In the previous chapters, we learned horses have two alleles of every gene. When breeding, a foal inherits one allele from each parent. We also learned how to write down and interprate these alleles. Now that we have this information, how can we use it to actually predict what the foal could look like?
A Punnett Square is a square diagram that shows all the possible outcomes of a specific cross. If we know the color genetics of the parents, we can use this to predict all possible foal colors and their chances.
Singe trait/ gene cross
Let's start simple and make a Punnett square for just one gene. We'll use the extension gene of these parents as an example:
Sire: E/e (bay/black)
Dam: e/e (chestnut)
Write the alleles of the sire on top of the square
Sire
E
e
Write the alleles of the dam on the left of the square
Sire
E
e
Dam
e
e
Fill in the squares on the inside by combining the allele on the top and on the left
Sire
E
e
Dam
e
E/e
e/e
e
E/e
e/e
The possible outcomes of this cross are the inside squares: E/e, e/e, E/e and e/e. That gives us:
50% E/e (black/bay)
50% e/e (chestnut)
So, this cross results in a 50% chance of getting a black or bay foal, and a 50% chance of a chestnut foal.
Two traits/ genes
Of course, most coat colors aren't determined by just one gene. For example, in the example above, we looked at the extension gene only. However, to know the base color of a horse, we need to look at the agouti gene as well. So, let's make a Punnett square again, this time using two genes.
Sire: E/e A/a (bay)
Dam: e/e A/a (chestnut)
Write all possible allele combinations of the sire on top of the square (The sire could pass on E + A, E + a, e + A, or e + a)
Sire
E A
E a
e A
e a
Write all possible allele combinations of the dam on the left of the square
Sire
E A
E a
e A
e a
Dam
e A
e a
e A
e a
Fill in the squares on the inside by combining the alleles on the top and on the left
Sire
E A
E a
e A
e a
Dam
e A
E/e A/A
E/e A/a
e/e A/A
e/e A/a
e a
E/e A/a
E/e a/a
e/e A/a
e/e a/a
e A
E/e A/a
E/e A/a
e/e A/A
e/e A/a
e a
E/e A/a
E/e a/a
e/e A/a
e/e a/a
The possible outcomes of this cross are the inside squares. This time, there are a lot more possibilities:
e/e _/_ (chestnut) = 8/16 or 50% (italic)
E/_ A/_ (bay) = 6/16 or 37.5% (normal)
E/_ a/a (black) = 2/16 or 12.5% (bold)
This cross gives us a 50% chance of getting a chestnut foal, 37.5% chance of a bay foal, and a 12.5% chance of a black foal.
Forked-line method
When two or even more genes get involved, Punnett squares become quite difficult to work with. A cross with four genes would result in 256 squares that need to be filled in! In cases like this, the forked line method can be used. We can solve the cross in the last example in this way:
Sire: E/e A/a (bay)
Dam: e/e A/a (chestnut)
Make simple Punnett squares for every gene involved (not necessary, but helps a lot)
Sire
E
e
Dam
e
E/e
e/e
e
E/e
e/e
Sire
A
a
Dam
A
A/A
A/a
a
A/a
a/a
Starting with the extension gene, we write down the possible outcomes, in this case, 1/2 E/e and 1/2 e/e, in the first row
E/e (1/2)
e/e (1/2)
This is where the fork part comes in. In the second row, we add the possible outcomes of agouti below every option. Here, we have 1/4 a/a, 1/2 A/a, and 1/4 A/A.
E/e (1/2)
a/a (1/4)
A/a (1/2)
A/A (1/4)
e/e (1/2)
a/a (1/4)
A/a (1/2)
A/A (1/4)
To get the chance of every outcome, we multiply the values along each path. For example, for E/e a/a we multiply 1/2 * 1/4 = 1/8 or 12.5%. If we add up all the e/e outcomes, we get 1/8 + 1/8+ 1/4 = 1/2 or 50%. The same result as the Punnett square method!
E/e (1/2)
a/a (1/4)
A/a (1/2)
A/A (1/4)
E/E a/a (1/8)
E/e A/a (1/4)
E/e A/A (1/8)
e/e (1/2)
a/a (1/4)
A/a (1/2)
A/A (1/4)
e/e a/a (1/8)
e/e A/a (1/4)
e/e A/A (1/8)
If we're interested in color outcomes only and not the chance of every genotype, we can simplify everything even more. A/a and A/A both have the same effect, so we can combine them. Here, we'll use 3/4 points and 1/4 body (referring to the restriction of black pigment).
Black/bay (1/2)
body (1/4)
points (3/4)
Black (1/8)
Bay (3/8)
chestnut (1/2)
body (1/4)
points (3/4)
chestnut (1/2)
Coat color calculators
Calculating all these chances can be a lot of work, especially when multiple genes get involved. Fortunately, there are some horse coat color calculators online that can do this automatically (they can be incomplete or outdated, so keep that in mind when using them!). Here are some I recommend:
