¶ Haplotypes, Linkage, and Meiotic Recombination
This is a more advanced lesson on inheritance. Please read Genetics Basics and Inheritance Part 1, first.
¶ If a horse is heterozygous at 2+ genes, does that mean the foal has a 50/50 chance of inheriting any of those alleles?
If we are talking about each gene individually, then the answer is yes*. If we are talking about 2 or more genes at once, not necessarily. If those genes are located on the same chromosome, then they are ‘linked’ and certain alleles will be more likely to be inherited together, while certain combinations will be far less frequent.
*Fun fact, this is actually a white lie. In the game this is true, but, in real life there are some alleles which can actually make it so they have a greater than 50% chance of being inherited through something called ‘meiotic drive.’ That’s irrelevant to the game though, so just FYI. If you are curious, one example is the t-haplotype in mice!
¶ What is linkage?
Linkage describes the skew of inheritance of certain haplotypes because the genes are located on the same chromosome. See figure A below.
¶ What is a haplotype?
A haplotype is a grouping of alleles that, because of linkage, tend to be inherited together.* See figure B.
*Note, there is another definition of haplotype that indicates the entire set of alleles, across all chromosomes, that the offspring inherited from one parent. So, in that case, some of the alleles described in the haplotype would not be linked. Just know that this definition exists, for the purpose of Eq, I will always use ‘haplotype’ to refer to linked genes and alleles.
¶ How are haplotype and genotype different?
A genotype describes all alleles the horse has for a specific gene or genes. A haplotype involves two or more genes, and tells you which alleles are physically linked to each other. So, a haplotype contains positional information of the alleles within a genotype.
For example, if you look at figure B, just chromosome 1,
The horse’s genotype would be:
Aa Bb
Their haplotypes would be:
AB ab
¶ How does linkage affect inheritance?
If genes A and B were not linked, then the foal would have a 25% chance of inheriting either AB, Ab, aB, or ab. See the ‘No Linkage’ example in figure C, further below.
But, because chromosomes are each one long strand of DNA, if two genes are linked, then they are physically connected to each other. Because of this, the parent in the figure C example would produce 50% foals with AB haplotypes, and 50% ab.
But, biology rarely lets anything be that simple. In this example, there is still a chance that A and b can be inherited together, or a and B. How? Because of something called meiotic recombination.
¶ What is meiotic recombination?
Meiotic recombination, or sometimes it's just referred to as recombination, is a special process that occurs during meiosis, where homologous chromosomes are physically broken, and their pieces are swapped. This typically happens in 1-2 places along each chromosome. So, if the break happens between genes A and B, then A and b or a and B could be inherited together.
¶ How does recombination affect inheritance?
Before I mentioned recombination, we learned the parent in figure C would produce 50% AB and 50% ab foals. With recombination though, there is a chance that a foal could be Ab or aB.
How high of a chance? It depends on how far apart genes A and B are on the chromosome. Basically, the further apart they are, the higher the chance recombination will occur between them.
Fun fact, there is a measurement in real life, called centimorgans (cM), that can tell us the chance. 1 cM = a 1% chance they will recombine. So, in the example in figure C, genes A and B were 4 cM apart (2 Ab + 2 aB).
¶ Are any genes in Eq linked to each other?
Yes! Simulating linkage in a game isn’t easy, but we have linked 7 pairs of genes in Eq (so far). Two of these pairs are based on genes that are linked in real life. We will make a future post about some of these genes.