A brief introduction to genetics

18.08.2014 - Lesezeit ca. 6 Min - 1200 Wörter

Introduction to mendelian genetics

I am interested in genetics. Therefore I would like to write a general-purpose library to calculate the results produced by the mating of two specimens of a species.

This project is the first step on the path to an application to calculate the results of corn snake pairings (colour, pattern, …).

This application must first be able to:

Later I would like to create the administration of the relevant genetic properties.

I’ll write it in Java, because I want to improve my skills (I usually work with C#).

Basics

To understand the explanations and examples below, it is necessary to have some skills on genetics. Here is a brief summary of the key terms:

You can find general information about mendelian inheritance in Wikipedia .

We use a capital letter to represent a dominant allele and a lower case letter for recessive one. You can read out that there are these three possible combinations of alleles (based on homozygous / heterozygous and on dominant / recessive values):

  1. Dominant homozygous ( AA)
  2. Recessive homozygous ( aa)
  3. Heterozygous ( Aa or aA)

How to calculate the outcome of a breeding

Obviously I can’t know the outcome of two particular individuals. My goal is to calculate the genotypes’ probability of the possible breeding’s outcome.

The Punnett square is one of the methods that is used to calculate these probabilities.

Punnett squares

Suppose we are crossing plants, this particular plant usually has yellow flowers, but in some cases the flowers are white. It is known that the allele for yellow flowers is dominant to the allele for white flowers. Therefore, we will represent the yellow flowers as A and white flowers as a.

There are six possible Punnett squares types for combinations of one locus.

  1. Dominant homozygous ( AA) x dominant homozygous ( AA)
  2. Recessive homozygous ( aa) x recessive homozygous ( aa)
  3. Dominant homozygous ( AA) x heterozygous ( Aa) or heterozygous ( Aa) x dominant homozygous ( AA)
  4. Recessive homozygous( aa) x heterozygous ( Aa) or heterozygous ( Aa) x recessive homozygous( aa)
  5. Dominant homozygous ( Aa) x recessive homozygous( aa) or recessive homozygous( aa) x dominant homozygous ( Aa)
  6. Heterozygous ( Aa) x heterozygous ( Aa)
Punnett square type 1
A
A
A
AA
AA
A
AA
AA
Punnett square type 2
a
a
a
aa
aa
a
aa
aa
Punnett square type 3
A
a
A
AA
Aa
A
AA
Aa
Punnett square type 4
A
a
a
aA
aa
a
aA
aa
Punnett square type 5
A
A
a
aA
aA
a
aA
aA
Punnett square type 6
A
a
A
AA
Aa
a
aA
aa

Summary

Aa and aA are equivalent for our purposes. So the above tables can be summarized as follows.

Legend:

In
Out
Info
Both dom. hom.
100% AA
100% dom. hom. All flowers are yellow
Both rec. hom.
100% aa
100% rec. hom. All flowers are white
Dom. hom. and het.
50% AA, 50% Aa
50% dom. hom., 50% het. All flowers are yellow.
Rec. hom. and het.
50% aa, 50% Aa
50% rec. hom., 50% het. 50% have white flowers and 50% yellow ones.
Dom. hom. and rec. hom.
100% Aa
100% het. All flowers are yellow.
Both het.
25% AA, 50% Aa, 25% aa
25% dom. hom., 50% het., 25% rec. hom. 75% have yellow flowers and 25% white flowers.

You can check the calculation for two locus on Wikipedia.

From genotype to phenotype

Once the genotype was calculated, it is possible to derive the phenotype. This is actually quite easy. Suppose that A means brown eyes and that a means blue eyes. Two parents with allele Aa have brown eyes but carry both the condition for blue eyes, which does not lead to retribution because it is recessive.

And suppose now we have the following calculation: Aa x Aa:

A a
A AA Aa
a aA aa

This combination results in the genotype: 25% AA, 50% Aa, 25% aa

As already explained, the visible properties form the phenotype. This means that in our Example, there are two phenotypes:

Another nomenclature

We have used a capital letter for Dominant and a lowercase letter for recessive. An allele combination was represented by two letters (eg AA, Aa or aa). This was advantageous for our examples and basic understanding.

There is a more detailed way of illustration:

Here are some examples:

First nomenclature New nomenclature
AA A +A +
Aa;aa A +A a;A aA a

But why do we need another notation? This is necessary if we consider a locus with two or more different mutations.

If we assume that locus X can take three different forms; a, b and c. a is dominant over b and c. And b is dominant over c.

It is possible that the a and c alleles are present at locus X. In the first notation would be represented as Ac. The information about the locus X is lost. If we have Ac and Bc, how can we know which locus is involved? It might be possible that a different locus Y is meant, a Locus that also has alleles b and c. This problem is eliminated by the new notation in which we represent the X locus with alleles a and c as XaXc.

Conclusion

Well, this was in broad terms, the necessary information to create the implementation.

See you soon.


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