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PILE-O LAVAS & LAVA CINDERS !!

I love snake pedigrees. This just shows the value of ACR- where, HAD it turned out to be important, we could have gone all the way back to the start and traced it. It's wonderful for when an unexpected gene pops up- you can go looking for it in aunts and uncles, etc.
 
DuxorW said:
Ok so here goes...

As stated above, it appears that some female het cinders throw all males, some throw all females (this seems less common), and some seem to have no trouble throwing either.

To explain this, I need to introduce the concept of genetic linkage. Imagine we have a snake that is homozygous for two recessive mutations we'll just refer to as Tender and Kisses (don't ask). We mate this snake to a wild type female to make babies that are het Tender het Kisses. We then mate these babies together. We would expect to get the classic 9:3:3:1 ratio of 3/16 Tender, 3/16 Kisses, 9/16 normal, and 1/16 Tender Kisses, correct?

Well, it turns out that we get 1/4 Tender Kisses and 3/4 normal. What? That 3:1 ratio is the ratio we'd expect if we were working with a single gene, not two genes! This is where linkage comes in.

These ratios we use on programs like corn calc assume that two mutant alleles like stripe and amel assort independently during meiosis so that the inheritance of one allele does not affect the inheritance of the other. This is true if the mutations are on different chromosomes, say chromosome 3 and 5. But what if the mutations are on the same chromosome? If mutations Tender and Kisses are on the same chromosome (let's use 9) they will always be inherited together unless a crossover occurs between them and separates them. In a het, this would create one chromosome 9 that has the Tender mutation on it on it but is wild type for Kisses, and the other chromosome 9 would be wild type for Tender and have the Kisses mutation. However, if crossover does not ever occur and they are always inherited together as a single unit, this would create the 1/4 Tender Kisses 3/4 normal ratio we saw.

If genes are really far apart on the same chromosome, they act like they are on different chromosomes because of the odds of single/double/triple crossovers occuring between them.

However, if two mutations are on the same chromosome and are far apart, there are factors that can still cause them to be inherited together. Large inversions on one of the chromosomes in the pair can suppress crossing over, causing the mutations to stay linked. However, this doesn't affect whether males or females are the ones who inherit the mutations together. Unless the mutations are on sex chromosomes.

This brings me back to cinder. I am reversing my earlier theory that crossovers between the cinder alleles on the Z and W chromosomes are rare! Instead, I think they are common! For reasons I won't go into, the recombination frequency between genes that are far apart on the same chromosome is 50%. I think the cinder locus is thus located on a large region of similarity between the Z and W chromosomes and thus experiences a 50% recombination rate, which is indistinguishable from independent assortment. However, I think that in CERTAIN lines of females, there may be an inversion or some other factor on the Z or W chromosome that is SUPPRESSING crossovers in these females. This prevention of a crossover will keep the cinder allele on the Z or W chromosome and skew the sex ratio of homo cinder offspring. This suppression is not 100% but is still very high.

This may sound wild but as a geneticist it makes perfect sense to me. It does make a prediction. A het cinder female who is throwing male cinders should do so in every clutch. A het cinder female throwing female cinders should continue to do so in every clutch. Because the crossover suppression is not 100%, there should be rare exceptions, but the pattern should stay the same for each individual het female. A het cinder female who makes male and female cinders should also continue to do so in future clutches.

If the inversion is on the Z chromosome, note that suppression of a crossover still has no effect in the sire. Assume he is het cinder. Since he is Z Z, a crossover can swap a cinder mutation from one Z chromosome to the other but the result on reproduction will not be different than if a crossover did not occur. A het cinder male has to give one of his Z chromosomes to both his male and female offspring. Whether or not crossover occurs, he would have 50% wt Z sperm and 50% cinder Z sperm.

What will be interesting is whether the suppressor of crossing over is on the Z chromosome. This is a disturbing possibility as male cinders/het cinders could pass this on to their daughters and cause them to have suppressed crossovers when producing offspring. Hopefully the suppressor of crossing over is on the W chromosome and hopefully the rare crossovers do not also encompass the suppressor of crossing over and move it to the Z chromosome in some individuals!!!

Again, this may sound crazy, but in the lab we actually take advantage of crossover suppression. Sometimes we want to make double or triple mutants of say, a fly. If the mutations are on the same chromosome we want them to be inherited together to increase our odds of recovering double and triple mutants when mating to another het. We use so-called "balancer" chromosomes that contain large inversions and suppress crossing over when they pair to the mutant chromosome, thus keeping all the mutant alleles together in a gamete.

Have I confused everyone yet?
Click to expand...

Uh, YEP !!!..................LOL

So, I take it this does not mean we can rule out your first hypothesis just yet ??
I'm still leaning towards it due to the outcomes I've had over the past 3 years.

Walter
:crazy02:BOUT' CORNS !!
 
Nanci said:
It makes sense to me. Now can you develop a simple genetic test for stargazer please? ;-)
Click to expand...

Lol, I wish it were simple to do so! It can be done it's just that the genome of the corn is not well characterized. The stargazer mutation needs to be mapped to a particular chromosome and narrowed down from there and it is very hard work, but once the nature of the mutation is identified, developing the test is simple. I do similar genetic tests in the lab and they are very cheap to perform on a single sample.

One interesting thing, going back to the cinders, is that if there is an inversion that suppresses crossover, it might be visible in a karyotype of a female that throws a single sex vs one that throws both. In corn snakes, the Z and W are heteromorphic, but not to the extent that the human X and Y chromosome are. Apparently once sex chromosomes become heteromorphic, as evolution proceeds they become more and more unalike. As one chromosome shrinks, genes that were originally on both will become isolated to the one that isn't shrinking. In the very distant future, cinder may only be on the Z chromosome! At that point, females carrying a single copy of the cinder mutant would always be cinder. A cinder male mated to a wild type female would produce all cinder females. Of course, we will all be dead by that point and it isn't going to happen in captivity.
 
So, I take it this does not mean we can rule out your first hypothesis just yet ??
I'm still leaning towards it due to the outcomes I've had over the past 3 years.
Click to expand...

Walter, in order for the sex ratio to be biased, the genes must be on the Z and W chromosomes. It is just that in some females crossing over will occur 50% of the time at the cinder locus which will make the cinder trait look like it is not linked to sex. But in some females that have Z and W chromosomes that differ structurally near the cinder locus, crossing over is going to be suppressed the vast majority of the time. This is what is going on in your females, crossing over is never occurring so the cinder allele is staying stuck on the Z chromosome of the mother, causing it to only be inherited by males. For your females you will continue to see the same result but may rarely get a crossover.

With Carol's female that is throwing both sexes equally, she will continue to get the same results from that female. However, the daughters may or may not have problems producing male or female cinders depending on if the Z chromosome they get from dad is compatible with crossing over to the W they get from the mom.
 
However, the daughters may or may not have problems producing male or female cinders depending on if the Z chromosome they get from dad is compatible with crossing over to the W they get from the mom.
Click to expand...

Of course this only applies to the het cinder daughters of that female.
 
DuxorW said:
Walter, in order for the sex ratio to be biased, the genes must be on the Z and W chromosomes. It is just that in some females crossing over will occur 50% of the time at the cinder locus which will make the cinder trait look like it is not linked to sex. But in some females that have Z and W chromosomes that differ structurally near the cinder locus, crossing over is going to be suppressed the vast majority of the time. This is what is going on in your females, crossing over is never occurring so the cinder allele is staying stuck on the Z chromosome of the mother, causing it to only be inherited by males. For your females you will continue to see the same result but may rarely get a crossover.

With Carol's female that is throwing both sexes equally, she will continue to get the same results from that female. However, the daughters may or may not have problems producing male or female cinders depending on if the Z chromosome they get from dad is compatible with crossing over to the W they get from the mom.
Click to expand...

So to simplify, (excluding my females) NOW all het Cinder X het Cinder breedings are a crap shoot to produce both male & female visual Cinders regardless if the hets were produced by a male or female Cinder ??? :shrugs:

Walter
:crazy02:BOUT' CORNS !!
 
Walter Smith said:
So to simplify, (excluding my females) NOW all het Cinder X het Cinder breedings are a crap shoot to produce both male & female visual Cinders regardless if the hets were produced by a male or female Cinder ??? :shrugs:

Walter
:crazy02:BOUT' CORNS !!
Click to expand...

My interpretation is yes, but once you have one clutch, you know what that female produces, and results will then be the same the following seasons.
 
Nanci said:
My interpretation is yes, but once you have one clutch, you know what that female produces, and results will then be the same the following seasons.
Click to expand...

GREAT...........LOL

Yeah, I gatherd that once you see the gender results of the visual Cinder offspring from the first breeding, you can expect the same all the time.

I take it this will only apply to het X het breedings ??
Breeding Cinder X Cinder should still automatically throw both genders correct ??? If so, what about those offspring ???

Walter
:crazy02:BOUT' CORNS !!
 
Well, we now have no idea how common the chromosomal variant that suppresses recombination is. It could be that many female het cinders can throw both sexes. Some of your female het offspring may even be able to produce both sexes, but I imagine they are also getting "incompatible" sex chromosomes from mom and dad (especially if mom and dad are related) and would thus throw males or females (most likely males). It would be interesting to mate the het cinder daughters with an unrelated homo cinder male.
 
Cinder x cinder will give both sexes. The female cinders from that pairing will throw both sexes. But if they have het cinder daughters, see above.
 
"It would be interesting to mate the het cinder daughters with an unrelated homo cinder male."
Sorry, this actually would make no difference. Breeding the het daughters back to their homo cinder dad will also show you if they can throw one or both sexes.
 
DuxorW said:
Cinder x cinder will give both sexes. The female cinders from that pairing will throw both sexes. But if they have het cinder daughters, see above.
Click to expand...

This is the way I am moving towards.

Also, I have a couple other het females that will be breeding for the first time next season, breeding back to their homo Cinder father to hit target.
I guess we'll see what kind of gender ratio I get with those two.

Walter
:crazy02:BOUT' CORNS !!
 
There are some ideal crosses that I will post later that will let me know if whatever is suppressing crossing over is on the Z or W chromosomes and whether it can move between them. I hope it is an inversion on the W chromosome because if so it will stay there and only be inherited through the maternal line.

Honestly I was originally expecting crossover between the Z and W chromosomes to be common near the cinder locus but the original data demanded they not be, so I figured the cinder allele was close enough to whatever the sex determining region is to he tightly linked to it. But now it looks like my original though as right and cinder is distant from it, and crossover suppression in a subset of females was confounding things. Carol's result was instrumental!
 
Walter Smith said:
This is the way I am moving towards.

Also, I have a couple other het females that will be breeding for the first time next season, breeding back to their homo Cinder father to hit target.
I guess we'll see what kind of gender ratio I get with those two.

Walter
:crazy02:BOUT' CORNS !!
Click to expand...

Since they got the cinder gene from their father, it is on the Z chromosome, which means they'll throw male cinders. Unless they are one of the females that can crossover more easily, in which case you'll get a normal sex ratio.
 
Unless they are one of the females that can crossover more easily, in which case you'll get a normal sex ratio.
Click to expand...

I have some idea on how to predict when this will be the case :)
 
Rather than go through a long drawn out logic for each of the multitude of possibilities, I will just go through the most plausible one and see if it can be validated.

For those of you having trouble wrapping your mind around this, I'll try to briefly summarize. Cinder appears to be on the Z and W chromosomes but normally assorts independently of sex, meaning if cinder is on the Z chromosome in a female (females are ZW) then in half the gametes the cinder allele will move to the W chromosome through crossing over. Thus if this female is mated to a homo cinder male, the visual cinder offspring will be half male and half female.

In some females, there appears to be a factor, probably a naturally occurring inversion, on one of the sex chromosomes of the female that is suppressing recombination. When mated to a homo cinder male, A Z cinder W wt female will thus produce almost all cinder males and a Z wt W cinder female will produce almost all cinder females. Again, only some females will do this, but for each individual female the results will be repeatable. Otherwise, a het cinder female will make both male and female cinders when mated to a homo cinder male, and will continue to do so in each clutch.

I think the most likely possibility is that the W chromosome of some females has the inversion (or something else that represses recombination). This leads to a few predictions.

I will refer to W chromosomes that are repressing recombination as Ws. The cinder allele will be a c and wild type for cinder will be +.

cinder male x het cinder female who is throwing males: The het cinder daughters of this clutch should be Zc Ws+. Since the dame is throwing males, she has Zc Ws+ chromosomes. All her daughters are getting a Zc from dad and a Ws+ from her.

If the supressor of recombination is on the W chromosome then these daughters should continue to throw males when mated to their father or another homo cinder male because they will give their Zc chromosome only to their sons and crossing over cannot move the cinder allele to the Ws chromosome except in very rare instances.

Jen has a female het cinder that is throwing females and I think this female or others like her will be critical. Again, if the supressor of recombination is on the W chromosome then this female should be Z+ Wsc. Mating her to a homo cinder male would produce all homo cinder daughters and they would not be efficient for further verifying this hypothesis. Pairing this female maker to a HET cinder or homozygous wt male would produce some het daughters that are Z+ Wsc unless there was a rare crossover. If the suppressor is on the W chromosome, these het female daughters should continue to be female makers when bred back to their father because the cinder allele on the Wsc chromosome is not able to swap with the + allele on the Z chromosome.

If the repressor is on the Z chromosome (Zs) some ugly things happen some of which aren't necessarily intuitive and I'm not sure I want to even go there if I can show the inversion is on the W chromosome! If the defect is truly an inversion it should not hop to the Z chromosome when a rare crossover does occur.

If it is on the W chromosome, suppressor W chromosomes could be out there having no effect on anything until cinder gets involved. So when starting new cinder projects there would be the possibility that your holdback het daughters could have suppressed crossing over at the cinder locus.
 
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