How can we study inheritance?

When spending time with your own family, friends, and neighbors, you may have noticed that
many traits run in families. For instance, members of a family may share similar facial features,
an uncommon hair color (like the brother and sister below), or a predisposition to health
problems such as diabetes. Characteristics that run in families often have a genetic basis,
meaning that they depend on genetic information a person inherits from his or her parents.

Image of a brother and sister who both have distinctive reddish hair.

Image credit "Brother, sister, portrait, russet," by Adina Voicu (CC0, public domain).
What if you wanted to figure out how genetic information is transmitted between generations?
For instance, you might be curious how traits can "skip" a generation, or why one child in a
family may suffer from a genetic disease while another does not. How could you go about asking
these kinds of questions scientifically?
An obvious first idea would be to study human inheritance patterns directly, but that turns out to
be a tricky proposition (see the pop-up below for details). In this article, we'll see how a
nineteenth-century monk named Gregor Mendel instead uncovered the key principles of
inheritance using a simple, familiar system: the pea plant.
[Why didn't Mendel study humans?]
The monk in the garden: Gregor Mendel
Johann Gregor Mendel (1822–1884), often called the “father of genetics,” was a teacher, lifelong
learner, scientist, and man of faith. It would be fair to say that Mendel had a lot of grit: he
persevered through difficult circumstances to make some of the most important discoveries in
biology.
As a young man, Mendel had difficulty paying for his education due to his family's limited
means, and he also suffered bouts of physical illness and depression; still, he persevered to
graduate from high school and, later, university^11start superscript, 1, end superscript. After
finishing university, he joined the Augustinian Abbey of St. Thomas in Brno, in what is now the
Czech Republic. At the time, the monastery was the cultural and intellectual hub of the region,
 and Mendel was immediately exposed to new teachings and ideas^11start superscript, 1, end
superscript.
His decision to join the order (against the wishes of his father, who expected him to carry on the
family farm) appears to have been motivated in part by a desire to continue his education and
pursue his scientific interests^22start superscript, 2, end superscript. Supported by the monastery,
he taught physics, botany, and natural science courses at the secondary and university levels.

Research on heredity

In 1856, Mendel began a decade-long research project to investigate patterns of inheritance.

Although he began his research using mice, he later switched to honeybees and plants, ultimately
settling on garden peas as his primary model system^22start superscript, 2, end superscript.
A model system is an organism that makes it easy for a researcher to investigate a particular
scientific question, such as how traits are inherited. By studying a model system, researchers can
learn general principles that apply to other, harder-to-study organisms or biological systems,
such as humans.
Mendel studied the inheritance of seven different features in peas, including height, flower color,
seed color, and seed shape. To do so, he first established pea lines with two different forms of a
feature, such as tall vs. short height. He grew these lines for generations until they were pure-
breeding (always produced offspring identical to the parent), then bred them to each other and
observed how the traits were inherited.
In addition to recording how the plants in each generation looked, Mendel counted the exact
number of plants that showed each trait. Strikingly, he found very similar patterns of inheritance
for all seven features he studied:
 One form of a feature, such as tall, always concealed the other form, such as short, in the first
generation after the cross. Mendel called the visible form the dominant trait and the hidden
form the recessive trait.
 In the second generation, after plants were allowed to self-fertilize (pollinate themselves), the
hidden form of the trait reappeared in a minority of the plants. Specifically, there were always
about 333 plants that showed the dominant trait (e.g., tall) for every 111 plant that showed the
recessive trait (e.g., short), making a 3:13:13, colon, 1 ratio.
 Mendel also found that the features were inherited independently: one feature, such as plant
height, did not influence inheritance of other features, such as flower color or seed shape.
Representation of results from one of Mendel's experiments. When a tall and short plant are
crossed, all of the offspring are tall. If the offspring self-fertilize, they produce tall and short
plants in a ratio of 3:1 in the next generation. Mendel's actual counts were 787 tall:277 short
plants in this generation (2.84:1 ratio).
 _Image modified from "Mendel seven characters," by Mariana Ruiz Villareal (public domain)._
In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the
local Natural History Society. Based on the patterns he observed, the counting data he collected,
and a mathematical analysis of his results, Mendel proposed a model of inheritance in which:
 Characteristics such as flower color, plant height, and seed shape were controlled by pairs of
heritable factors that came in different versions.
 One version of a factor (the dominant form) could mask the presence of another version (the
recessive form).
 The two paired factors separated during gamete production, such that each gamete (sperm or
egg) randomly received just one factor.
 The factors controlling different characteristics were inherited independently of one another.
We'll take a closer look at how Mendel reached these conclusions in the articles on the law of
segregation and the law of independent assortment. In 1866, Mendel published his observations
and his model of inheritance, under the title Experiments in Plant Hybridization^{3,4}3,4start
superscript, 3, comma, 4, end superscript, in the Proceedings of the Natural History Society of
Brünn.

Scientific legacy
Mendel's work went largely unnoticed by the scientific community during his lifetime. How
could this have been the case?
In part, Mendel's contemporaries failed to recognize the the importance of his work because his
findings went against prevailing (popular) ideas about inheritance. In addition, although we now
see Mendel's mathematical approach to biology as innovative and pioneering, it was new,
unfamiliar, and perhaps confusing or unintuitive to other biologists of the time^55start
superscript, 5, end superscript.
In the mid-1800s, when Mendel was doing his experiments, most biologists subscribed to the
idea of blending inheritance. Blending inheritance wasn't a formal, scientific hypothesis, but
rather, a general model in which inheritance involved the permanent blending of parents'
characteristics in their offspring (producing offspring with an intermediate form of a
characteristic)^66start superscript, 6, end superscript. The blending model fit well with some
observations of human inheritance: for instance, children often look a bit like both of their
parents.
But the blending model could not explain why Mendel crossed a tall and a short pea plant and
got only tall plants, or why self-fertilization of one of those tall plants would produce a 3:13:13,
colon, 1 ratio of tall to short plants in the next generation. Instead, if the blending model were
correct, a tall plant crossed with a short plant should produce a medium plant, which would go
on to produce more medium plants (see below).
Image comparing the predictions of the blending model with Mendel's actual results for a cross
between a tall pea plant and a short pea plant.
The blending model predicts that all the offspring from the cross should be of medium height,
and that if those offspring self-fertilize, all the plants in the next generation will also be of
medium height.
Mendel instead observed that all the offspring of the cross were tall, and that when they self-
fertilized, they produced tall and short plants in a ratio of 3:1.

_Image modified from "Mendel seven characters," by Mariana Ruiz Villareal (public domain)._
As it turns out, both pea plant height and human height (along with many other characteristics in
a wide range of organisms) are controlled by pairs of heritable factors that come in distinctive
versions, just as Mendel proposed. In humans, however, there are many different factors (genes)
that contribute fractionally to height and vary among individuals. This makes it difficult to see
the contribution of any one factor and produces inheritance patterns that can resemble blending.
In Mendel's experiments, in contrast, there was just one factor that differed between the tall and
short pea plants, allowing Mendel to clearly see the underlying pattern of inheritance.
In 1868, Mendel became abbot of his monastery and largely set aside his scientific pursuits in
favor of his pastoral duties. He was not recognized for his extraordinary scientific contributions
during his lifetime. In fact, it was not until around 1900 that his work was rediscovered,
reproduced, and revitalized. Its rediscoverers were biologists on the brink of discovering the
chromosomal basis of heredity – that is, about to realize that Mendel's “heritable factors” were
carried on chromosomes.

Mendel’s model system: The pea plant

Mendel carried out his key experiments using the garden pea, Pisum sativum, as a model system.
Pea plants make a convenient system for studies of inheritance, and they are still studied by some
geneticists today.
Useful features of peas include their rapid life cycle and the production of lots and lots of seeds.
Pea plants also typically self-fertilize, meaning that the same plant makes both the sperm and the
egg that come together in fertilization. Mendel took advantage of this property to produce true-
breeding pea lines: he self-fertilized and selected peas for many generations until he got lines
that consistently made offspring identical to the parent (e.g., always short).
Pea plants are also easy to cross, or mate in a controlled way. This is done by transferring pollen
from the anthers (male parts) of a pea plant of one variety to the carpel (female part) of a mature
pea plant of a different variety. To prevent the receiving plant from self-fertilizing, Mendel
painstakingly removed all of the immature anthers from the plant’s flowers before the cross.
Diagram of pea flowers, showing how a cross is performed. First, a flower on the female parent
is emasculated, meaning that the male parts (anthers) are removed with forceps or scissors. Then,
pollen is collected from a flower on the male parent plant using a paintbrush. The pollen is
dabbed onto the female part (carpel) of the female parent flower that was previously emasculated.
Because peas were so easy to work with and prolific in seed production, Mendel could perform
many crosses and examine many individual plants, making sure that his results were consistent
(not just a fluke) and accurate (based on many data points).

Mendel’s experimental setup

Once Mendel had established true-breeding pea lines with different traits for one or more
features of interest (such as tall vs. short height), he began to investigate how the traits were
inherited by carrying out a series of crosses.
First, he crossed one true-breeding parent to another. The plants used in this initial cross are
called the \text PPP generation, or parental generation.
Mendel collected the seeds from the \text PPP generation cross and grew them up. These
offspring were called the \text F_1F1F, start subscript, 1, end subscript generation, short for
first filial generation. (Filius means “son” in Latin, so this name is slightly less weird than it
seems!)
Once Mendel examined the \text F_1F1F, start subscript, 1, end subscript plants and recorded
their traits, he let them self-fertilize naturally, producing lots of seeds. He then collected and
grew the seeds from the \text F_1F1F, start subscript, 1, end subscript plants to produce an \text
F_2F2F, start subscript, 2, end subscript generation, or second filial generation. Again, he
carefully examined the plants and recorded their traits.
Diagram of a cross between a tall plant and a short plant, labeling the P, F1, and F2 generations.

_Image modified from "Mendel seven characters," by Mariana Ruiz Villareal (public domain)._
Mendel's experiments extended beyond the \text F_2F2F, start subscript, 2, end
subscript generation to \text F_3F3F, start subscript, 3, end subscript, \text F_4F4F, start
subscript, 4, end subscript, and later generations, but his model of inheritance was based mostly
on the first three generations (\text PPP, \text F_1F1F, start subscript, 1, end subscript, and \text
F_2F2F, start subscript, 2, end subscript).
Mendel didn’t just record what his plants looked like in each generation (e.g., tall vs. short).
Instead, he counted exactly how many plants with each trait were present. This may sound
tedious, but by recording numbers and thinking mathematically, Mendel made discoveries that
eluded famous scientists of his time (such as Charles Darwin, who carried out similar
 experiments but didn’t grasp the significance of his results)^{5}5start superscript, 5, end
superscript.
You can use the links below to learn more about Mendel's laws of inheritance:
 The law of segregation, describing how individual traits are inherited.
 The law of independent assortment, describing how two or more traits are inherited relative to
one another.

The law of segregation

Key points:

 Gregor Mendel studied inheritance of traits in pea plants. He proposed a model where pairs of
"heritable elements," or genes, specified traits.
 Genes come in different versions, or alleles. A dominant allele hides a recessive allele and
determines the organism's appearance.
 When an organism makes gametes, each gamete receives just one gene copy, which is selected
randomly. This is known as the law of segregation.
 A Punnett square can be used to predict genotypes (allele combinations)
and phenotypes (observable traits) of offspring from genetic crosses.
 A test cross can be used to determine whether an organism with a dominant phenotype is
homozygous or heterozygous.
 Introduction
Today, we know that many of people's characteristics, from hair color to height to risk of
diabetes, are influenced by genes. We also know that genes are the way parents pass
characteristics on to their children (including things like dimples, or—in the case of me and my
father—a terrible singing voice). In the last hundred years, we've come to understand that genes
are actually pieces of DNA that are found on chromosomes and specify proteins.
But did we always know those things? Not by a long shot! About 150150150 years ago, a monk
named Gregor Mendel published a paper that first proposed the existence of genes and presented
a model for how they were inherited. Mendel's work was the first step on a long road, involving
many hard-working scientists, that's led to our present understanding of genes and what they do.
In this article, we’ll trace the experiments and reasoning that led Mendel to formulate his model
for the inheritance of single genes.
Mendel's model: It started with a 3:13:13, colon, 1 ratio
Mendel studied the genetics of pea plants, and he traced the inheritance of a variety of
characteristics, including flower color, flower position, seed color, and seed shape. To do so, he
started by crossing pure-breeding parent plants with different forms of a characteristic, such as
violet and white flowers. Pure-breeding just means that the plant will always make more
offspring like itself, when self-fertilized over many generations.
[What is self-fertilization?]
What results did Mendel find in his crosses for flower color? In the parental, or \text
PPP generation, Mendel crossed a pure-breeding violet-flowered plant to a pure-breeding white-
flowered plant. When he gathered and planted the seeds produced in this cross, Mendel found
that 100100100 percent of the plants in the next generation, or \text F_1F1F, start subscript, 1,
end subscript generation, had violet flowers.
Conventional wisdom at that time would have predicted that the hybrid flowers should be pale
violet—that is, that the parents' traits should blend in the offspring. Instead, Mendel’s results
showed that the white flower trait had completely disappeared. He called the trait that was visible
in the \text F_1F1F, start subscript, 1, end subscriptgeneration (violet flowers) the dominant
trait, and the trait that was hidden or lost (white flowers) the recessive trait.

The diagram shows a cross between pea plants that are true-breeding for purple flower color and
plants that are true-breeding for white flower color. This cross-fertilization of the P generation
resulted in an F{1} generation with all violet flowers. Self-fertilization of the F{1} generation
resulted in an F_{2} generation that consisted of 705 plants with violet flowers, and 224 plants
with white flowers.
Importantly, Mendel did not stop his experimentation there. Instead, he let the \text F_1F1F, start
subscript, 1, end subscript plants self-fertilize. Among their offspring, called the \text F_2F2F,
start subscript, 2, end subscript generation, he found that 705705705 plants had violet flowers
and 224224224 had white flowers. This was a ratio of 3.153.153, point, 15 violet flowers to one
white flower, or approximately 3:13:13, colon, 1.
This 3:13:13, colon, 1 ratio was no fluke. For the other six characteristics that Mendel examined,
both the \text F_1F1F, start subscript, 1, end subscript and \text F_2F2F, start subscript, 2, end
subscript generations behaved in the same way they did for flower color. One of the two traits
would disappear completely from the \text F_1F1F, start subscript, 1, end subscriptgeneration,
only to reappear in the \text F_2F2F, start subscript, 2, end subscript generation in a ratio of
roughly 3:13:13, colon, 1
[See Mendel's data for all seven characteristics]

\text F_2F, start subscript, 2, end \text F_2F, start subscript, 2, end
subscript subscript
6022602220012001 3.01:13, point, 01, colon, 1
5474547418501850 2.96:12, point, 96, colon, 1
428428152152 2.82:12, point, 82, colon, 1
882882299299 2.95:12, point, 95, colon, 1
787787277277 2.84:12, point, 84, colon, 1
705705224224 3.15:13, point, 15, colon, 1
651651207207 3.14:13, point, 14, colon, 1
Seven characteristics of Mendel’s pea plants are illustrated. The flowers can be purple or white.
The peas can be yellow or green, or smooth or wrinkled. The pea pods can be inflated or
constricted, or yellow or green. The flower position can be axial or terminal. The stem length can
be tall or dwarf.
As it turned out, the 3:13:13, colon, 1 ratio was a crucial clue that let Mendel crack the puzzle of
inheritance. Let's take a closer look at what Mendel figured out.

Mendel's model of inheritance

Based on his results (including that magic 3:13:13, colon, 1 ratio), Mendel came up with a model
for the inheritance of individual characteristics, such as flower color.
In Mendel's model, parents pass along “heritable factors," which we now call genes, that
determine the traits of the offspring. Each individual has two copies of a given gene, such as the
gene for seed color (Y gene) shown below. If these copies represent different versions, or alleles,
of the gene, one allele—the dominant one—may hide the other allele—the recessive one. For
seed color, the dominant yellow allele Y hides the recessive green allele y.
A graphic with 2 columns, the first with the heading “Phenotype” and the second with the
heading “Genotype.” In the phenotype column, one yellow pea plant cross-fertilizes with one
green pea plant. The first generation of offspring is 100 percent yellow pea plants. After self-
fertilization of these yellow pea offspring, 75 percent of the second generation offspring have
yellow peas and 25 percent have green peas. The genotype column shows the first generation
offspring as 100 percent Yy, and the second generation as 25 percent YY, 50 percent Yy, and 25
percent yy.
The set of alleles carried by an organism is known as its genotype. Genotype
determines phenotype, an organism's observable features. When an organism has two copies of
the same allele (say, YY or yy), it is said to be homozygousfor that gene. If, instead, it has two
different copies (like Yy), we can say it is heterozygous. Phenotype can also be affected by the
environment in many real-life cases, though this did not have an impact on Mendel's work.

Mendel's model: The law of segregation

So far, so good. But this model alone doesn't explain why Mendel saw the exact patterns of
inheritance he did. In particular, it doesn't account for the 3:13:13, colon, 1 ratio. For that, we
need Mendel's law of segregation.
According to the law of segregation, only one of the two gene copies present in an organism is
distributed to each gamete (egg or sperm cell) that it makes, and the allocation of the gene copies
is random. When an egg and a sperm join in fertilization, they form a new organism, whose
genotype consists of the alleles contained in the gametes. The diagram below illustrates this idea:
This illustration shows a monohybrid cross. In the P generation, one parent has a dominant
yellow phenotype and the genotype YY, and the other parent has the recessive green phenotype
and the genotype yy. Each parent produces one kind of gamete, resulting in an F{1} generation
with a dominant yellow phenotype and the genotype Yy. Self-pollination of the F{1} generation
results in an F_{2} generation with a 3 to 1 ratio of yellow to green peas. One out of three of the
yellow pea plants has a dominant genotype of YY, and 2 out of 3 has the heterozygous genotype
Yy. The homozygous recessive plant has the green phenotype and the genotype yy.
The four-squared box shown for the \text F_2F2F, start subscript, 2, end subscript generation is
known as a Punnett square. To prepare a Punnett square, all possible gametes made by the
parents are written along the top (for the father) and side (for the mother) of a grid. Here, since it
is self-fertilization, the same plant is both mother and father.
The combinations of egg and sperm are then made in the boxes in the table, representing
fertilization to make new individuals. Because each square represents an equally likely event, we
can determine genotype and phenotype ratios by counting the squares.
[Why are the boxes all equally likely?]
1122111:2:11, colon, 2, colon, 1\text F_2F, start subscript, 2, end subscript3:13, colon, 1The test
cross
Mendel also came up with a way to figure out whether an organism with a dominant phenotype
(such as a yellow-seeded pea plant) was a heterozygote (Yy) or a homozygote (YY). This
technique is called a test cross and is still used by plant and animal breeders today.
In a test cross, the organism with the dominant phenotype is crossed with an organism that is
homozygous recessive (e.g., green-seeded):

In a test cross, a parent with a dominant phenotype but unknown genotype is crossed with a
recessive parent. If the parent with the unknown genotype is homozygous dominant, all the
resulting offspring will have at least one dominant allele. If the parent with the unknown
genotype is heterozygous, 50 percent of the offspring will inherit a recessive allele from both
parents and will have the recessive phenotype.
If the organism with the dominant phenotype is homozygous, then all of the \text F_1F1F, start
subscript, 1, end subscript offspring will get a dominant allele from that parent, be heterozygous,
and show the dominant phenotype. If the organism with the dominant phenotype organism is
 instead a heterozygote, the \text F_1F1F, start subscript, 1, end subscript offspring will be half
heterozygotes (dominant phenotype) and half recessive homozygotes (recessive phenotype).
The fact that we get a 1:11:11, colon, 1 ratio in this second case is another confirmation of
Mendel’s law of segregation.
Is that Mendel's complete model of inheritance?
Not quite! We've seen all of Mendel's model for the inheritance of single genes. However,
Mendel's complete model also addressed whether genes for different characteristics (such as
flower color and seed shape) influence each other's inheritance. You can learn more about
Mendel's model for the inheritance of multiple genes in the law of independent
assortment article.
One thing I find pretty amazing is that Mendel was able to figure out his entire model of
inheritance simply from his observations of pea plants. This wasn't because he was some kind of
crazy super genius, but rather, because he was very careful, persistent, and curious, and also
because he thought about his results mathematically (for instance, the 3:13:13, colon, 1 ratio).
These are some of the qualities of a great scientist—ones that anyone, anywhere, can develop!

Check your understanding

1. Imagine that you are a rabbit breeder with two purebred rabbits, a male with black fur and a
female with tan fur. When you cross your rabbits, all of the \text F_1F1F, start subscript, 1, end
subscript kits (baby rabbits) have tan fur.
Which trait is dominant, and which is recessive?
A)Black fur is dominant, while tan fur is recessive
B)Tan fur is dominant, while black fur is recessive
C)Both tan fur and black fur are dominant
D)Neither tan fur nor black fur is dominant
2. Which statement best describes the relationship between genotype and phenotype?
A)Genotype always completely determines phenotype
B)Phenotype always completely determines genotype
C)Genotype determines phenotype, but with influence from the environment
D)Phenotype determines genotype, but with influence from the environment
The law of independent assortment
Introduction

The law of segregation lets us predict how a single feature associated with a single gene is
inherited. In some cases, though, we might want to predict the inheritance of two characteristics
associated with two different genes. How can we do this?

[Refresher on the law of segregation]

To make an accurate prediction, we need to know whether the two genes are inherited
independently or not. That is, we need to know whether they "ignore" one another when they're
sorted into gametes, or whether they "stick together" and get inherited as a unit.
When Gregor Mendel asked this question, he found that different genes were inherited
independently of one another, following what's called the law of independent assortment. In
this article, we'll take a closer look at the law of independent assortment and how it is used to
make predictions. We'll also see when and why the law of independent assortment does (or
doesn't!) hold true.
Note: If you are not yet familiar with how individual genes are inherited, you may want to check
out the article on the law of segregation or the introduction to heredity video before you dive into
this article.
What is the law of independent assortment?
Mendel's law of independent assortment states that the alleles of two (or more) different genes
get sorted into gametes independently of one another. In other words, the allele a gamete
receives for one gene does not influence the allele received for another gene.
Example: Pea color and pea shape genes
Let's look at a concrete example of the law of independent assortment. Imagine that we cross two
pure-breeding pea plants: one with yellow, round seeds (YYRR) and one with green, wrinkled
seeds (yyrr). Because each parent is homozygous, the law of segregation tells us that the gametes
made by the wrinkled, green plant all are ry, and the gametes made by the round, yellow plant
are all RY. That gives us \text F_1F1F, start subscript, 1, end subscript offspring that are all RrYy.
The allele specifying yellow seed color is dominant to the allele specifying green seed color, and
the allele specifying round shape is dominant to the allele specifying wrinkled shape, as shown
by the capital and lower-case letters. This means that the \text F_1F1F, start subscript, 1, end
subscript plants are all yellow and round. Because they are heterozygous for two genes, the \text
F_1F1F, start subscript, 1, end subscript plants are called dihybrids (di- = two, -hybrid =
heterozygous).
A cross between two dihybrids (or, equivalently, self-fertilization of a dihybrid) is known as
a dihybrid cross. When Mendel did this cross and looked at the offspring, he found that there
were four different categories of pea seeds: yellow and round, yellow and wrinkled, green and
round, and green and wrinkled. These phenotypic categories (categories defined by observable
traits) appeared in a ratio of approximately 9:3:3:19:3:3:19, colon, 3, colon, 3, colon, 1.

Illustration of the hypothesis that the seed color and seed shape genes assort independently.
In this diagram, the Y and R alleles of the yellow, round parent and the y and r alleles of the
green, wrinkled parent are not inherited as units. Instead, the alleles of the two genes are inherited
as independent units.
P generation: A yellow, round plant (YYRR) is crossed with a green, wrinkled plant (yyrr). Each
parental generation can produce only one type of gamete, YR or yr.
F1 generation: The F1 dihybrid seeds are yellow and round, with a genotype of YyRr. The F1
plants can produce four different types of gametes: YR, Yr, yR, and yr. We can predict the
genotypes of the F2 plants by placing these gametes along the top and side axes of a 4X4 Punnett
square and filling in the boxes to represent fertilization events.
F2 generation: Completion of the Punnett square predicts four different phenotypic classes of
offspring, yellow/round, yellow/wrinkled, green/round, and green/wrinkled, in a ratio of 9:3:3:1.
This is the prediction of the model in which the seed shape and seed color genes assort
independently.
Punnett square:

YR Yr yR yr
YR YYRR YYRr YyRR YyRr
Yr YYRr YYrr YyRr Yyrr
yR YyRR YyRr yyRR yyRr
yr YyRr Yyrr yyRr yyrr
Plain text = yellow, round phenotypeItalic text= yellow, wrinkled phenotypeBold text= green,
round phenotypeBold, italic text= green, wrinkled phenotype
This ratio was the key clue that led Mendel to the law of independent assortment. That's because
a 9:3:3:19:3:3:19, colon, 3, colon, 3, colon, 1 ratio is exactly what we'd expect to see if the \text
F1F1F, 1 plant made four types of gametes (sperm and eggs) with equal frequency: YR, Yr, yR,
and yr. In other words, this is the result we'd predict if each gamete randomly got a Y or y allele,
and, in a separate process, also randomly got an R or r allele (making four equally probable
combinations).
We can confirm the link between the four types of gametes and the 9:3:3:19:3:3:19, colon, 3,
colon, 3, colon, 1ratio using the Punnett square above. To make the square, we first put the four
equally probable gamete types along each axis. Then, we join gametes on the axes in the boxes
of the chart, representing fertilization events. The 161616 equal-probability fertilization events
that can occur among the gametes are shown in the 161616 boxes. The offspring genotypes in
the boxes correspond to a 9:3:3:19:3:3:19, colon, 3, colon, 3, colon, 1ratio of phenotypes, just as
Mendel observed.
[More about two-gene Punnett squares]
44441616

Independent assortment vs. linkage

The section above gives us Mendel's law of independent assortment in a nutshell, and lets us see
how the law of independent assortment leads to a 9:3:3:19:3:3:19, colon, 3, colon, 3, colon,
1 ratio. But what was the alternative possibility? That is, what would happen if two
genes didn't follow independent assortment?
In the extreme case, the genes for seed color and seed shape might have always been inherited as
a pair. That is, the yellow and round alleles might always have stayed together, and so might the
green and wrinkled alleles.
To see how this could work, imagine that the color and shape genes are physically stuck together
and cannot be separated, as represented by the boxes around the alleles in the diagram below. For
instance, this could happen if the two genes were located very, very close together on a
chromosome (an idea we'll explore further at the end of the article).
Illustration of the hypothesis that the seed shape and seed color genes display complete linkage.
In this diagram, the Y and R alleles are represented as a unit (Y-R), as are the y and r alleles (y-
r).
P generation: a (Y-R)(Y-R) yellow, round parent is crossed with a (y-r)(y-r) green, wrinkled
parent. Each parent produces just one type of gamete, containing either a (Y-R) unit or a (y-r)
unit.
F1 generation: the F1 dihybrid is heterozygous for both genes and has a yellow, round phenotype.
The allele pairs remain as indivisible units in the F1 dihybrid: (Y-R)(y-r). When the F1 dihybrid
self-fertilizes, it can produce two types of gametes: a gamete containing a (Y-R) unit and a
gamete containing a (y-r) unit. These two types of gametes will each be produced 50% of the
time, and we can predict the genotypes of the F2 offspring by listing the two gamete types along
the axes of a 2X2 Punnett square and then filling in the boxes to simulate fertilization events.
F2 generation: When the Punnett square is completed, we get three different genotypes in a 1:2:1
ratio: (Y-R)(Y-R), (Y-R)(y-r), and (y-r)(y-r). These genotypes correspond to a 3:1 ratio of
yellow, round:green, wrinkled seeds. This is the prediction of the model in which the seed shape
and seed color genes are completely linked. (Note: this model is not actually correct for these two
genes. This is just one of the two hypotheses that Mendel was testing).
Rather than giving a color allele and, separately, giving a shape allele to each gamete, the \text
F_1F1F, start subscript, 1, end subscript dihybrid plant would simply give one “combo unit” to
each gamete: a YR allele pair or a yr allele pair.
We can use a Punnett square to predict the results of self-fertilization in this case, as shown
above. If the seed color and seed shape genes were in fact always inherited as a unit,
or completely linked, a dihybrid cross should produce just two types of offspring, yellow/round
and green/wrinkled, in a 3:13:13, colon, 1 ratio. Mendel's actual results were quite different from
this (the 9:3:3:19:3:3:19, colon, 3, colon, 3, colon, 1 ratio we saw earlier), telling him that the
genes assorted independently.

The reason for independent assortment

To see why independent assortment happens, we need to fast-forward half a century and discover
that genes are physically located on chromosomes. To be exact, the two copies of a gene carried
by an organism (such as a Y and a yallele) are located at the same spot on the two chromosomes
of a homologous pair. Homologous chromosomes are similar but non-identical, and an
organism gets one member of the pair from each of its two parents.
The physical basis for the law of independent assortment lies in meiosis I of gamete formation,
when homologous pairs line up in random orientations at the middle of the cell as they prepare to
separate. We can get gametes with different combos of "mom" and "dad" homologues (and thus,
the alleles on those homologues) because the orientation of each pair is random.
To see what this means, compare chromosome arrangement 1 (top) and chromosome
arrangement 2 (bottom) at the stage of metaphase I in the diagram below. In one case, the red
"mom" chromosomes go together, while in the other, they split up and mix with the blue "dad"
chromosomes. If meiosis happens many times, as it does in a pea plant, we will get both
arrangements—and thus RY, Ry, rY, and ry classes of gametes—with equal frequency.

Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis.
The homologous chromosomes, with their different versions of each gene, are randomly
segregated into daughter nuclei, resulting in a variety of possible genetic arrangements.
Genes that are on different chromosomes (like the Y and R genes) assort independently. The seed
color and seed shape genes are on chromosomes 1 and 7 of the pea genome, respectively, in real
life^11start superscript, 1, end superscript. Genes that are far apart on the same chromosome also
assort independently thanks to the crossing over, or exchange of homologous chromosome bits,
that occurs early in meiosis I.
[See a picture]
 There are, however, gene pairs that do not assort independently. When genes are close together
on a chromosome, the alleles on the same chromosome tend to be inherited as a unit more
frequently than not. Such genes do not display independent assortment and are said to be linked.
We'll take a closer look at genetic linkage in other articles and videos.
[See a picture]

Check your understanding

1. Suppose you cross a pure-breeding, black-coated dog with curly fur to a pure-breeding, yellow-
coated dog with straight fur. In the F1mgeneration, all the puppies have straight, black coats.
Next, you interbreed the F1 dogs with one another to get F2 generation.

P generation: Pure-breeding dog with black, curly fur is crossed to pure-breeding dog with
yellow, straight fur.
F1 generation: All F1 dogs have black, straight fur. F1 dogs are crossed to produce an F2
generation.
F2 generation: What fraction of F2 puppies will have yellow, straight fur?
If coat color and coat texture are controlled by two genes that assort independently, what
fraction of the F2 puppies are expected to have yellow, straight fur?
Choose 1 answer:
Choose 1 answer:
A)1/4
B)3/4
C)3/16
D)1/16
Since all of the \text F_1F1F, start subscript, 1, end subscript dogs are black and straight-furred,
we know that black fur color and straight fur texture are dominant over yellow fur color and
curly fur texture. If we call the color gene B/b and the texture gene C/c, and use capital letters for
the dominant form of each gene and lowercase letters for the recessive form, we can assign the
two parental dogs genotypes of BBcc (black and curly) and bbCC (yellow and straight-furred).
When the parental dogs are crossed, they produce black, straight-furred \text F_1F1F, start
subscript, 1, end subscript dogs that are dihybrids: BbCc.
A cross between two \text F_1F1F, start subscript, 1, end subscript dihybrid dogs results in the
Punnett square shown below. The \text F_1F1F, start subscript, 1, end subscript dogs can make
four different types of gametes, which are represented along the two axes of the Punnett square.
The squares of the table represent fertilization events in which the gametes on the axes combine.
Since all of the gamete types are equally likely to be produced (because the genes assort
independently, i.e., do not influence each other's inheritance), all the squares in the table
represent equal-probability events, ones that occur 1/161/161, slash, 16 of the time
Now, we need to find the squares that correspond to the outcome we are interested in: a puppy
with yellow, straight fur. To have yellow, straight fur, the puppy must get two recessive alleles
for fur color (bbgenotype) and at least one dominant allele for fur texture (Cc or CCgenotype). If
we go through the table and circle the genotypes that match these requirements, we'll find
that 333 out of the 161616 boxes correspond to yellow, straight-furred puppies. Thus, we would
expect 3/16 of the F2, puppies to have yellow, straight fur.
Answer: 3/16.

Probabilities in genetics
Introduction

The Punnett square is a valuable tool, but it's not ideal for every genetics problem. For instance,
suppose you were asked to calculate the frequency of the recessive class not for
an Aa x Aa cross, not for an AaBb x AaBb cross, but for an AaBbCcDdEe x AaBbCcDdEe cross.
If you wanted to solve that question using a Punnett square, you could do it – but you'd need to
complete a Punnett square with 102410241024 boxes. Probably not what you want to draw
during an exam, or any other time, if you can help it!
The five-gene problem above becomes less intimidating once you realize that a Punnett square is
just a visual way of representing probability calculations. Although it’s a great tool when you’re
working with one or two genes, it can become slow and cumbersome as the number goes up. At
some point, it becomes quicker (and less error-prone) to simply do the probability calculations
by themselves, without the visual representation of a clunky Punnett square. In all cases, the
calculations and the square provide the same information, but by having both tools in your belt,
you can be prepared to handle a wider range of problems in a more efficient way.
In this article, we’ll review some probability basics, including how to calculate the probability of
two independent events both occurring (event X and event Y) or the probability of either of two
mutually exclusive events occurring (event X or event Y). We’ll then see how these calculations
can be applied to genetics problems, and, in particular, how they can help you solve problems
involving relatively large numbers of genes.
[Solution to the five-gene cross problem]
1/21, slash, 2
P(abcde) = P(a) \cdot P(b) \cdot P(c) \cdot P(d) \cdot P(e)P, left parenthesis, a, b, c, d, e, right
parenthesis, equals, P, left parenthesis, a, right parenthesis, dot, P, left parenthesis, b, right
parenthesis, dot, P, left parenthesis, c, right parenthesis, dot, P, left parenthesis, d, right
parenthesis, dot, P, left parenthesis, e, right parenthesis
P(abcde) = (1/2) \cdot (1/2) \cdot (1/2) \cdot (1/2) \cdot (1/2) =(1/2)^5 = 1/32P, left parenthesis,
a, b, c, d, e, right parenthesis, equals, left parenthesis, 1, slash, 2, right parenthesis, dot, left
parenthesis, 1, slash, 2, right parenthesis, dot, left parenthesis, 1, slash, 2, right parenthesis, dot,
left parenthesis, 1, slash, 2, right parenthesis, dot, left parenthesis, 1, slash, 2, right parenthesis,
equals, left parenthesis, 1, slash, 2, right parenthesis, start superscript, 5, end superscript, equals,
1, slash, 32
 P(aabbccddee) = P(abcde_{\text {parent A}}) \cdot P(abcde_{\text {parent B}})P, left
parenthesis, a, a, b, b, c, c, d, d, e, e, right parenthesis, equals, P, left parenthesis, a, b, c, d, e,
start subscript, p, a, r, e, n, t, space, A, end subscript, right parenthesis, dot, P, left parenthesis, a,
b, c, d, e, start subscript, p, a, r, e, n, t, space, B, end subscript, right parenthesis
P(aabbccddee) = (1/32) \cdot (1/32) = 1/1024P, left parenthesis, a, a, b, b, c, c, d, d, e, e, right
parenthesis, equals, left parenthesis, 1, slash, 32, right parenthesis, dot, left parenthesis, 1, slash,
32, right parenthesis, equals, 1, slash, 1024
1/10241, slash, 10241110241024

Probability basics

Probabilities are mathematical measures of likelihood. In other words, they’re a way of

quantifying (giving a specific, numerical value to) how likely something is to happen. A
probability of 111 for an event means that it is guaranteed to happen, while a probability
of 000 for an event means that it is guaranteed not to happen. A simple example of probability is
having a 1/21/21, slash, 2 chance of getting heads when you flip a coin, as Sal explains in
this intro to probability video.
Probabilities can be either empirical, meaning that they are calculated from real-life
observations, or theoretical, meaning that they are predicted using a set of rules or assumptions.
 The empirical probability of an event is calculated by counting the number of times that event
occurs and dividing it by the total number of times that event could have occurred. For instance,
if the event you were looking for was a wrinkled pea seed, and you saw it 1{,}8501,8501,
comma, 850 times out of the 7{,}3247,3247, comma, 324 total seeds you examined, the
empirical probability of getting a wrinkled seed would be 1{,}850/7{,}324 =
0.2531,850/7,324=0.2531, comma, 850, slash, 7, comma, 324, equals, 0, point, 253, or very
close to 111 in 444 seeds.
 The theoretical probability of an event is calculated based on information about the rules and
circumstances that produce the event. It reflects the number of times an event is expected to
occur relative to the number of times it could possibly occur. For instance, if you had a pea plant
heterozygous for a seed shape gene (Rr) and let it self-fertilize, you could use the rules of
probability and your knowledge of genetics to predict that 111 out of every 444 offspring would
get two recessive alleles (rr) and appear wrinkled, corresponding to a 0.250.250, point,
25 (1/41/41, slash, 4) probability. We’ll talk more below about how to apply the rules of
probability in this case.
In general, the larger the number of data points that are used to calculate an empirical
probability, such as shapes of individual pea seeds, the more closely it will approach the
theoretical probability.

The product rule

One probability rule that's very useful in genetics is the product rule, which states that the
probability of two (or more) independent events occurring together can be calculated by
multiplying the individual probabilities of the events. For example, if you roll a six-sided die
once, you have a 1/61/61, slash, 6 chance of getting a six. If you roll two dice at once, your
chance of getting two sixes is: (probability of a six on die 1) x (probability of a six on die 2)
= (1/6) \cdot (1/6) = 1/36(1/6)⋅(1/6)=1/36left parenthesis, 1, slash, 6, right parenthesis, dot, left
parenthesis, 1, slash, 6, right parenthesis, equals, 1, slash, 36.
In general, you can think of the product rule as the “and” rule: if both event X and event Y must
happen in order for a certain outcome to occur, and if X and Y are independent of each other
(don’t affect each other’s likelihood), then you can use the product rule to calculate the
probability of the outcome by multiplying the probabilities of X and Y.
We can use the product rule to predict frequencies of fertilization events. For instance, consider a
cross between two heterozygous (Aa) individuals. What are the odds of getting an aa individual
in the next generation? The only way to get an aa individual is if the mother contributes
an a gamete and the father contributes an a gamete. Each parent has a 1/21/21, slash, 2 chance of
making an a gamete. Thus, the chance of an aa offspring is: (probability of mother
contributing a) x (probability of father contributing a) = (1/2) \cdot (1/2) = 1/4(1/2)⋅(1/2)=1/4left
parenthesis, 1, slash, 2, right parenthesis, dot, left parenthesis, 1, slash, 2, right parenthesis,
equals, 1, slash, 4.

Illustration of how a Punnett square can represent the product rule.

Punnett square:

A a
A AA Aa
a Aa aa
 There's a 1/2 chance of getting an a allele from the male parent, corresponding to the rightmost
column of the Punnett square. Similarly, there's a 1/2 chance of getting an a allele from the
maternal parent, corresponding to the bottommost row of the Punnett square. The intersect of
these the row and column, corresponding to the bottom right box of the table, represents the
probability of getting an a allele from the maternal parent and the paternal parent (1 out of 4
boxes in the Punnett square, or a 1/4 chance).
This is the same result you’d get with a Punnett square, and actually the same logical process as
well—something that took me years to realize! The only difference is that, in the Punnett square,
we'd do the calculation visually: we'd represent the 1/21/21, slash, 2 probability of an a gamete
from each parent as one out of two columns (for the father) and one out of two rows (for the
mother). The 111-square intersect of the column and row (out of the 444 total squares of the
table) represents the 1/41/41, slash, 4 chance of getting an a from both parents.

The sum rule of probability

In some genetics problems, you may need to calculate the probability that any one of several
events will occur. In this case, you’ll need to apply another rule of probability, the sum rule.
According to the sum rule, the probability that any of several mutually exclusive events will
occur is equal to the sum of the events’ individual probabilities.
For example, if you roll a six-sided die, you have a 1/61/61, slash, 6 chance of getting any given
number, but you can only get one number per roll. You could never get both a one and a six at
the same time; these outcomes are mutually exclusive. Thus, the chances of getting either a
one or a six are: (probability of getting a 1) + (probability of getting a 6) = (1/6) +(1/6) =
1/3(1/6)+(1/6)=1/3left parenthesis, 1, slash, 6, right parenthesis, plus, left parenthesis, 1, slash, 6,
right parenthesis, equals, 1, slash, 3.
You can think of the sum rule as the “or” rule: if an outcome requires that either event X or event
Y occur, and if X and Y are mutually exclusive (if only one or the other can occur in a given
case), then the probability of the outcome can be calculated by adding the probabilities of X and
Y.
As an example, let's use the sum rule to predict the fraction of offspring from an Aa x Aa cross
that will have the dominant phenotype (AA or Aa genotype). In this cross, there are three events
that can lead to a dominant phenotype:
 Two A gametes meet (giving AA genotype), or
 A gamete from Mom meets a gamete from Dad (giving Aa genotype), or
 a gamete from Mom meets A gamete from Dad (giving Aa genotype)
In any one fertilization event, only one of these three possibilities can occur (they are mutually
exclusive).
Since this is an “or” situation where the events are mutually exclusive, we can apply the sum
rule. Using the product rule as we did above, we can find that each individual event has a
probability of 1/41/41, slash, 4. So, the probability of offspring with a dominant phenotype is:
(probability of A from Mom and A from Dad) + (probability of A from Mom and a from Dad) +
(probability of a from Mom and A from Dad) = (1/4) + (1/4) + (1/4)=
3/4(1/4)+(1/4)+(1/4)=3/4left parenthesis, 1, slash, 4, right parenthesis, plus, left parenthesis, 1,
slash, 4, right parenthesis, plus, left parenthesis, 1, slash, 4, right parenthesis, equals, 3, slash, 4.

Illustration of how a Punnett square can represent the sum rule.

Punnett square:

A a
A AA Aa
a Aa aa
The boldedboxes represent events that result in a dominant phenotype (AA or AA genotype). In
one, an A sperm combines with an A egg. In another, an A sperm combines with an a egg, and in
a third, an a sperm combines with an A egg. Each event has a 1/4 chance of happening (1 out of 4
boxes in the Punnett square). The chance that any of these three events will occur is 1/4+1/4+1/4
= 3/4.
Once again, this is the same result we’d get with a Punnett square. One out of the four boxes of
the Punnett square holds the dominant homozygote, AA. Two more boxes represent
heterozygotes, one with a maternal A and a paternal a, the other with the opposite combination.
Each box is 111 out of the 444boxes in the whole Punnett square, and since the boxes don't
overlap (they’re mutually exclusive), we can add them up (1/4 + 1/4 + 1/4 =
3/41/4+1/4+1/4=3/41, slash, 4, plus, 1, slash, 4, plus, 1, slash, 4, equals, 3, slash, 4) to get the
probability of offspring with the dominant phenotype.

The product rule and the sum rule

Product rule Sum rule

For independent events X and Y, the For mutually exclusive events X and Y, the
 Product rule Sum rule
probability (PPP) of them both occurring probability (PPP) that one will occur (X or Y)
(X and Y) is P(X) \cdot P(Y)P(X)⋅P(Y)P, left is P(X) + P(Y)P(X)+P(Y)P, left parenthesis, X,
parenthesis, X, right parenthesis, dot, P, left right parenthesis, plus, P, left parenthesis, Y,
parenthesis, Y, right parenthesis. right parenthesis.

Applying probability rules to dihybrid crosses

Direct calculation of probabilities doesn’t have much advantage over Punnett squares for single-
gene inheritance scenarios. (In fact, if you prefer to learn visually, you may find direct
calculation trickier rather than easier.) Where probabilities shine, though, is when you’re looking
at the behavior of two, or even more, genes.
For instance, let’s imagine that we breed two dogs with the genotype BbCc, where dominant
allele B specifies black coat color (versus b, yellow coat color) and dominant allele C specifies
straight fur (versus c, curly fur). Assuming that the two genes assort independently and are not
sex-linked, how can we predict the number of BbCc puppies among the offspring?
One approach is to draw a 161616-square Punnett square. For a cross involving two genes, a
Punnett square is still a good strategy. Alternatively, we can use a shortcut technique involving
four-square Punnett squares and a little application of the product rule. In this technique, we
break the overall question down into two smaller questions, each relating to a different genetic
event:
1. What’s the probability of getting a Bb genotype?
2. What’s the probability of getting an Cc genotype?
In order for a puppy to have a BbCc genotype, both of these events must take place: the puppy
must receive Bb alleles, and it must receive Cc alleles. The two events are independent because
the genes assort independently (don't affect one another's inheritance). So, once we calculate the
probability of each genetic event, we can multiply these probabilities using the product rule to
get the probability of the genotype of interest (BbCc).
Diagram illustrating how 2X2 Punnett squares can be used in conjunction with the product rule
to determine the probability of a particular genotype in a dihybrid cross.
Upper panel:
Question: when two BbCc dogs are crossed, what is the likelihood of getting a BbCc offspring
individual?
Lower panel:
Solution: probability of BbCc = (probability of Bb) x (probability of Cc)
Punnett square for fur color:

B b
B BB Bb
b Bb bb
Probability of Bb genotype: 1/2
Punnett square for fur texture:

C c
C CC Cc
c Cc cc
Probability of Cc genotype: 1/1
Probability of BbCc = (probability of Bb) x (probability of Cc) Probability of BbCc = (1/2) x
(1/2) = 1/4
To calculate the probability of getting a Bb genotype, we can draw a 444-square Punnett square
using the parents' alleles for the coat color gene only, as shown above. Using the Punnett square,
you can see that the probability of the Bb genotype is 1/21/21, slash, 2. (Alternatively, we could
have calculated the probability of Bb using the product rule for gamete contributions from the
two parents and the sum rule for the two gamete combinations that give Bb.) Using a similar
Punnett square for the parents' fur texture alleles, the probability of getting an Cc genotype is
also 1/21/21, slash, 2. To get the overall probability of the BbCcgenotype, we can simply
multiply the two probabilities, giving an overall probability of 1/41/41, slash, 4.
[Let's check that with a Punnett square]

16-square Punnett square illustrating the same solution reached using the probability method.

BC Bc bC bc
BBC
BC BBCC c BbCC BbCC
Bc BBCc BBcc BbCc Bbcc
bC BbCC BbCc bbCC bbCc
bc BbCc Bbcc bbCc Bbcc
Fraction of progeny of BbCcgenotype: 4/16 = 1/4
You can also use this technique to predict phenotype frequencies. Give it a try in the practice
question below!
 Check your understanding
In dogs, black coat color (B) is dominant to yellow coat color (b), and straight fur (C) is
dominant to curly fur (c). The coat color gene and the fur texture gene are on different
chromosomes, so they assort independently, and are not sex linked.
In a cross between two BbCc parents, predict the fraction of offspring with black coat color
and straight fur.
a) 1/16
b) 9/16
c) ¾
d) 15/16
We can break the question down into two smaller questions:
1. What fraction of offspring will have black coat color?
2. What fraction of offspring will have straight fur?
Since black coat color and straight fur are dominant traits, all BB and Bbpuppies will have black
coats, and all CC and Cc puppies will have straight fur, corresponding to 3/4 of puppies in each
case. (You can draw out the individual Punnett squares for the color and texture genes to confirm
these frequencies.)
To get the probability of a puppy having both black coat color and straight fur, you can multiply
the probabilities of these two independent events: (3/4).(3/4) = 9/16
9/16 of the puppies will have black coats and straight fur.

Beyond dihybrid crosses

The probability method is most powerful (and helpful) in cases involving a large number of
genes.
For instance, imagine a cross between two individuals with various alleles of four unlinked
genes: AaBbCCdd x AabbCcDd. Suppose you wanted to figure out the probability of getting
offspring with the dominant phenotype for all four traits. Fortunately, you can apply the exact
same logic as in the case of the dihybrid crosses above. To have the dominant phenotype for all
four traits, and organism must have: one or more copies of the dominant allele A and one or
 more copies of dominant allele B and one or more copies of the dominant allele C and one or
more copies of the dominant allele D.
Since the genes are unlinked, these are four independent events, so we can calculate a probability
for each and then multiply the probabilities to get the probability of the overall outcome.
 The probability of getting one or more copies of the dominant A allele is 34. (Draw a Punnett
square for Aa x Aa to confirm for yourself that 333 out of the 444 squares are either AA or Aa.)
 The probability of getting one or more copies of the dominant B allele is 1/2. (Draw a Punnett
square for Bb x bb: you’ll find that half the offspring are Bb, and the other half bb.)
 The probability of getting one or more copies of the dominant C allele is 111. (If one of the
parents is homozygous CC, there’s no way to get offspring without a C allele!)
 The probability of getting one or more copies of the dominant D allele is 1/2, as for B. (Half the
offspring will be Dd, and the other half will be dd.)
To get the overall probability of offspring with the dominant phenotype for all four genes, we
can multiply the probabilities of the four independent events
3/4. 1/2. 1 . 1/2 . = 3/16

Check your understanding

For the same cross described in the section above (AaBbCCdd x AabbCcDd), what are the odds
of getting offspring with the recessive phenotype for all four traits?
A) 0
B) 1/64
C) 1/32
D) 1/6
It’s not possible to get a quadruple homozygous recessive individual out of this cross.
That’s because the probability of getting two recessive c alleles is zero. The first parent
has only dominant alleles for this gene, ensuring that each of the offspring will receive at
least one dominant C allele (and thus cannot display the recessive phenotype).
How does the zero probability of a cc genotype figure in mathematically? To get the
overall probability of the aabbccdd genotype, we'd have to multiply the probabilities of
the desired genotypes for the other three genes (aa,1/4; bb,1/2; dd,1/2) by the zero
corresponding to the cc genotype, giving an overall probability
of zero.
P(aabbccdd) = P(aa) . P(bb) . P(cc) . P(dd)
= P(1/4). P(1/2) . P(o) . P(1/2) = 0
The probability of getting an individual with a recessive phenotype for all four genes
is 000.
Introduction to heredity review
Key terms

Term Meaning
Genetics The study of biological inheritance
Trait A specific characteristic of an invidual
Gene A unit of heredity that is passed from parent to offspring
Allele One of different forms of a gene
Genotype The genetic makeup of an organism (ex: TT)
Phenotype The physical characteristics of an organism (ex: tall)
Dominant
allele Allele that is phenotypically expressed over another allele
Recessive
allele Allele that is only expressed in absence of a dominant allele
Homozygous Having two identical alleles for a particular gene
Heterozygous Having two different alleles for a particular gene
Diagram that can be used to predict the genotypes and phenotypes resulting
Punnett square from a genetic cross

Mendelian inheritance

Gregor Mendel's principles of heredity, observed through patterns of inheritance in pea plants,
form the basis of modern genetics.
Mendel proposed that traits were specified by "heritable elements" called genes. Genes come in
different versions, or alleles, with dominant allelesbeing expressed over recessive alleles.
Recessive alleles are only expressed when no dominant allele is present.
In most sexually reproducing organisms, each individual has two alleles for each gene (one from
each parent). This pair of alleles is called a genotype and determines the organism's appearance,
or phenotype.

Mendel's laws
 Table showing how genes exchange according to segregation or independent assortment during
meiosis and how this translates into the Mendel's Laws.
Laws of segregation and independent assortment. Image modified from Wikimedia, Public
domain
When an organism makes gametes, each gamete receives just one gene copy, which is selected
randomly. This is known as the law of segregation.
Mendel's second law is the law of independent assortment, which states that the alleles for one
gene sort into gametes independently of the alleles of another gene.

Punnett squares and probability

A Punnett square can be used to predict genotype and phenotypes of offspring from genetic
crosses. A single-gene, or monohybrid cross is pictured below.
 This illustration shows a monohybrid cross. In the P generation, one parent has a dominant
yellow phenotype and the genotype YY, and the other parent has the recessive green phenotype
and the genotype yy. Each parent produces one kind of gamete, resulting in an F{1} generation
with a dominant yellow phenotype and the genotype Yy. Self-pollination of the F{1} generation
results in an F_{2} generation with a 3 to 1 ratio of yellow to green peas. One out of three of the
yellow pea plants has a dominant genotype of YY, and 2 out of 3 has the heterozygous genotype
Yy. The homozygous recessive plant has the green phenotype and the genotype yy.
Monohybrid Punnett square. Image modified from OpenStax, CC BY 4.0
A test cross can be used to determine whether an organism with a dominant phenotype is
homozygous or heterozygous.
 In a test cross, a parent with a dominant phenotype but unknown genotype is crossed with a
recessive parent. If the parent with the unknown genotype is homozygous dominant, all the
resulting offspring will have at least one dominant allele. If the parent with the unknown
genotype is heterozygous, 50 percent of the offspring will inherit a recessive allele from both
parents and will have the recessive phenotype.
Example test cross. Image credit: OpenStax, CC BY 4.0
Punnett squares can be used for a two-gene crosses, or dihybrid crosses by following the same
basic rules as for a monohybrid cross. However, since there are now more gamete types, there
must also be more squares in the table.

Illustration of the hypothesis that the seed color and seed shape genes assort independently.
 In this diagram, the Y and R alleles of the yellow, round parent and the y and r alleles of the
green, wrinkled parent are not inherited as units. Instead, the alleles of the two genes are inherited
as independent units.
P generation: A yellow, round plant (YYRR) is crossed with a green, wrinkled plant (yyrr). Each
parental generation can produce only one type of gamete, YR or yr.
F1 generation: The F1 dihybrid seeds are yellow and round, with a genotype of YyRr. The F1
plants can produce four different types of gametes: YR, Yr, yR, and yr. We can predict the
genotypes of the F2 plants by placing these gametes along the top and side axes of a 4X4 Punnett
square and filling in the boxes to represent fertilization events.
F2 generation: Completion of the Punnett square predicts four different phenotypic classes of
offspring, yellow/round, yellow/wrinkled, green/round, and green/wrinkled, in a ratio of 9:3:3:1.
This is the prediction of the model in which the seed shape and seed color genes assort
independently.
Punnett square:

YR Yr yR yr
YR YYRR YYRr YyRR YyRr
Yr YYRr YYrr YyRr Yyrr
yR YyRR YyRr yyRR yyRr
yr YyRr Yyrr yyRr yyrr
Plain text = yellow, round phenotypeItalic text= yellow, wrinkled phenotypeBold text= green,
round phenotypeBold, italic text= green, wrinkled phenotype
Probabilities in genetics
The two probability rules that are most relevant to Punnett squares are the product rule and
the sum rule.
The product rule states that the probability of two (or more) independent events occurring
together can be calculated by multiplying the individual probabilities of the events.
 Illustration of how a Punnett square can represent the product rule.
Punnett square:

A a
A AA Aa
a Aa aa
There's a 1/2 chance of getting an a allele from the male parent, corresponding to the rightmost
column of the Punnett square. Similarly, there's a 1/2 chance of getting an a allele from the
maternal parent, corresponding to the bottommost row of the Punnett square. The intersect of
these the row and column, corresponding to the bottom right box of the table, represents the
probability of getting an a allele from the maternal parent and the paternal parent (1 out of 4
boxes in the Punnett square, or a 1/4 chance).
Example of the product rule using a Punnett square.
In some genetics problems, you may need to calculate the probability that any one of several
events will occur. In this case, you’ll need to apply another rule of probability, the sum rule.
According to the sum rule, the probability that any of several mutually exclusive events will
occur is equal to the sum of the events’ individual probabilities.
 Illustration of how a Punnett square can represent the sum rule.
Punnett square:

A a
A AA Aa
a Aa aa
The boldedboxes represent events that result in a dominant phenotype (AA or AA genotype). In
one, an A sperm combines with an A egg. In another, an A sperm combines with an a egg, and in
a third, an a sperm combines with an A egg. Each event has a 1/4 chance of happening (1 out of 4
boxes in the Punnett square). The chance that any of these three events will occur is 1/4+1/4+1/4
= 3/4.
Example of the sum rule using a Punnett square.

Common mistakes and misconceptions

 Dominant traits are not always the most common. Some people may think that dominant trait
is the most likely to be found in the population, but the term "dominant" only refers to the fact
that the allele is expressed over another allele. An example of this is Huntington's disease. Even
though Huntington's is caused by a dominant allele, it only affects about 30,000 people in the
United States
 Traits are not always the product of a single gene. For example, there are at least 3 different
genes that are associated with eye color in humans. In addition, there are sometimes more than
two alleles for each gene. For example, there are 3 different alleles of one gene determine coat
color of cats.
A male bird is homozygous recessive for both wacky wings (w) and flashy
feathers (f). He is crossed with a female who is homozygous dominant
(normal wings and normal feathers) for both traits.

What are the genotypes of these birds? (male; female)

A)wwFF; WwFf
(In this answer choice, the male is homozygous recessive for wacky wings (ww) and
homozygous dominant for flashy feathers (FF). The female is heterozygous at both traits (Ww
and Ff).
)
B)wwff; WWFF
(The homozygous recessive genotypes for wacky wings and flashy feathers are ww and ff,
respectively. The homozygous dominant genotypes for normal wings and normal feathers are
WW and FF, respectively.
)
C)WwFf; wwff
In this answer choice, the male is heterozygous at both traits (Ww and Ff). The female is
homozygous recessive at both traits (ww and ff).
()

D)WWFF; wwff

In this answer choice, the male is homozygous dominant at both traits (WW and FF). The female
is homozygous recessive at both traits (ww and ff).