Now I'm going to expand on my post to hopefully clarify some things.
The notation I am going to use for the genotypes is something like this: Vc/vC. That is a het lava het charcoal, but I've used the slash to indicate how the alleles are arranged on each member of the chromosome pair. So one chromosome is Vc and the other is vC, and the only gametes that animal can produce, without an apparently rare recombination event, are Vc and vC. So that animal would not be able to produce a
diamond in the first generation, no matter what you mate it to, unless a rare recombination event occurred to produce a vc gamete.
Here are some crosses to illustrate how to use the concept:
1) Lava x Charcoal= Lava (vC/vC) x Charcoal (Vc/Vc)
The lava can only make vC gametes, and the charcoal can only make Vc gametes, so all offspring will be vC/Vc
2) Het lava het charcoal offspring from 1 crossed to each other = vC/Vc x vC/Vc
The only gametes that can be produced without recombination are vC and Vc. So offspring are
¼ vC/vC (lava not het charcoal)
¼ Vc/Vc (charcoal not het lava)
½ vC/Vc (het lava het charcoal)
Note that the allelic arrangement is the same as both parents, ie you never see a vc or VC chromosome. So we haven't made any headway. If you cross lavas not het charcoal to charcoals not het lava, you will not get any diamonds. There is a possibility of getting diamonds from cross 2, though. I will return to this later.
3) Crossing the lavas not het charcoal to the charcoals not het lava from above is the same as doing cross number 1. Crossing the het lava het charcoals is the same as doing cross number 2.
From cross number two, there is a small possibility of recombination. Normally those snakes can only produce vC and Vc gametes. But when a vC and Vc chromosome line up during meiosis before separating, something can happen. Basically what I've done below is draw a horizontal line representing the chromosome, and with the charcoal and lava loci (pronounced LOW-sigh, by the way) labeled. They are one below the other, and an X indicates crossing over (recombination). What is happening is that the chromosomes break where the X is drawn, and reconnect to their partner. So in the top chromosome, follow along until the X, then move down to the lower chromosome. That gives you one of the outcomes of a crossover. Follow the bottom chromosome until the X, and move up to the top chromosome, to get the other outcome. I color-coded parts of the chromosomes, so you easily understand what is happening. The result is two new chromosomes that have the same LOCI on them, but the alleles that occupy them are a different combination than what we saw before. When a crossover happens between a Vc and vC chromosome in the region between the lava and charcoal loci, the outcome is a VC chromosome and a vc chromosome.
So when these recombinant chromosomes separate during meiosis, a small amount of VC and vc gametes will be produced. A vc gamete is what you need to produce a
diamond, because a
diamond results from the union of a vc sperm and vc egg. You can see now why a recombination event is rare between loci that are close together on the same chromosome. Since recombination is a random event, the further apart two loci are, the more likely it is that the region a crossover occurs in will be between the two loci, instead of outside them. You might be wondering if the lava and charcoal loci were FAR apart on the same chromosome, would recombination always happen between them, resulting in gametes that never have the same allelic arrangement as the parents? This does not happen, because if loci are far apart, more than one recombination event can happen between them. An odd number of crossovers results in recombinant chromosomes relative to the two loci in question, and an even number of crossover events results in nonrecombinant chromosomes, relative to the two loci in question.
So in this cross, almost all gametes will be Vc and vC, but a very small portion will be vc or VC. So the odds of a
diamond are very small, because it requires the union of TWO recombinant gametes.
However, some potentially useful offspring can be produced that require only one recombinant gamete instead of two. If a recombinant vc gamete unites with nonrecombinant Vc or vC gametes, you will get vc/Vc or vc/vC offspring. These are lavas het charcoal and charcoals het lava. These can be used to produce diamonds. However, most of the lava and charcoal offspring from cross #2 would be vC/vC or Vc/Vc, ie homozygous for one trait but NOT het for the other. You’d have to prove out the ph hets from the lavas and charcoals to find the rare ones that are recombinant and actually het for lava or charcoal. But from a het lava het charcoal x same (vC/Vc x vC/Vc) you are more likely to produce lavas het charcoal or charcoals het lava than you are a
diamond, because one type requires the union of a recombinant and nonrecombinant gamete, whereas the other requires two recombinant gametes. But these lavas het charcoal and charcoals het lava can be used to easily produce diamonds.
Say you held back all of the lava ph charcoal and charcoal ph lava offspring, and managed to find one that was indeed homozygous for one trait and het for the other. Maybe you didn’t get lucky enough to get two that proved out their hets. If you did, though, you could mate them together. Assume you had a lava het charcoal and a charcoal het lava. The arrangement of their alleles on the chromosomes would be vC/vc for the lava het charcoal, and Vc/vc for the charcoal het lava. Crossing the two would give
4) Lava het charcoal (vC/vc) x charcoal het lava (vc/Vc)
¼ vC/Vc (normal het charcoal het lava)
¼ vC/vc (lava het charcoal)
¼ vc/Vc (charcoal het lava)
¼ vc/vc (
diamond)
So a ¼ probability of producing diamonds!
Notice that the normals het charcoal het lava do not have an allelic arrangement that would be useful for rapidly producing more diamonds. They’d have to have another rare recombination event to produce any vc gametes.
You also produce more lavas het charcoal and charcoals het lava that have the vc arrangement on one of their chromosome pairs, so these could be mated to each other or back to the parents to create more diamonds.
Note that in this cross, recombination can’t come back to bite you. Since the parents were vC/vc and Vc/vc, recombination can’t change the allelic arrangements to undo all your hard work. Recombination between a vC and vc chromosome produces vc and vC chromosomes, the same two types that you had before.
In all likelihood, you won’t be able to prove out the ph for two separate charcoals/lavas, unless you have a huge collection. You’ll probably just get one or the other. Say you got a lava ph charcoal that proved out lava het charcoal. You can still create diamonds easily by mating it to anything, and crossing the offspring back to the lava het charcoal. Just say you mated it to a het charcoal het lava Vc/vC.
5) lava het charcoal (vC/vc) x het charcoal het lava (Vc/vC) gives
¼ vC/Vc (het lava het charcoal, same arrangement as parent)
¼ vC/vC (lavas not het charcoal)
¼ vc/Vc (charcoals het lava)
¼ vc/vC (lavas het charcoal)
This kind of stinks because you get ½ lavas, but only half of those have a vc chromosome, which you need to make more diamonds. But the charcoals should all have one vc chromosome. So mating them to each other or to the lava het charcoal parent would produce more diamonds.
You could get diamonds in this cross, if a recombination event occurred in the het charcoal het lava parent. You could also get normals (vc/VC), and those normals would be good for diamond-making.
Try this instead
6) Cross lava het charcoal (vC/vc) to a charcoal (Vc/Vc) and get
½ vC/Vc (het lava het charcoal, not a favorable arrangement for
diamond making)
½ vc/Vc (charcoal het lava, favorable arrangement for
diamond making)
In this cross, half of the offspring were suitable for making more diamonds, and they are all charcoal, which is an immediate visual indicator of which offspring to hold back. Note that any recombination event during gamete formation in the parents does not change anything. Recombination between a vC and vc chromosome generates a vc and vC chromosome, the same as what you started with. Same for the chromosomes of the charcoal parent, obviously, since both of their chromosomes are identical with regards to lava and charcoal. This is good, because you KNOW that all the charcoal offspring are suitable for diamond-making.
When you do get a
diamond, here are a few crosses and what the expected results are.
7)
Diamond (vc/vc) x het lava het charcoal (vC/Vc)
½ vc/vC (lavas het charcoal)
½ vc/Vc (charcoals het lava)
Both types are good for making more diamonds. However, since once parent was vC/Vc, recombination in that parent can produce vc and VC gametes. So a small fraction of your offspring would be
vc/vc (
diamond)
vc/VC (het lava het charcoal).
Notice that any het lava het charcoal offspring from cross 7 are DIFFERENT from their het lava het charcoal parents! They can be used to easily create more diamonds, unlike the parent.
8)
Diamond (vc/vc) x wt
All offspring are vc/VC, and can make more diamonds when crossed to each other, a
diamond, a lava het charcoal, or a charcoal het lava.
9)
Diamond (vc/vc) x lava het charcoal (vC/vc)
½ vc/vC (lavas het charcoal)
½ vc/vc (diamonds)
10)
Diamond (vc/vc) x het lava het charcoal offspring from cross 8 (vc/VC)
1/2 normals het charcoal lava (vc/VC)
1/2 diamonds (vc/vc).
Recombination in the het lava het charcoal could produce vC and cV gametes, so a small proportion of the offspring would be lavas het charcoal and charcoals het lava.
Notice that with unlinked genes, for example amel and cinder, if you mated amel cinder x het amel het cinder, you would only get 1/4 offspring that are homozygous for both mutations. For closely linked genes, it is 1/2, if the allelic arrangement is favorable in the het parent, or close to zero, if it is not.
I hope this helps! Let me know if you have any questions, so that I can improve this post.