LESSON 3: Genotype and Phenotype

Intended Learning Outcomes:

At the end of the lesson, you must have:

➢ Determine the genotype and phenotype as well as the genotypic and

phenotypic ratio;
➢ Explain the effects of the genotype of an organism and environment to its
phenotype;

Acquire New Knowledge:

What is Genotype?
The set of genes in our DNA which is responsible for a particular trait. Hence, it is the
information stored within a gene.
The word genotype can be used to refer a particular gene or set of genes which are carried by
an individual. Genotype of an individual is its complete heritable genetic identity, which is
unique to an organism or individual. It also refers to the alleles or variants of a gene, which are
carried by an organism. Humans are diploid organism, which means they have two alleles at a
given locus, wherein one comes from father and the other one from mother. These alleles
represent the genotype of a specific gene. Genotype, along with epigenetic factors, determines
the phenotype
Genotype is internally coded inheritable information which is carried by all organisms. This
coded information is used as a blueprint for building and maintaining a living creature. This
information is present in all cells and is passed on to next generation at the time of cell division.
These coded instructions control everything such as formation of protein, regulation of
metabolism.
The examples of genotype include genes responsible for the stripes on cat, size of a bird’s beak,
height, hair color, eye color, etc. Let us assume the eye color of human being; we have different
colors like blue, brown, green, black, etc. Why we all have a different eye color? This is because
of the difference in the amount of eye pigment, melanin which is present in iris. Eye color is an
inherited trait and there have been evidences that up to 16 genes can influence the color of eye
(Sturm and Larsson 2009). There are three known alleles that control the shade of eye color.
These alleles assort independently during gamete formation. Every individual has four alleles
for controlling their eye color; B allele (brown) is always dominant over G allele (green). The
blue trait is always recessive (Table 1). We can see that two or more than two different
genotypes can give the same phenotype, so two different individual shaving brown eyes may
have different genotype.
Table 1 Genotype and phenotype of eye color
Genotype Phenotype

BBGG Brown
BbGG Brown

BBGg Brown

BbGg Brown
BBgg Brown

Bbgg Brown

bbGg Green
bbGG Green
Bbgg Blue

Genotypic Ratio
The number of times a genotype would appear in the offsprings after a cross between both
parents will be the genotypic ratio. The value depends upon the genotype of parents. It can be
calculated by Punnett square. Let us assume that two organisms with same genotype (Aa, A is
dominant and a is recessive) are allowed to mate, the offspring will have the genotype: AA, Aa,
and aa and the resulting genotypic ratio will be 1:2:1, whereas the resulting phenotypic ratio
will be 3:1.
THE PUNNET SQUARE

Genotyping
The process of determining differences in the genetic make-up of an individual by examining an
individual’s DNA sequence and comparing it to another individual’s sequence or a reference
sequence. The most widely used methods for genotyping include polymerase chain reaction
(PCR), DNA sequencing, random amplified polymorphic detection (RAPD), amplified fragment
length polymorphism, allele-specific polymerase chain reaction, and hybridization to DNA
microarrays. Genotyping finds its application in prenatal disease diagnosis, for which two
widely used techniques are “amniocentesis” (Hessner et al. 1998) and “chorionic villi sampling.”
Apart from prenatal disease diagnosis, genotyping is routinely used for determining blood
group, genetic counseling, and personalized medicine. Genotyping can be done right from
humans to microorganisms. For microorganisms, genotyping can be used for controlling the
spreading of pathogens. Similarly, transgenic organisms can also be genotyped. A transgenic
mouse can be genotyped by a simple polymerase chain reaction (PCR) technique.
Effect of Environment on Genotype
Genotype of an organism is its inherited map which is carried with in its genetic code. All
organisms that have the same genotype do not look or behave the same way as phenotype and
behavior are modified by environmental factors. When two different genotypes respond to
environmental factors in a different way, it is referred to as gene environment interaction. Such
interactions can provide a better insight for the genetic epidemiology of certain diseases.
What is a Phenotype?
Phenotype is attribute or observable appearances/ characteristic of an individual organism
demonstrating its distinctive morphological, developmental, physiological, biochemical, or
behavioral assets.
In the early twentieth century, Danish botanist and geneticist Wilhelm Ludvig Johannsen
introduced the word phenotype to describe the visible and measurable individualities of
organisms (he also introduced the word genotype, in reference to the hereditary units of
organisms). When two or more conspicuously diverse phenotypes exist in the similar
population of a species, the species is called polymorphic. A well-documented example of
polymorphism is Labrador retriever coloring; although the coat color depends on several genes,
it is perceptibly seen in the environment as brown, yellow, and black color. An individual’s
phenotype may change continuously through their entire life due to changes in environmental
conditions and the morphological and physiological changes related with aging.
Phenotypic Variation
Phenotypic variation (due to pivotal inherited genetic change) is an essential requirement for
evolution by natural selection. Natural selection interrupts the genetic organization of a
population indirectly through the contribution of phenotypes. In natural selection, evolution
would be not possible without phenotypic variation (Lewontin1970). The communication
between genotype and phenotype has been hypothesized by the subsequent relationship:
Genotype (G) + Environment (E) ⟶ Phenotype (P)

A more apparent kind of the relationship is:

Genotype (G) + Environment (E) + Genotype and Environment Interactions (GE) ⟶ Phenotype
(P)
Genotypes frequently have ample flexibility in the modification and appearance of phenotypes;
in several organisms these phenotypes are very diverse under variable environmental
conditions (ecophenotypic variation). For example, the plant Hieracium umbellatum is
established in two opposite habitats in Sweden. One habitat is rocky, seaside cliffs, where the
plants are bushy with broad leaves and prolonged inflorescences; the other is amid sand banks
where plants grow prostrate with narrow leaves and dense 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 (Bergfeld et al. 2009). The plants possess their habitat-
specific appearance under standardized experimental conditions.
The Extended Phenotype
Extended phenotype term pronounced by Richard Dawkins. According to Dawkins, a phenotype
comprised all response that a gene has on its environments/surroundings, involving other
organisms known as an extended phenotype (Dawkins 1978). For example, an organism such as
a persist amends its environment by constructing a beaver barrier; this can be contemplated an
expression of its genes, such as incisor teeth which uses to alter its environment. Likewise,
while a bird feeds a breed parasite, e.g., a cuckoo, it is accidentally spreading its phenotype; and
when genes in an orchid interrupt orchid bee behavior to enhance pollination, or genes in a
peacock disturbing copulatory verdicts of peahens ,once more, the phenotype is being extended.
Another example, in the caddis’ salivary gland, the caddis house constructed by a silk which is
wrapped to prevent against predators and boost the mate selection. According to Dawkins’s
view, genes are designated by their phenotypic effects (Dawkins 1982). Many of the scientists
generally support that extended phenotype concept is significant; however its role is regularly
illustrative, instead of supporting in the strategy of experimental tests (Hunter 2009).

Phenotypic Adaption
Evolutionary adaptations to new environments commonly reverse plastic phenotypic changes.
In a new environment, phenotypic adaptation can consist of two phases: plastic change and
genetic change. In the first phase, the environmental shift activates phenotypic changes
without mutation; such types of changes are recognized to as plastic changes (PCs) regardless
of their fitness effects. In the second phase, phenotypes are changed by mutations that accrue
during adaptive evolution. It is proposed that the plastic phenotypic alterations are frequently
required for organism existence in a new environment, which is compulsory because adaptive
evolution is not possible, if the environmental adaptation destroys all individuals. Moreover, it
is recommended that genetic adaptations in the second phase are alleviated by the PCs in the
first phase. For instance, plasticity can change the phenotypic value of an organism closer to the
adapted state in the new environment and provide as a stepping stone to adaptation. For a trait,
the plastic phenotypic variation influenced by an environmental shift and the successive
genetic change (GC) during the adaptation to the new environment could be in the similar
direction toward the ideal phenotypic value in the new environment. Figure 1b indicates that
the PC is reinforced by the adaptive GC and thus is deliberated adaptive. The PC and the
subsequent GC could also be in reverse directions. Figure 1 c shows that the PC is reversed by
the adaptive GC and is hence usually considered non adaptive.

Photo from https://www.researchgate.net/publication/332370410_Phenotype

In the photo above shows the gene expression changes in experimental evolution. (a) Phenotypic
adaptation is considered by comprising the phenotypic standards of a trait at three stages: ancestral
organisms adapted to the primitive environment controlled in the primitive environment (stage o);
ancestral organisms measured in the new environment (stage p); and developed organisms adapted
to the new environment distinguished in the new environment (stage a). Plastic alterations refer to
alterations from stage o to p, while genetic alterations refer to alterations from stage p to a. (b)
When a pair of plastic and genetic phenotypic alterations of a trait, both are larger than a
predetermined cutoff and are in the similar (same) direction known as reinforcing. (c) When a pair of
plastic and genetic phenotypic alterations of a trait, both are larger than a predetermined cutoff and
are in the dissimilar (opposite) direction known as reversing.

Difference between Genotype and Phenotype

PHENOTYPE GENOTYPE

“physical manifestation” “genetic constitution”

Application and Assessment:

A. Use the Punnet square to determine the genotype and phenotype of an organism and its
genotypic and phenotypic ratio. (2 pts each)

1. A male and female bird have 4 un-hatched eggs. The female

is on the left heterozygous; the male on the right is
homozygous recessive. Use B or b for your genotypes.

a. What are the genotypes of the 4 un-hatched

eggs?

F: Bb
 M: bb

b. What are the phenotypes of the 4 un-hatched eggs?

F: BB
M: Bb
c. What is the genetic ratio and phenotypic ratio?

GR: BB

PR: Bb

2. A human male having a homozygous dominant allele for a blue eye is genetically crossed to a
female with homozygous recessive brown eyes. Use A or a for your genotypes.

a. What are the genotypes of their offspring or the F2 generation?

M- aa

F- Aa

b. What are the phenotypes?

M- aa

F- Aa

c. What is the genotypic ratio?

Aa

d. What is the phenotypic ratio?

aa

B.

1. How the genotype of an organism and the environment does affect its phenotype? Explain
your answer. (5pts)
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.

2. Cite an example situation that shows the environment influences the phenotype or the trait
of an organism. (5pts)
 Environmental factors such as diet, temperature, oxygen levels, humidity, light cycles, and
the presence of mutagens can all impact which of an animal's genes are expressed, which
ultimately affects the animal's phenotype.

3. What do you think is the reason why all hereditary possibilities in the genotype are not
expressed in the phenotype? (5pts)
All inherited possibilities in the genotype are not expressed in the phenotype, because some
are the result of latent, recessive, or inhibited genes.

C. Write a reflection on what you have learned in this lesson. (5 points)

In this lesson I learned that, Genotype is the set of genes in our DNA which is responsible for a
particular trait. Hence, it is the information stored within a gene. Also, the number of times a
genotype would appear in the offspring after a cross between both parents will be the genotypic
ratio. The value depends upon the genotype of parents. It can be calculated by Punnett square.
Also I learned a lot about genotype and phenotype.