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The Cultivars (morphs)/Genetics Issues Discussions about genetics issues and/or the various cultivars for cornsnakes commercially available.

Palmetto question
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Old 12-24-2015, 06:10 PM   #21
DuxorW
The thing is that an ultramel corn snake would really be no more or less of a hybrid than any non ultra/ultramel corn snake descended, even distantly, from an ultra-containing corn. If the allele was truly not derived from corn snakes and instead came from a gray rat, then sequences from the gray rat will already be dispersed throughout much our captive population.
 
Old 12-26-2015, 12:58 AM   #22
BeauBoi
Quote:
Originally Posted by DuxorW View Post
What would you even look for with a palmetto corn? A restriction fragment length polymorphism? It wouldn't be cheap or trivial to prove any polymorphism you saw was from hybridization. Maybe if the palmetto locus was actually cloned (a time consuming and expensive task), the sequence of the coding region or the introns of the palmetto allele (the sequence of introns changes more rapidly during evolution, so two related species would generally show more sequence divergence in the introns than the exons) of the palmetto allele could be informative as to whether it was derived from corn snakes. The morph is new and the hets look like regular corns, I suspect it is no more of a hybrid than a wild corn snake is.

As far as the ultra mutation, the group that identified the locus responsible for amelanism in corns are sequencing the ultra allele. Depending on how thorough their analysis is, they should be able to demonstrate if it arose from a mutation in the wt corn snake allele or if it is not derived from corns.
I believe that the palmetto morph is actually a lucistic mutation that was crossed into the corn snake genome, similar to the recent addition of the scaleless mutation, if that is the case then I should be able use the corn snake DNA map that was recently created and contrast it with that of a palmetto corn. If they prove to be (as expected; the mutation will differ reguardles of where it came from) then I will compare it with sequences from other snake species that show similar mutations--the Calic Beauty Snake being a good example.

~Beau
 
Old 12-26-2015, 01:02 AM   #23
BeauBoi
Quote:
Originally Posted by Dragonling View Post
I think the origin of ultra is more worth looking into. I tend to trust Don's opinion, particularly when he's put so much effort into the palmetto project. I mean he had $12,000 riding on it just being reproducible, so you know he did ever bit of homework he could.
The Ultra gene is another I would be interested in looking into, but I feel that the answer to wether it is intra-species specific has already been answered to my satisfaction. Regardless, should I be able to answer definitively as to the origin of the palmetto, I would definitely be interested in also confirming the Ultra.

~Beau
 
Old 12-26-2015, 10:14 AM   #24
DuxorW
Quote:
Originally Posted by BeauBoi View Post
I believe that the palmetto morph is actually a lucistic mutation that was crossed into the corn snake genome, similar to the recent addition of the scaleless mutation, if that is the case then I should be able use the corn snake DNA map that was recently created and contrast it with that of a palmetto corn. If they prove to be (as expected; the mutation will differ reguardles of where it came from) then I will compare it with sequences from other snake species that show similar mutations--the Calic Beauty Snake being a good example.

~Beau
You do realize it is not this easy, right? Even with the highly fragmented genome sequence published, in order to identify the palmetto locus you would have to spend thousands of dollars and use next generation sequencing. Any corn snake you sequence will differ from the draft sequence at a ton of nucleotides that are irrelevant. You would need to map the mutation to a candidate region either by sequencing pooled samples from siblings with and without the palmetto mutation and identifying the regions that segregate only with the palmetto corns (which merely narrows your list of candidate genes), or by doing some other form of linkage analysis. Both are time consuming and expensive. Look at all the effort this group had to go through, even after sequencing the corn snake genome, just to identify the locus containing the amel mutation. They did whole exome sequencing followed by linkage analysis. But what they generated will not be that useful to you, you would essentially have to repeat their strategy.
 
Old 12-26-2015, 10:34 AM   #25
BeauBoi
Quote:
Originally Posted by DuxorW View Post
You do realize it is not this easy, right? Even with the highly fragmented genome sequence published, in order to identify the palmetto locus you would have to spend thousands of dollars and use next generation sequencing. Any corn snake you sequence will differ from the draft sequence at a ton of nucleotides that are irrelevant. You would need to map the mutation to a candidate region either by sequencing pooled samples from siblings with and without the palmetto mutation and identifying the regions that segregate only with the palmetto corns (which merely narrows your list of candidate genes), or by doing some other form of linkage analysis. Both are time consuming and expensive. Look at all the effort this group had to go through, even after sequencing the corn snake genome, just to identify the locus containing the amel mutation. They did whole exome sequencing followed by linkage analysis. But what they generated will not be that useful to you, you would essentially have to repeat their strategy.
I am quite aware of the processes involved. Nothing worth doing is ever "easy", however the sense of satisfaction one gains from finally answering a burning question makes it all worth while!

I expect that it will take years to accomplish.

~Beaux
 
Old 12-26-2015, 11:15 AM   #26
Distaff
Quote:
Originally Posted by DuxorW View Post
You do realize it is not this easy, right? Even with the highly fragmented genome sequence published, in order to identify the palmetto locus you would have to spend thousands of dollars and use next generation sequencing. Any corn snake you sequence will differ from the draft sequence at a ton of nucleotides that are irrelevant. You would need to map the mutation to a candidate region either by sequencing pooled samples from siblings with and without the palmetto mutation and identifying the regions that segregate only with the palmetto corns (which merely narrows your list of candidate genes), or by doing some other form of linkage analysis. Both are time consuming and expensive. Look at all the effort this group had to go through, even after sequencing the corn snake genome, just to identify the locus containing the amel mutation. They did whole exome sequencing followed by linkage analysis. But what they generated will not be that useful to you, you would essentially have to repeat their strategy.
Well, I did not realize it would be so complicated! I grew up reading Steven J. Gould, Biology was the only subject I cared about in HS, and I can have a basic idea about the double helix. I guess, I figured that if a hundred bucks can get you an ethnic history from "23 And Me," and about the same amount of cash will verify the dog's pedigree...

Good to know.
Thanks.
 
Old 12-26-2015, 11:20 AM   #27
DuxorW
Quote:
Originally Posted by Distaff View Post
Well, I did not realize it would be so complicated! I grew up reading Steven J. Gould, Biology was the only subject I cared about in HS, and I can have a basic idea about the double helix. I guess, I figured that if a hundred bucks can get you an ethnic history from "23 And Me," and about the same amount of cash will verify the dog's pedigree...

Good to know.
Thanks.
Yeah, the human genome is very well annotated and many single nucleotide polymorphisms (SNPs) have been found that correlate with specific traits or diseases. That is what they test for with 23 and Me, they use something called a SNP array. But this required a ton of prior knowledge that we just don't have yet with the corn snake. Generating that knowledge is the expensive and time consuming part.
 
Old 12-26-2015, 11:43 AM   #28
DuxorW
Quote:
Originally Posted by BeauBoi View Post
I am quite aware of the processes involved. Nothing worth doing is ever "easy", however the sense of satisfaction one gains from finally answering a burning question makes it all worth while!

I expect that it will take years to accomplish.

~Beaux
Sorry, the way you framed approaching the question made me think you didn't (I have a PhD in molecular genetics). I remain skeptical that anyone outside the field of reptile genetics/genomics will carry out such a task given the resources required and the huge financial/time commitment. Plus you are likely to be proven wrong about the palmetto mutation.
 
Old 12-26-2015, 11:57 AM   #29
DuxorW
Plus isn't the black rat leucistic mutation incomplete dominant?
 
Old 12-26-2015, 12:53 PM   #30
BeauBoi
Quote:
Originally Posted by DuxorW View Post
Sorry, the way you framed approaching the question made me think you didn't (I have a PhD in molecular genetics). I remain skeptical that anyone outside the field of reptile genetics/genomics will carry out such a task given the resources required and the huge financial/time commitment. Plus you are likely to be proven wrong about the palmetto mutation.
You don't necessarily start out with hybridization probes (although, even if you did, all you are really taking about is a centrifuge and and spectrometer w/ a camera; yes equipment is expensive, if you buy it, same with computer time but that's the great thing about being a research student...).
Now that the genome has been mapped, we can start with spastical analysis of palmetto DNA samples against the mapped genome, and then work our way up from there.

I'm no molecular biologist. I am just an environmental engineer who decided to return to college after 20 years working in fossil fuel industry and agriculture R&D, but reverse-engineering is kinda what I do.

~Beau
 

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