Andrew Almendarez

MEEN 3310.001
Use of Matrices to Determine Genetic Probability
Matrices are rectangular arrays of numbers, symbols, or expressions, arranged in rows
and columns. Through prescribed manipulations and interpretations matrices can be used to
represent and solve physical problems. One such problem is finding the probability of a certain
genotype within a population over multiple generations.
The ability to predict the probability of a certain genotype is useful to those in several
industries where the genetic makeup of an organism can affect the profitability of the organism.
An example is the trying to breed cows that produce the most milk. If cows of a certain genotype
were known to produce more milk than others it is useful to know how many cows of that
genotype there will be after a number of generations, and what will maximize the proportion of
that genotype in the future. This is where the Punnett is used in conjunction with matrices.
The Punnett square is a tool used to calculate the probability of a certain genotype or
phenotype to show up in the offspring of two parents with known genes. The two types of alleles
are dominant and recessive, dominant meaning that when paired with a recessive the dominant
trait is the one that is present in the offspring. A basic Punnett square is shown below.

FIGURE 1: Basic Punnett square

Andrew Almendarez
MEEN 3310.001
In the previous figure it is seen that from a crossing of an Aa combination with another Aa
combination yields a 25% chance of AA and aa, and 50% chance Aa. This tool can be used for
breeding of plants and animals in order to maximize the possibility of having an organism with a
desired trait. Punnett squares can also be used to determine the probability of a combination of
traits as well as long as the two traits are independent of each other in development, leading to
the larger dihybrid square below.

FIGURE 2: Dihybrid cross Punnett square

This version of the Punnett square can be used to achieve a preferred combination of two traits.
For example, a dog breeder may want dogs with soft fur and a nonaggressive nature, both of
which are stored in the dominant genes. So to maximize the chance of breeding such dogs only
dogs with the combination AABB are bred with the other combinations. This situation can be
represented with matrices as well as the proportions of future generations.
The possible outcomes for the offspring include the nine combinations AABB, AABb,
AaBB, AaBb, AAbb, Aabb, aaBB, aaBb, and aabb. The probability of each of these outcomes
will become the rows for the matrix. Then the columns will represent the crossing of AABB with
the rest of the gene combinations. This will give a matrix 9x9 matrix A

Andrew Almendarez
MEEN 3310.001
Probablilit

Crossed With

y
AABB
AABb
AaBB
AaBb
AAbb
Aabb
aaBB
aaBb
aabb

AABB
1
0
0
0
0
0
0
0
0

AABb
1/2
1/2
0
0
0
0
0
0
0

AAbb
0
1
0
0
0
0
0
0
0

AaBB
1/2
0
1/2
0
0
0
0
0
0

AaBb
1/4
1/4
1/4
1/4
0
0
0
0
0

Aabb
0
1/2
0
1/2
0
0
0
0
0

aaBB
0
0
1
0
0
0
0
0
0

aaBb
0
0
1/2
1/2
0
0
0
0
0

This matrix A is the transition matrix representing a transformation of population distribution

from one generation to the next. Assuming the initial population of dogs has an equal
distribution the initial distribution vector x0 is

[]

1/9
1/9
1/9
1/9
x 0= 1/9
1/9
1/9
1/9
1/9

One generation later the distribution will be x1 = Ax0

aabb
0
0
0
1
0
0
0
0
0

Andrew Almendarez
MEEN 3310.001

][ ] [ ]

1 1/2 0 1/2 1/4 0 0 0 0 1/ 9

1/4
0 1/2 1 0 1/4 1/ 2 0 0 0 1/ 9
1/4
0 0 0 1/2 1/4 0 1 1/2 0 1/ 9
1/4
0 0 0 0 1/4 1/ 2 0 1/2 1 1/ 9
1/4
x 1= 0 0 0 0
0
0 0 0 0 1/ 9 = 0
0 0 0 0
0
0 0 0 0 1/ 9
0
0 0 0 0
0
0 0 0 0 1/ 9
0
0 0 0 0
0
0 0 0 0 1/ 9
0
0 0 0 0
0
0 0 0 0 1/ 9
0

After another generation x2 = Ax1 = A2x0 which equals (1/2,3/8,1/8,0,0,0,0,0,0)T. Then xn = Anx0
and as n approaches infinity xn approaches (1,0,0,0,0,0,0,0,0)T, but in actuality it takes about 14
generations before there is a 99.99% chance of getting AABB and a 0.01% chance of getting
AABb. If the breeder wishes to know the population distribution after n generations all they
would need to do is to calculate An and multiply by x0, but that involves a large amount of
calculation and may result in computational error. To reduce the chances of error diagonalization
can be used.
The basic premise of diagonalization is that the matrix An = PDnP-1, where

n
D= 0

0 0
2 0

0 k

with k being the eigenvalues, and P is the linear combination of the eigenvectors. The
eigenvalues can be found by solving the det(A- I) = 0, which is in this case

Andrew Almendarez
MEEN 3310.001

1
1/ 2
0
1/2 1/4
0
0
0
0
0
1/2
1
0
1/4 1/2
0
0
0
0
0
0 1/2 1/4
0
1
1/2
0
0
0
0
0 1/4 1/2
0
1/2
1
0
0
0
0
0
0
0
0
0 =0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0

The determinant is equal to the product of the diagonal since this matrix is triangular which leads
to 1 = 1, 2 = 1/2, and 3 = 4 = 5 = 6 = 7 = 8 = 9 = 0. The eigenvectors are found by solving
(A- 1I)x = 0

|[ ]

1
1/2
0
1/2 1/4
0
0
0
0
0
1/2
1
0
1/4 1/2
0
0
0
0
0
0 1/2 1/4
0
1
1/2
0
0
0
0
0 1/4 1/2
0
1/2
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0

x1
x2
x3
x4
x5 =0
x6
x7
x8
x9

and the same for the rest of the eigenvalues. This leads to the eigenvectors (1,0,0,0,0,0,0,0,0)T, (

2
,
2

2 ,0,0,0,0,0,0,0)T, (0.4082,-0.8165,0.4082,0,0,0,0,0,0)T,
2

(-0.4082,0.8165,-0.4082,0,0,0,0,0,0)T, (0.4082,-0.8165,0.4082,0,0,0,0,0,0)T,
(0.4082,-0.8165,0.4082,0,0,0,0,0,0)T, (-0.4082,0.8165,-0.4082,0,0,0,0,0,0)T,
(0.4082,-0.8165,0.4082,0,0,0,0,0,0)T, and (0.4082,-0.8165,0.4082,0,0,0,0,0,0)T. Then

Andrew Almendarez
MEEN 3310.001

[
[

1 0 0 0 0 0 0 0 0
0 1/2 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0
D= 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0
and

1 2/2 0.4082 0.4082 0.4082

0.4082 0.4082 0.4082
0.4082
0 2/ 2 0.8165 0.8165 0.8165 0.8165 0.8165 0.8165 0.8165
0
0.4082 0.4082 0.4082
0.4082 0.4082 0.4082
0.4082
0
0
0
0
0
0
0
0
0
0
P= 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0

As it turns out this particular case is not solvable with diagonalization as in order to be
diagonizable A needs to have n linearly independent eigenvectors, and this is not the case as
several of the vectors are identical meaning they are linearly dependent. Given this outcome
manual calculations had to be performed in order to predict future populations. Below is a chart
showing the population distributions over generations.

Andrew Almendarez
MEEN 3310.001

Population Distribution

AABB

AABb

AaBB

AaBb

Aabb

aaBB

aaBb

aabb

AAbb

FIGURE 3: Population distribution graph

With this data it is clear that selective breeding does have a significant effect on
the population distribution, and that by breeding only dogs with the gene combination AABB
yields and even greater percentage of the sought after traits. While the desired outcome of
breeding only AABB was not solvable through diagonalization, other combinations in which
every possible outcome has a possibility of being, AaBb crossed with AaBb for example, would
lead to linearly independent eigenvectors and therefore be diagonizable. Even so the concept of
transition matrices in addition with Punnett squares were able to graph the distribution of
phenotypes among generations of animals.