Download document

From Genes to Phenotypes



At one level, geneticists tend to think of genes in isolation. In reality,
genes don't act in isolation. The proteins and RNAs they encode
contribute to specific cellular pathways that also receive input from
the products of many other genes. Furthermore, expression of a
single gene is dependent on many factors, including the specific
genetic backgrounds of the organism and a range of environmental
conditions, temperature, nutritional conditions, population density,
and so on.
Gene action is a term that covers a very complex set of events, and
there is probably no case where we understand all the events that
transpire from the level of expression of a single gene to the level of
an organism's phenotype.
Two important generalizations about the complexity of gene action:


1. There is a one-to-many relationship of genes to phenotypes.
2. There is a one-to-many relationship of phenotypes to genes.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
One-to-many relationship of genes to phenotypes

This relationship is called pleiotropy. Pleiotropy is inferred from the observation
that mutations selected for their effect on one specific character are often found to
affect other characters of the organism. This might mean that there are related
physiological pathways contributing to a similar phenotype in several tissues.


For example, the white eye-color mutation in Drosophila results in lack of pigmentation
not only in compound eyes but also in ocelli (simple eyes), sheaths of tissue surrounding
the male gonad, and the Malpighian tubules (the fly's kidneys). In all these tissues,
pigment formation requires the uptake of pigment precursors by the cells. The white
allele causes a defect in this uptake, thereby blocking pigment formation in all these
tissues.
Often, pleiotropy involves multiple events that are not obviously physiologically
related.

For example, the dominant Drosophila mutation Dichaete causes the wings to be held out
laterally but also removes certain hairs on the back of the fly; furthermore, the mutation
is inviable when homozygous. This example shows a real limitation in the way
dominant and recessive mutations are named. The reality is that a single mutation can
be both dominant and recessive, depending on which aspect of its pleiotropic phenotype
is under consideration. In general, genetic terminology is not up to the task of
representing this level of pleiotropy and complexity in one symbol, and there is a certain
arbitrary or historical aspect as to how we name alleles.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
One-to-many relationship of phenotypes to genes


This concept is based on the observation that many different genes can
affect a single phenotype. This is easy to understand in terms of a
character such as eye color, in which there are complex metabolic
pathways with numerous enzymatic steps, each encoded by one or
more gene products. Genetic heterogeneity is the term used to refer
to a given condition that may be caused by different genes.
One goal of genetic analysis is to identify all the genes that affect a
specific phenotype and to understand their genetic, cellular,
developmental, and molecular roles. To do this, we need ways of
sorting mutations and genes.


We first will consider how we can use genetic analysis to determine if two
mutants are caused by mutational hits in the same gene (that is, they are alleles)
or in different genes.
Later, we will consider how genetic analysis can be used to make inferences
about gene interactions in developmental and biochemical pathways.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The complementation test

The allelism test that finds widest application is the complementation
test, which is illustrated in the following example.


Consider a species of flower in which the wild-type color is blue. We have
induced three white-petaled mutants and have obtained pure-breeding strains (all
homozygous). We can call the mutant strains $, £, and ¥, using currency symbols
to avoid prejudicing our thinking concerning dominance. In each case the results
show that the mutant condition is determined by the recessive allele of a single
gene. However, are they three alleles of one gene, or of two or three genes? The
question can be answered by asking if the mutants complement each other.
Complementation is the production of a wild-type phenotype
when two recessive mutant alleles are united in the same cell.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Performing the complementation test

In a diploid organism the complementation test is performed by intercrossing
homozygous recessive mutants two at a time and observing whether or not the
progeny have wild-type phenotype. If recessive mutations represent alleles of the
same gene, then obviously they will not complement because they both represent
lost gene function. Such alleles can be thought of generally as a’ and a", using
primes to distinguish between two different mutant alleles of a gene whose wildtype allele is a+. These alleles could have different mutant sites but would be
functionally identical. The heterozygote a’/a" would be

However, two recessive mutations in different genes would have wild-type function
provided by the respective wild-type alleles. Here we can name the genes a1 and a2,
after their mutant alleles. Heterozygotes would be a1/+ ; +/a2 (unlinked genes) or
a1+/+a2 (linked genes), and we can diagram them as follows:
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Mutants that complement

We now return to the flower example and intercross the mutant strains
to test for complementation. Assume the results of intercrossing
mutants $, £, and ¥ are as follows:

From this set of results we would conclude that mutants $ and £ must
be caused by alleles of one gene (say w1) because they do not
complement; but ¥ must be caused by a mutant allele of another gene
(w2).
The molecular explanation of such results is often in terms of
biochemical pathways in the cell. How does complementation work at
the molecular level? Although it is conventional to say that it is
mutants that complement, in fact the active agents in complementation
are the proteins produced by the wild-type alleles.

Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The biochemical explanation

The normal blue color of the flower is caused by a blue pigment called anthocyanin. Pigments
are chemicals that absorb certain parts of the visible spectrum; in the case of the harebell the
anthocyanin absorbs all wavelengths except blue, which is reflected into the eye of the
observer. However, this anthocyanin is made from chemical precursors that are not pigments;
that is, they do not absorb light of any specific wavelength and simply reflect back the white
light of the sun to the observer, giving a white appearance. The blue pigment is the end
product of a series of biochemical conversions of nonpigments. Each step is catalyzed by a
specific enzyme coded by a specific gene. We can accommodate the results with a pathway as
follows:

A mutation in either of the genes in homozygous condition will lead to the accumulation of a
precursor, which will simply make the plant white. Now, the mutant designations can be
written as follows:
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Complementation
Three phenotypically identical white
mutants, $, £, and ¥, are intercrossed
to form heterozygotes whose
phenotypes reveal whether or not the
mutations complement each other.
(Only two of the three possible
crosses are shown here.) If two
mutations are in different genes (such
as £ and ¥), then complementation
results in the completion of the
biochemical pathway (the end
product is a blue pigment in this
example). If mutations are in the
same gene (such as $ and £), no
complementation occurs because the
biochemical pathway is blocked at
the step controlled by that gene, and
the intermediates in the pathway are
colorless (white).
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Interactions Between the Alleles of One Gene
Incomplete Dominance

Four-o'clocks are plants native to tropical America. Their name comes from the fact
that their flowers open in the late afternoon. When a wild-type four-o'clock plant
with red petals is crossed with a pure line with white petals, the F1 has pink petals. If
an F2 is produced by selfing the F1, the result is

Because of the 1:2:1 ratio in the F2, we can deduce an inheritance pattern based on
two alleles of a single gene. However, the heterozygotes (the F1 and half the F2) are
intermediate in phenotype, suggesting an incomplete type of dominance. Inventing
allele symbols, we can list the genotypes of the four-o'clocks in this experiment as
c+/c+ (red), c/c (white), and c+/c (pink).
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Incomplete dominance

Incomplete dominance describes the general situation in which the phenotype of a
heterozygote is intermediate between the two homozygotes on some quantitative
scale of measurement.

This figure gives terms for all the theoretical positions on the scale, but in practice it
is difficult to determine exactly where on such a scale the heterozygote is located. At
the molecular level, incomplete dominance is generally caused by a quantitative
effect of the number of "doses" of a wild-type allele; two doses produce most
functional transcript and therefore most functional protein product; one dose
produces less transcript and product, whereas zero doses have no functional
transcript or product. In cases of full dominance, in the wild-type/mutant
heterozygote either half of the normal amount of transcript and product is adequate
for normal cell function (the gene is haplo-sufficient), or the wild-type allele is "upregulated" to bring the concentration of transcript up to normal levels.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Codominance

The human ABO blood groups are determined by three alleles of one gene that show
several types of interaction to produce the four blood types of the ABO system. The
allelic series includes three major alleles, i, IA, and IB, but of course any person can
have only two of the three alleles (or two copies of one of them). There are six
different genotypes, the three homozygotes and three different types of
heterozygotes:

In this allelic series, the alleles IA and IB each determine a unique antigen, which is
deposited on the surface of the red blood cells. These are two forms of a single
protein. However, the allele i results in no antigenic protein of this type. In the
genotypes IA/i and IB/i, the alleles IA and IB are fully dominant to i. However, in the
genotype IA/IB each of the alleles produces its own antigen, so they are said to be
codominant.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Relativity of dominance relationships

The human disease sickle-cell anemia gives interesting insight into dominance. The
gene concerned affects the molecule hemoglobin, which transports oxygen and is the
major constituent of red blood cells. The three genotypes have different phenotypes,
as follows:

In regard to the presence or absence of anemia, the HbA allele is obviously
dominant. In regard to blood cell shape, however, there is incomplete dominance.
Finally, in regard to hemoglobin itself there is codominance, as the two hemoglobin
molecules HbA and HbS can be visualized simultaneously by means of
electrophoresis
Sickle-cell anemia illustrates that the terms dominance, incomplete dominance, and
codominance are somewhat arbitrary. The type of dominance inferred depends on the
phenotypic level at which the observations are being made, organismal, cellular, or
molecular. Indeed the same caution can be applied to many of the categories that scientists
use to classify structures and processes; these categories are devised by humans for
convenience of analysis
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
An anomalous segregation ratio



Normal wild-type mice have coats with a rather dark overall pigmentation. A
mutation called yellow (a lighter coat color) illustrates an interesting allelic
interaction. If a yellow mouse is mated to a homozygous wild-type mouse, a 1:1
ratio of yellow to wild-type mice is always observed in the progeny. This
observation suggests (1) that a single gene with two alleles determines these
phenotypic alternatives, (2) that the yellow mouse was heterozygous for these
alleles, and (3) that the allele for yellow is dominant to an allele for normal color.
However, if two yellow mice are crossed with each other, the result is always as
follows:
Note two interesting features in these results. First, the 2:1 phenotypic ratio is a
departure from the expectations for a monohybrid self-cross. Second, because no
cross of yellow × yellow ever produced all yellow progeny, as there would be if
either parent were a homozygote, it appears that it is impossible to obtain
homozygous yellow mice
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Letal alleles

The explanation for such results is that all yellow mice are heterozygous for one
special allele. A cross between two heterozygotes would be expected to yield a
monohybrid genotypic ratio of 1:2:1. However, if all the mice in one of the
homozygous classes died before birth, the live births would then show a 2:1 ratio of
heterozygotes to the surviving homozygotes. The allele AY for yellow is dominant to
the wild-type allele A with respect to its effect on color, but AY acts as a recessive
lethal allele with respect to a character we would call viability. Thus, a mouse with
the homozygous genotype AY/AY dies before birth and is not observed among the
progeny. All surviving yellow mice must be heterozygous AY/A, so a cross between
yellow mice will always yield the following results:
The expected monohybrid ratio of 1:2:1 would be
found among the zygotes, but it is altered to a 2:1 ratio
in the progeny born because zygotes with a lethal AY/AY
genotype do not survive to be counted. This hypothesis
is supported by the removal of uteri from pregnant
females of the yellow × yellow cross; one-fourth of the
embryos are found to be dead.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
What goes wrong in lethal mutations?


In many cases it is possible to trace the cascade of events that leads to death. A
common situation is that the allele causes a deficiency in some essential chemical
reaction. The human diseases PKU and cystic fibrosis are good examples of this
kind of deficiency. In other cases there is a structural defect. Sickle-cell anemia is
another example.
Whether an allele is lethal or not often depends on the environment in which the
organism develops. Whereas certain alleles would be lethal in virtually any
environment, others are viable in one environment but lethal in another. Human
hereditary diseases provide examples. Cystic fibrosis is a disease that would be
lethal without treatment, and individuals with PKU would not survive in a natural
setting in which the special diet would be impossible. As another example, many of
the alleles favored and selected by animal and plant breeders would almost certainly
be eliminated in nature as a result of competition with the members of the natural
population. Modern grain varieties provide good examples; only careful nurturing
by the farmer has maintained such alleles for our benefit.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Complex gene interactions in coat color


The analysis of coat color in mammals is a beautiful example of how
different genes cooperate in the determination of overall coat
appearance. The mouse is a good mammal for genetic studies because
it is small and thus easy to maintain in the laboratory, and because its
reproductive cycle is short.
It is the best-studied mammal with regard to the genetic determination
of coat color. The genetic determination of coat color in other
mammals closely parallels that of mice, and for this reason the mouse
acts as a model system. We shall look at examples from other
mammals as our discussion proceeds. At least five major genes
interact to determine the coat color of mice: the genes are A, B, C, D,
and S
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The A gene

This gene determines the distribution of pigment in the hair. The wildtype allele A produces a phenotype called agouti. Agouti is an overall
grayish color with a brindled, or "salt-and-pepper," appearance. It is a
common color of mammals in nature. The effect is caused by a band
of yellow on the otherwise dark hair shaft.
In the nonagouti phenotype (determined by
the allele a), the yellow band is absent, so
there is solid dark pigment throughout. The
lethal allele AY, discussed in an earlier
section, is another allele of this gene; it
makes the entire shaft yellow. Still another
allele at results in a "black-and-tan" effect,
a yellow belly with dark pigmentation
elsewhere.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The B gene


This gene determines the color of pigment. There are two major
alleles, B coding for black pigment and b for brown. The allele B
gives the normal agouti color in combination with A but gives solid
black with a/a. The genotype A/- ; b/b gives a streaked brown color
called cinnamon, and a/a ; b/b gives solid brown.
In horses, the breeding of domestic lines seems to have eliminated the
A allele that determines the agouti phenotype, although certain wild
relatives of the horse do have this allele. The color we have called
brown in mice is called chestnut in horses, and this phenotype also is
recessive to black.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The C gene



The wild-type allele C permits color expression, and the allele c
prevents color expression. The c/c constitution is epistatic to the other
color genes. The c/c animals are of course albinos. Albinos are
common in many mammalian species and have also been reported
among birds, snakes, and fish.
In most cases, the gene codes for the melanin-producing enzyme
tyrosinase. In rabbits an allele of this gene, the ch (Himalayan) allele,
determines that pigment will be deposited only at the body
extremities. In mice the same allele also produces the phenotype
called Himalayan, and in cats the same allele produces the phenotype
called Siamese.
The allele ch can be considered a version of the c allele with heatsensitive expression. It is only at the colder body extremities that ch is
functional and can make pigment. In warm parts of the body it is
expressed just like the albino allele c. This allele shows clearly how
the expression of an allele depends on the environment.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The D gene

The D gene controls the intensity of pigment specified by the other coat color genes.
The genotypes D/D and D/d permit full expression of color in mice, but d/d "dilutes"
the color, making it look milky. The effect is due to an uneven distribution of
pigment in the hair shaft. Dilute agouti, dilute cinnamon, dilute brown, and dilute
black coats all are possible. A gene with such an effect is called a modifier gene.
In horses, the D allele shows
incomplete dominance. The
figure shows how dilution
affects the appearance of
chestnut and bay horses. Cases
of dilution in the coats of house
cats also are commonly seen.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
The S gene

The S gene controls the presence or absence of spots by controlling the migration of
clumps of melanocytes (pigment-producing cells) across the surface of the
developing embryo. The genotype S/- results in no spots, and s/s produces a
spotting pattern called piebald in both mice and horses. This pattern can be
superimposed on any of the coat colors discussed earlier, with the exception of
albino, of course. Piebald mutations are also known in humans.
We see that the normal coat appearance in wild
mice is produced by a complex set of
interacting genes determining pigment type,
pigment distribution in the individual hairs,
pigment distribution on the animal's body, and
the presence or absence of pigment. Such
interactions are deduced from modified ratios in
dihybrid crosses. The figure illustrates some of
the pigment patterns in mice. Interacting genes
such as these determine most characters in
any organism.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Modifier genes


Modifier gene action can be based on many different molecular mechanisms. One
case involves regulatory genes that bind to the upstream region of the gene near the
promoter and affect the level of transcription. Positive regulators increase ("upregulate") transcription rates, and negative regulators decrease ("down-regulate")
transcription rates.
As an example, consider the regulation of a gene G. G is the normal allele coding
for active protein, whereas g is a null allele (caused by a base-pair substitution) that
codes for inactive protein. At an unlinked locus, R codes for a regulatory protein that
causes high levels of transcription at the G locus, whereas r yields protein that
allows only a basal level. If a dihybrid G/g ; R/r is selfed, a 9:3:4 ratio of protein
activity is produced, as follows:
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini
Penetrance and Expressivity

Penetrance is defined as the percentage of individuals with a given genotype who
exhibit the phenotype associated with that genotype. For example, an organism may
have a particular genotype but may not express the corresponding phenotype
because of modifiers, epistatic genes, or suppressors in the rest of the genome or
because of a modifying effect of the environment. Alternatively, absence of a gene
function may intrinsically have very subtle effects that are difficult to measure in a
laboratory situation.

Another term for describing the range of phenotypic
expression is called expressivity. Expressivity
measures the extent to which a given genotype is
expressed at the phenotypic level. Different degrees
of expression in different individuals may be due to
variation of the allelic constitution of the rest of the
genome or to environmental factors. This figure
illustrates the distinction between penetrance and
expressivity.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini