I'm a geneticist but I cannot wrap my head around the snake color genetics you talk about. Whenever you talk about it, I'm just like *nod nod* I hope you get the colors you want!
achievement unlocked: major dialogue trigger!
SO. Welcome to my big nerdery thing re: corn snakes!!!! Long post incoming, I am NOT SORRY!
The very *very* basics for the people who are not geneticists-
Normal henceforth refers to the basic wild-type color and/or pattern, and genetics.
Morph refers to alterations to this wild-type, be it mutation-based like recessive, incomplete dominant, and dominant genes, or selectively bred.
The vast majority of corn snake morphs are simple recessive. This means that in order to display a particular trait the animal must have two matching copies of the gene. In order to get two copies, each parent must have at least one copy to potentially pass down to offspring. Everyone remember that (actually highly inaccurate) lesson about blue eyes vs brown eyes in grade school biology? Like that.
Some corn snake morphs are incomplete dominant. These are (maybe?) red factor (likely 3+ versions btw), palmetto, masque and halo. This means that if they have one copy of the gene they look a particular way (other than normal) and if they get two copies they look another way. Palmetto is the most extreme example of this.
Some corn snake morphs are dominant. These are tessera and buf/toffee (increasing speculation these are the same thing). Dominant means that the snake only needs one copy to express the trait AND that two copies makes no difference to how that trait looks.
Some corn snake morphs are selectively bred. These are morphs like okeetee-phase, miami-phase, sunglow, candycane and.... my onyx-line charcoals. These are basically 'breeds' of corn snake and require meticulous selection (often not done by many breeders...) to maintain the appearance that makes these selectively bred morphs distinct from the parent morph or from normals. For examples, okeetee-phase snakes are *supposed* to be selectively bred for extremely thick black borders around the markings of the snakes, but many snakes sold as okeetees have borders that are barely thicker than a standard normal. These should not be sold as okeetees. They do not qualify.
Both dominant and incomplete dominant morphs are a "you either have it or you don't" type situation - If the animal is not visual, it does not carry the gene. period. A recessive gene will be 'hidden' when there's only one copy. A snake with a single recessive gene will not visually show the trait, but paired to the right mate can produce offspring that *will* show it.
Having one normal gene and one mutant gene is referred to as being 'het' for a gene/trait. Het is short for heterozygous, meaning "different pair". Having two copies is often referred to as 'homo', short for homozygous which means "same pair".
When it comes to passing down a trait, an animal that is homozygous for a trait will *always* pass one copy of that gene down to its offspring. If that baby is not a visual for a recessive trait, it will be 100% het for it, there's no other option for the parent to have given. If it's a dominant or incomplete dominant trait, every single baby will be showing the trait.
An animal that is het for a trait only has a 50% chance of passing on the mutant gene. It can either give the mutant gene or a normal gene and it's a complete toss-up over which will be provided.
However, most of the time when people refer to 'hets' in corn snakes, they're talking about recessive genes. Hets and possible hets (where there's a *chance* they carry the gene, but not a certainty) are often referred to with percentages. 100%, 66%, and 50%. You cannot go lower than 50%.
If you breed something homozygous recessive to something het for the same trait, roughly 50% of the babies will be visual for the trait and 50% will be 100% het. Only half the babies will be visual because the homozygous parent MUST give a mutant gene, but the het parent only has a 50% chance to provide it. The non-visual babies will ALL be 100% het for the trait, because that homozygous parent has no other option to provide it. Behold... a punnet square showing how that works. cc is homozygous charcoal, and we'll say Nc (not the actual way these things are shown, but it makes more sense this way) is a Normal gene and a charcoal gene.
Half the squares are cc - visual charcoals, two copies of the charcoal gene because the cc parent *had* to give a c. The Nc parent only gave a c half the time, and an N the other half. The Nc babies have one Normal gene and one charcoal gene.
Things get weirder when you breed two animals that are both het. Each parent only has a 50% chance of providing the mutant gene. With this pairing, only a quarter of the babies will be visuals. Of the non-visual babies, 2/3rds will have gotten one copy of the mutant gene, and 1/3 will have received NO copy! These none visual babies are referred to as being 66% possible het for a trait.
This 66% number tends to confuse a lot of people. A lot think it should be 75% (with that being the halfway point between a 50% het and a 100% het) but they're failing to subtract the visual babies from the equation.
Punnet square time again!
There are.... 4 squares. >_>
These squares show all the potential genetic combinations from pairing a het to a het for charcoal. One visual, 2 hets, one normal. But we're interested purely in the hets right now. We know for a fact that the visual charcoal got copies of the genes. That's not in question. So remove that square. We're now left with 3 squares. 2 of these 3 squares (66%...) have babies that are het for charcoal. One square has a baby that got no charcoal genes at all.
Visually, these 3 babies *all look the same*. You cannot tell by looking who is het for a recessive trait and who is not. Therefore, all the babies in the clutch have a 66% chance of carrying the gene.
50% hets show up when only one parent is het for a trait. Because the other parent has no ability to pass on a mutant gene, none of the babies will be visuals. And because the first parent is only het, it can give either a normal gene or a mutant gene. Again, all these babies look normal and you cannot tell who is het and who isn't. All the babies have only a 50% chance of having received the mutant gene.
As for my main breeding lines, the gene I'm working primarily with is charcoal which is recessive. They're also all at least het masque(incomplete dominant) but it really doesn't do much and I don't care about it so I ignore it. All of my current batch of charcoals are either het for, or homozygous diffused(recessive) as well.
The mother of most of my line was a charcoal het diffused, hypo(recessive), amel(recessive). The father of many of them was a pewter (charcoal + diffused) het anery(recessive), lavender(recessive).
So let's break this down. Both animals are homozygous charcoal. They will each give, for sure, a charcoal gene. Therefore ALL the babies will also be homozygous, visual charcoals. The female is het for diffused, the male is homozygous diffused. Half their babies will be pewters and half will be 100% diffused.
But now look at the rest of those hets. The female has hypo and amel. The male has anery and lavender. None of those match up. They each only have a 50% chance of giving their babies a copy of any particular het trait. So all the babies are 50% possible het for hypo, amel, anery and lavender!
Thanks to the wonders of genetic testing I know which babies were given the amel trait (Larune and Marquina), which were given the lavender trait (Dusk), and which got neither (Jet and Coal).
Previously (and this is still the case for most corn snake morphs, but they are working on it), the only way to know which possible hets a corn snake actually received was through test breeding. This is not great because it produces a lot of babies that are 'byproducts' rather than the main goal and gives you fewer years to achieve your goal with any given female.
Larune and Coal's clutch was a two-fer: It's a chance to get myself some more onyx-line worthy charcoals AND let me test Larune for her 50% diffused het and Coal's 50% hypo het. And as I got a pewter baby, that shows that she does indeed carry the diffused gene... and because what is unquestionably a phantom nose is now peeking through an egg, Coal proved to be carrying the hypo gene.
Now, my end goal with my charcoals is selectively breeding towards a solid black snake. To that end I am keeping the darkest babies from each clutch to pair together to get even darker babies.
Having hets for genes that make for lighter babies (amel, hypo, lavender and anery as *totally* random examples) is not ideal towards that end goal. The main gene I want to completely weed out is anery. I just don't find carbons (anery + charcoal) to be interesting looking. The amel gene is completely counterproductive (charcoal + amel = solid white snake) but blizzards are uncommon and popular so I wouldn't have been entirely sad to produce those. However, neither of my main males carries the gene at all which is actually a benefit to having as many snakes as possible to choose dark babies from. Lavender makes for a nice medium gray snake when paired with charcoal. Doesn't really help my goal to make dark snakes, and as neither of my main males carries the gene it's not something I really have to worry about in this generation. Hypomelanism makes for light gray snakes when paired with charcoal. This really doesn't help with my end goal either. Would rather than Coal was *not* het for hypo, and I still don't know if Jet is or not. I'll find out next year when I pair him to Larune.... or sooner if they develop a DNA test.
....
Okay, I'm done now!
