mutation responsible can occur spontaneously before embryonic development, or it can be inherited from two parents who are carriers of a faulty gene or from a parent with the disorder. When the genetic disorder is inherited from one or both parents, it is also classified as a hereditary disease. Some disorders are caused by a mutation on the X chromosome and have X-linked inheritance. Very few disorders are inherited on the Y chromosome or mitochondrial DNA.

<span class="mw-page-title-main">Heredity</span> Passing of traits to offspring from the species parents or ancestor

Heredity, also called inheritance or biological inheritance, is the passing on of traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic information of their parents. Through heredity, variations between individuals can accumulate and cause species to evolve by natural selection. The study of heredity in biology is genetics.

<span class="mw-page-title-main">Mendelian inheritance</span> Type of biological inheritance

Mendelian inheritance is a type of biological inheritance following the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 by Hugo de Vries and Carl Correns, and later popularized by William Bateson. These principles were initially controversial. When Mendel's theories were integrated with the Boveri–Sutton chromosome theory of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics. Ronald Fisher combined these ideas with the theory of natural selection in his 1930 book The Genetical Theory of Natural Selection, putting evolution onto a mathematical footing and forming the basis for population genetics within the modern evolutionary synthesis.

<span class="mw-page-title-main">Dominance (genetics)</span> One gene variant masking the effect of another in the other copy of the gene

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 the second is called recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked; these have an inheritance and presentation pattern that depends on the sex of both the parent and the child. Since there is only one copy of the Y chromosome, Y-linked traits cannot be dominant or recessive. Additionally, there are other forms of dominance, such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes and co-dominance, in which different variants on each chromosome both show their associated traits.

Penetrance in genetics is the proportion of individuals carrying a particular variant of a gene that also expresses an associated trait. In medical genetics, the penetrance of a disease-causing mutation is the proportion of individuals with the mutation that exhibit clinical symptoms among all individuals with such mutation. For example, if a mutation in the gene responsible for a particular autosomal dominant disorder has 95% penetrance, then 95% of those with the mutation will develop the disease, while 5% will not.

Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together. Markers on different chromosomes are perfectly unlinked, although the penetrance of potentially deleterious alleles may be influenced by the presence of other alleles, and these other alleles may be located on other chromosomes than that on which a particular potentially deleterious allele is located.

<span class="mw-page-title-main">Punnett square</span> Tabular summary of genetic combinations

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 the probability of an offspring having a particular genotype. The Punnett square is a tabular summary of possible combinations of maternal alleles with paternal alleles. These tables can be used to examine the genotypical outcome probabilities of the offspring of a single trait (allele), or when crossing multiple traits from the parents. The Punnett square is a visual representation of Mendelian inheritance. For multiple traits, using the "forked-line method" is typically much easier than the Punnett square. Phenotypes may be predicted with at least better-than-chance accuracy using a Punnett square, but the phenotype that may appear in the presence of a given genotype can in some instances be influenced by many other factors, as when polygenic inheritance and/or epigenetics are at work.

<span class="mw-page-title-main">Equine coat color genetics</span> Genetics behind the equine coat color

Equine coat color genetics determine a horse's coat color. Many colors are possible, but all variations are produced by changes in only a few genes. Bay is the most common color of horse, followed by black and chestnut. A change at the agouti locus is capable of turning bay to black, while a mutation at the extension locus can turn bay or black to chestnut.

<span class="mw-page-title-main">Monohybrid cross</span> Cross between two organisms with different variations at one genetic locus of interest

A monohybrid cross is a cross between two organisms with different variations at one genetic locus of interest. The character(s) being studied in a monohybrid cross are governed by two or multiple variations for a single location of a gene. Then carry out such a cross, each parent is chosen to be homozygous or true breeding for a given trait (locus). When a cross satisfies the conditions for a monohybrid cross, it is usually detected by a characteristic distribution of second-generation (F2) offspring that is sometimes called the monohybrid ratio.

<span class="mw-page-title-main">Non-Mendelian inheritance</span> Type of pattern of inheritance

Non-Mendelian inheritance is any pattern in which traits do not segregate in accordance with Mendel's laws. These laws describe the inheritance of traits linked to single genes on chromosomes in the nucleus. In Mendelian inheritance, each parent contributes one of two possible alleles for a trait. If the genotypes of both parents in a genetic cross are known, Mendel's laws can be used to determine the distribution of phenotypes expected for the population of offspring. There are several situations in which the proportions of phenotypes observed in the progeny do not match the predicted values.

<span class="mw-page-title-main">Human genetics</span> Study of inheritance as it occurs in human beings

Human genetics is the study of inheritance as it occurs in human beings. Human genetics encompasses a variety of overlapping fields including: classical genetics, cytogenetics, molecular genetics, biochemical genetics, genomics, population genetics, developmental genetics, clinical genetics, and genetic counseling.

In genetics, expressivity is the degree to which a phenotype is expressed by individuals having a particular genotype. Alternatively, it may refer to the expression of a particular gene by individuals having a certain phenotype. Expressivity is related to the intensity of a given phenotype; it differs from penetrance, which refers to the proportion of individuals with a particular genotype that share the same phenotype.

<span class="mw-page-title-main">Test cross</span>

Under the law of dominance in genetics, an individual expressing a dominant phenotype could contain either two copies of the dominant allele or one copy of each dominant and recessive allele. By performing a test cross, one can determine whether the individual is heterozygous or homozygous dominant.

Pseudodominance is the situation in which the inheritance of a recessive trait mimics a dominant pattern.

<span class="mw-page-title-main">Hereditary carrier</span> Organism with a recessive genetic allele that does not display the recessive trait

A hereditary carrier, is a person or other organism that has inherited a recessive allele for a genetic trait or mutation but usually does not display that trait or show symptoms of the disease. Carriers are, however, able to pass the allele onto their offspring, who may then express the genetic trait.

<span class="mw-page-title-main">Zygosity</span> Degree of similarity of the alleles in an organism

Zygosity 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.

Classical genetics is the branch of genetics based solely on visible results of reproductive acts. It is the oldest discipline in the field of genetics, going back to the experiments on Mendelian inheritance by Gregor Mendel who made it possible to identify the basic mechanisms of heredity. Subsequently, these mechanisms have been studied and explained at the molecular level.

Mendelian traits behave according to the model of monogenic or simple gene inheritance in which one gene corresponds to one trait. Discrete traits with simple Mendelian inheritance patterns are relatively rare in nature, and many of the clearest examples in humans cause disorders. Discrete traits found in humans are common examples for teaching genetics.

This glossary of genetics and evolutionary biology is a list of definitions of terms and concepts used in the study of genetics and evolutionary biology, as well as sub-disciplines and related fields, with an emphasis on classical genetics, quantitative genetics, population biology, phylogenetics, speciation, and systematics. Overlapping and related terms can be found in Glossary of cellular and molecular biology, Glossary of ecology, and Glossary of biology.

References

  1. ↑ "What is genotype? What is phenotype? – pgEd". pged.org. Retrieved 2020-06-22.
  2. ↑ "Genotype". Genome.gov. Retrieved 2021-11-09.
  3. ↑ Pierce, Benjamin (2020). Genetics A Conceptual Approach. NY, New York: Macmillian. ISBN   978-1-319-29714-5.
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  5. ↑ Johannsen W (1903). "Om arvelighed i samfund og i rene linier". Oversigt Birdy over Det Kongelige Danske Videnskabernes Selskabs Forhandlingerm (in Danish). 3: 247–70. German ed. "Erblichkeit in Populationen und in reinen Linien" (in German). Jena: Gustav Fischer. 1903. Archived from the original on 2009-05-30. Retrieved 2017-07-19.. Also see his monograph Johannsen W (1905). Arvelighedslærens elementer horse[The Elements of Heredity] (in Danish). Copenhagen.{{cite book}}: CS1 maint: location missing publisher (link) which was rewritten, enlarged and translated into German as Johannsen W (1905). Elemente der exakten Erblichkeitslehre (in German). Jena: Gustav Fischer. Archived from the original on 2009-05-30. Retrieved 2017-07-19.
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  14. 1 2 Alliance, Genetic; Health, District of Columbia Department of (2010-02-17). Classic Mendelian Genetics (Patterns of Inheritance). Genetic Alliance.
  15. 1 2 "4.4.1: Inheritance patterns for X-linked and Y-linked genes". Biology LibreTexts. 2020-06-24. Retrieved 2021-11-15.
  16. 1 2 3 "14.2: Penetrance and Expressivity". Biology LibreTexts. 2021-01-13. Retrieved 2021-11-19.
  17. 1 2 3 "Phenotype Variability: Penetrance and Expressivity | Learn Science at Scitable". www.nature.com. Retrieved 2021-11-19.
  18. ↑ Caron, Nicholas S.; Wright, Galen EB; Hayden, Michael R. (1993), Adam, Margaret P.; Ardinger, Holly H.; Pagon, Roberta A.; Wallace, Stephanie E. (eds.), "Huntington Disease", GeneReviews®, Seattle (WA): University of Washington, Seattle, PMID   20301482 , retrieved 2021-11-19
  19. ↑ "Genetic Dominance: Genotype-Phenotype Relationships | Learn Science at Scitable". www.nature.com. Retrieved 2021-11-15.
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  25. ↑ Mackay, T. F. (December 1995). "The genetic basis of quantitative variation: numbers of sensory bristles of Drosophila melanogaster as a model system". Trends in Genetics. 11 (12): 464–470. doi:10.1016/s0168-9525(00)89154-4. ISSN   0168-9525. PMID   8533161.
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