DuxorW

This exchange happened in Joe Pierce's 2015 season thread, but I thought I would post it here so it would have some more visibility.

Joe noticed that he was having no luck producing a diamond corn snake.

From Steve Roylance:
My response, slightly edited for clarity:
"Sometimes when people get results like that, it makes me wonder if any of the corn snake mutations are "linked," a term describing two loci that are close together on the same chromosome. When this is the case, the alleles at those two loci are no longer inherited independently of each other, which has implications when you are trying to make a double homozygous animal.

For example, say you crossed a lava (vvCC) and a charcoal (VVcc) to make het lava het charcoals (VvCc). If the lava and charcoal loci are on the same chromosome, in the het offspring one member of the chromosome pair has the V and c alleles (inherited from the charcoal parent), and the other chromosome has the v and C alleles (inherited from the lava parent). Normally, you would expect these hets to be able to make Vc, VC, vC, and vc sperm/eggs, but linkage would prevent this, because the v allele is stuck on the chromosome with the C allele, and the V allele is stuck on the chromosome with the c allele, so when the members of the chromosome pair separate and go their separate ways into the gametes, v and C (or V and c) get dragged together into the same egg/sperm. So only two types of egg/sperm are produced, vC and Vc, making it impossible to produce diamonds, as no gamete carries both lava and charcoal mutations simultaneously. When two vC gametes unite, you get lavas not het charcoal. When two Vc gametes unite, you get charcoals not het lava. When a vC and Vc gamete unite, you get het lavas het charcoals, but again the mutant charcoal allele is not on the same member of the chromosome pair as the mutant lava allele.

How do we explain the existence of diamonds, if it should be impossible? The reason it's not impossible in reality is this: During egg/sperm formation, members of a chromosome pair line up and exchange segments of genetic material with each other, mixing up the allelic arrangements on those chromosomes in a process called crossing over. If an exchange happens between the lava and charcoal loci in the het lava charcoal animals described above, you would be able to produce VC and vc gametes (these gametes are called recombinant because their allelic arrangement is different from the original arrangement of Vc or vC in the parental chromosomes). However, the closer two loci are on the same chromosome, the less likely it is that a crossover event happens between them. If they are really far apart, a recombination happens at the maximum rate of 50%, generating results that are indistinguishable from independent assortment (the normal pattern of inheritance you get when genes aren't on the same chromosome). If they are really close together, recombination is very infrequent. Whether lava and charcoal are linked is just speculation but accurate and detailed clutch data could disprove it.

If the linkage were very tight you would expect this result:
If you breed a charcoal to a lava to produce double hets, and cross these double hets to each other, you would get

1/4 lavas NOT het charcoal (inherited a vC chromosome from both parents), 1/4 charcoals NOT het lava (inherited a Vc chromosome from both parents), 1/2 het diamonds (received a Vc from one parent and a vC from the other).

Some types of normals (VVCC, VvCC, VVCc) and diamonds (vvcc) would be rare, as would charcoals het lava (Vvcc) and lavas het charcoal (vvCc), because those would require the inheritance of one or two recombinant chromosomes (vc or VC). Is this anyone's experience?

To see how I got that result, when genes are tightly linked you can kind of treat them as the same locus on a Punnett square. The gametes produced by the double het animals would be either mutant for lava and wt for charcoal, or wt for lava and mutant for charcoal. So either Vc or vC. Here is the square, treating the charcoal and lava loci as a unit:

____Vc__vC
Vc| VVcc VvCc
vC| VvCc vvCC

So only 3 genotypic/phenotypic classes.
VVcc=charcoal, not het lava
vvCC=lava, not het charcoal
VvCc=normal, het lava het charcoal.

This assumes perfect linkage, so even if the loci are linked, deviations from this result are normal. But this result is very different from what you would expect from independent assortment (the way we normally calculate the result of crosses involving more than one locus). Offspring deviating from the above square had to have inherited a recombinant chromosome, allowing us to calculate the "recombination frequency" between lava and charcoal. In a normal cross that involves 2 loci assumed to be on different chromosomes, the recombination frequency is 50% (you can prove this by comparing the results from a normal Punnett square to the one above), so frequencies between 0 (loci are really close together) and 50% (loci are really far apart or on different chromosomes) are suggestive of linkage.

There is a somewhat hilarious implication of this. If lava and charcoal were actually linked, if you did hit a diamond in the above cross, you might be tempted to mate it with its charcoal or lava littermates to produce more diamonds. But the Punnett square above should caution you against that, since the charcoals are probably not het lava, and the lavas are probably not het charcoal!

But you have to mate it to something, and there is still hope: all offspring of your diamond will automatically inherit a chromosome with the vc arrangement (since the diamond has two vc chromosomes, which is why it's vvcc). Thus, those offspring can easily produce vc gametes without recombination, allowing you to easily produce more diamonds when you mate a diamond to its offspring. If your pairing was diamond x homozygous wt, the offspring will be VvCc, but one of their chromosomes will be vc and the other will be VC. Thus, assuming tight linkage, roughly half their gametes will carry the vc chromosomes and half will cary VC. So your odds of getting more diamonds when you cross the diamond to its het diamond offspring should be closer to 1/2 than to the 1/4 you would normally predict! Note that in this case you DON'T get the same result if you cross the diamond to its het diamond SIBLINGS. In that case you would only get lavas and charcoals! However, a diamond produced from a diamond parent can be paired with its siblings to easily produce more diamonds. The arrangement of the alleles on the homologous chromosomes has to be considered when predicting the outcome of crosses involving linked genes, not just the genotype of the parents.

Sorry for the long post, sometimes a simple concept leads you down several roads."

From Steve:
I think the observation that the charcoals/lavas Steve held back were not het for lava/charcoal supports my hypothesis of linkage, although more data is needed. He is testing possible hets from at least 5 more holdbacks this year.

This explanation might seem pretty technical to some of you, but my initial audience was Joe and Steve, who seem to have done their homework, and Mitchell Mulks, who has a formal background in the life sciences. So I will be happy to clarify anything that doesn't make sense.

Also, would love to have clutch data from people performing breedings that could potentially have produced diamonds, to see if the results conform to what we'd expect from genetic linkage. Corn snakes have 18 chromosome pairs, and there are more than 18 described mutations in corn snake, so it would not be surprising at all that at least two of them share a chromosome, and are close enough together to exhibit linkage.

Thanks for reading!

Please see post #6, for an expanded explanation!