This blog post was written by: HolyCow

Genetics #1: Back to the Basics 1.0

Introduction
Hello! 
Welcome to the first of a series of blogs about genetics! In these genetic blogs we will start at the basics of genetics, and go further in depth later on in the series. Needless to say, horses will be the main focus of these blogs! 

Genetics can be complex. Ofcourse we want as much of our playerbase to understand this material. Because of this, we will try to simplify a bit. However: even the basics can be a bit hard to understand without any prior biology knowledge. If you have any questions, don’t be afraid to ask them! 

The first few blog will be all about the basics, as they are in real life genetics. Readers already familiar with these, might find the challenge in these a bit lacking.  I realise a lot of horse people are passionate about genetics, and might get slightly annoyed with the nuances lost by simplifying all the information, or the lack of depth. I ask you to be patient! If these blogs are a success, we will go deeper into the subject to a point where there is more place for nuance and discussion (as we already have on the dutch server), as well as discuss the specific in-game genetics systems.

So, back to the material!

Basic Concepts
In genetics, some concepts are used that are very important to understand and somewhat differentiate from each other. This is not always easy, given that the meaning of some often-used words overlap or are similar.

What you can see about an organism, the traits (such as coat colour, character, etc), is the phenotype. This is partly hereditary, but the environment also has an influence on this.

DNA is a very large molecule in which hereditary information is stored. This makes up most of the genetic / hereditary material in your body. DNA forms a kind of code that your body can read and use. 

The genome is all the genetic material within an organism. In the case of mammals, this consists mainly of DNA. So these are all the genes, but also the remaining DNA.
Besides the genome, you also have the concept of a genotype: A genotype is all the genetic material within an individual. The change from ‘organism’ to ‘individual’ is a small detail, but the implications are different. Whereas ‘genome’ often refers more to groups of organisms (e.g. horses, humans, dogs) or breeds (Arabians, Haflingers, Friesians), ‘genotype’ is used more for an individual, e.g: Bella, that one pony standing in the meadow opposite the cattle farm. So a genotype distinguishes more between the different variants an individual can have, where the genome is more globally about the different genes.

A gene is a small piece of hereditary material (piece of DNA code) that codes for a particular function. Usually a gene codes for a protein, but not always. The name of a gene is often based on the name of the protein they code for. For example, the protein ‘Agouti-signaling protein’, abbreviated ASIP, is encoded by the ASIP gene. The other gene that determines basic colour in horses is called Extension of MCR1 (after ‘Melanocortin 1 receptor’, the protein) (This naming after the encoded protein is not always the case, by the way. Slightly outdated is the naming of a gene based on the disease they cause. In addition, the name of a genes that exists similarly in different animal species and also code for the same proteins can sometimes have different names)

The locus is the spot within the genome where a particular gene can be found. So this is (usually) at a particular spot on a chromosome. In practice, the (informal) name of the gene is often used for this. Compare that to discussing eating together at McDonalds. You can sent your friends exactly the coordinates that determine where on earth a particular address is located, or simply: ‘See you at Maccies’

Most DNA is stored as chromosomes. Chromosomes consist of DNA densely folded around special proteins. Chromosomes are inside the nucleus of the cell. 
Virtually the entire DNA genome is divided among these chromosomes. There usually are two of each type of chromosome in each cell: a pair of chromosomes. Each chromosome of these pairs contain the same genes. For example, a horse has 32 chromosome pairs, and therefore 64 chromosomes in most cells. 
Imagine that Chromosome 1 contains: Gene for basic colour, gene for speed, and gene for character, than the second Chromosome 1 in that pair also contains these genes. And then on both of the Chromosomes 2 there is, for example, the gene for endurance, gene for white pattern. (This is mostly used as an example: In reality, all these traits are determined by multiple genes, on multiple pairs of chromosomes)

So having a pair of chromosomes means you have duplicates of most of the genes. So using the previous example: you have 2x the gene for base colour, because you actually have 2x Chromosome 1. Because the chromosomes of such a pair of chromosomes have the same genes, we call them homologous to each other. 

These chromosomes are called homologous, and not exactly the same, because several variants of a gene are often possible: 
An allele or ‘gene variant’ is a variant of a gene. On MH, the term ‘gene’ is usually used for this. For example: ‘Red gene’ and ‘Black gene’. Actually, it should be ‘Red allele’ and a ‘black allele’ on the gene ‘Base colour’. But the terms gene and allele are often used interchangeably. (Even in real life, it has become semi-accepted to talk about a gene instead of an allele or gene variant).
Another example: If you have the gene for eye colour, you can have an allele ‘brown eyes’ and an allele ‘blue eyes’. Both are variants of the ‘eye colour’ gene.

It is possible that on one chromosome 1, gene ‘Basic colour’ has the variant ‘Black’, and on the other chromosome 1, that same gene has the variant ‘Red. These chromosomes would be homologous (having the same genes in roughly the same order), but not the same (having different gene variants)

When such a pair of chromosomes both have the same allele on a certain gene, we call it homozygous. When both chromosomes have a different allele on that same gene, we call it heterozygous. 
To take the example of the gene ‘Base colour’ again: 2x a black allele = homozygous. 2x a chestnut allele = homozygous. 1x black and 1x chestnut allele = heterozygous. 



When there are different types of alleles within a gene that are both present (i.e. when you are heterozygous for a certain gene), it is often the case that one allele is expressed, while the other cannot be expressed. In the example of coat colour, it may be that the allele for black is ‘stronger’ than the allele for red, meaning an animal heterozygous for coat colour (1x Red, 1x Black), ends up having a black coat. 
When this is the case, we call the allele that is visible in the phenotype ( e.g. black allele) dominant, and the allele that is suppressed / (almost) not visible in the phenotype (e.g. red allele) recessive. 

This was the first part. Next part, I will briefly discuss how alleles inherit, and how to note the genotypes!