Genotype

An organism's genotype is not visible to the naked eye. It's not even visible under a microscope. To determine it in a laboratory either takes endless sets of microarrays and DNA-PCR or the power of super-computers and mass-sequencing technology. Yet genotype, in combination with environmental effects, determines so much of what you look like and how you behave - from eye color to height to personality to food preferences. Ultimately, your genotype is an orderly sequence of DNA that encodes the proteins that make you, you.

Definition of Genotype

Genotype is defined as the genetic makeup of an organism. In terms of a particular trait, genotype describes the nature of the alleles of that trait. Every living thing has genes, and the particular alleles of those genes help determine how that organism looks and behaves - its phenotype.

Terms for Describing Genotype

What are some terms we must understand when describing genotype?

Homozygosity is the state of a homozygous organism for a given trait. In other words, both of its alleles for that gene are the same. Let's use cystic fibrosis to examine this. There are two possible alleles on the gene that control whether someone gets cystic fibrosis or not. F is the normal variant, and f is the mutated cystic fibrosis variant. F is the dominant allele, which means there must only be one copy of it for an individual not to have cystic fibrosis. If f is the recessive allele, there must be two copies of it for the individual to have the disease. There are two possible homozygous genotypes at this gene: either someone is homozygous dominant, has the genotype (FF), and doesn't have cystic fibrosis, or someone is homozygous recessive, has the genotype ff, and has cystic fibrosis.

Heterozygosity is the state of a heterozygous organism for a given trait; its alleles for that gene are different. Let's continue with our previous example. For someone to be heterozygous at the gene controlling cystic fibrosis, their genotype would have to be Ff. Because this gene acts on the principles of Mendelian inheritance (one allele exhibits complete dominance over the other), this person would NOT have cystic fibrosis. They would be a carrier; their genotype shows the presence of a mutant allele, but their phenotype is the same as someone who is homozygous dominant and doesn't have any mutant alleles at all.

Although we've mentioned this word previously, we will also use this opportunity to define what an allele is. We will define three terms that - as different as they sound - have similar meanings and usages. All three words are important when describing genotype:

1. Allele

2. Mutation

3. Polymorphism

Allele Definition:

An allele is a variant of a gene. In the cystic fibrosis gene mentioned above, the two alleles are F and f. Alleles can be dominant or recessive. They are organized into pairs on chromosomes, which are the total physical representation of our DNA and genetic material. Some genes have more than two alleles, but there are always at least two present because, by definition, they require variation.

Mutation Definition:

For an allele to be called a mutation, it usually has three factors -

1. It appeared spontaneously in an organism.
   • Such as a cancer cell developing a mutation or if something goes wrong during reproduction and a newly formed organism develops a mutation.
2. It is deleterious.
   • Deleterious means that it is harmful to the organism.
3. It is rare.
   • Typically it has to be an allele present in less than 1% of the population!

Polymorphism Definition:

Polymorphism refers to any allele that is not a mutation: thus, it occurs more frequently than mutations, is not typically deleterious, and does not necessarily appear spontaneously (or de-novo) in an organism for the first time.

Types of Genotypes

With genes that have only two possible alleles, which follow the principles outlined by Mendelian genetics, there are three types of genotypes:

1. Homozygous dominant

2. Homozygous recessive

3. Heterozygous

Dominant Genotypes:

There are two types of dominant genotypes when following the patterns of Mendelian Inheritance. One is the homozygous dominant genotype (AA), which has two copies of the dominant allele. The other is the heterozygous genotype. We do not call this 'heterozygous dominant' because the dominance is implied. The implication is that when an organism is heterozygous at a gene, there are two different alleles, and according to Mendelian genetics, one of the alleles shines through in the phenotype and is dominant. So saying 'heterozygous dominant' would be redundant.

Dominant genotypes always have dominant alleles, they may have recessive alleles, and they occur more commonly in a population. This phenomenon occurs because of Mendel's Law of Dominance, which states that the dominant allele will always control the phenotype of a heterozygote. Thus, dominant phenotypes will naturally be the most prolific in any population because this phenotype encompasses both homozygous dominant and heterozygous genotypes.

Recessive Genotype

When following the patterns of Mendelian Inheritance, there is only one type of recessive genotype. It is the homozygous recessive genotype (for example, aa). It is typically denoted with two lower case letters, but it can also be capitalized. When it is capitalized, it will be followed by some mark like an apostrophe or asterisk (F'), or the recessive allele will be explicitly obvious to you.

What are the Tools We Have for Determining Genotype?

When determining the genotype, we can use Punnett squares. These are used primarily in Mendelian patterns of inheritance. Punnett squares are tools in biology that help us analyze the prospective genotypes of offspring of two organisms (often plants) when we cross them. When we know the genotype of the two parents, we can see the ratios of the genotypes of their future children. For example, if two homozygous dominants are crossed, we can see that all of their offspring will be heterozygotes (Fig. 1).

Homozygous cross leading to 100% heterozygote offspring.

Sometimes, a Punnett square is not enough, especially when examining genotypes for human disorders (like cystic fibrosis). It can tell us the genotype of parents, but not grandparents and other ancestors. When we want a bigger picture demonstration of a genotype, we use something called a pedigree.

An example of a pedigree for a family

Examples of Genotype

Genotypes are best understood in relation to the phenotype they contribute to. The table below will show a possible genotype and phenotype pair (Table 1).

Table 1: Some examples of genotypes and the phenotypes they cause.

Remember that not all characteristics follow the principles of Mendelian inheritance. Human blood types, for example, have three possible alleles for each gene; A, B, and O. A and B exhibit codominance, meaning they both are expressed simultaneously; while O is recessive to both of them. These three alleles combine to produce four possible different blood types - A. B, O, and AB. (Fig. 3).

Possible human blood types, due to codominance, and multiple alleles