DNA testing for herps?

[batwrangler]

DNA testing is becoming common and affordable for horses, dogs, cats, and birds. Does anyone know if DNA testing is available for herps as well? I think the contents of a cornsnake DNA database could be very interesting.

 

[Intravenous]

It depends what you mean by DNA testing...

Yes, you could run the DNA of a cornsnake and compare it to another cornsnake but you can't really learn anything from that. Without actually working out where the genes are in the DNA and what they do (which is a very expensive process) its pretty much useless.

 

[batwrangler]

It depends what you mean by DNA testing...

Yes, you could run the DNA of a cornsnake and compare it to another cornsnake but you can't really learn anything from that. Without actually working out where the genes are in the DNA and what they do (which is a very expensive process) its pretty much useless.

I'm sure that there's already been considerable work done on mapping snake DNA and that it won't be much of a stretch to get to where it would be useful for amateur herpers.

For instance, a quick google turns up this gentleman (http://www.life.uiuc.edu/pjw/snake.htm) who is using "DNA-based genetic markers for determining kinship and characterizing population structure" in snakes, and is studying a bunch of rat snake species, too, judging from his publications.

 

[Intravenous]

I'm sure that there's already been considerable work done on mapping snake DNA and that it won't be much of a stretch to get to where it would be useful for amateur herpers.

For instance, a quick google turns up this gentleman (http://www.life.uiuc.edu/pjw/snake.htm) who is using "DNA-based genetic markers for determining kinship and characterizing population structure" in snakes, and is studying a bunch of rat snake species, too, judging from his publications.

That just looks like he's using genetics to moniter population size and diversity...that can either be done by measuring the size and change in certain regions of non-coding DNA between individuals, generally not by finding out where the gene actually lies in the genome . To actually map out the whole snake genome and find out where certain genes are would cost several (probably hundreds of) million dollars...what kind of breeder/herper is going to want to put money in that? It's not an investment, its an interest.

I'm not saying it can't be done...at the moment it is possible, but the cost would be too large to make it too expensive for anyone to do it.

I would think so anyway :shrugs:.

 

[Susan]

Personally, I'm not going to trust any of this DNA testing for awhile. There are 2 companies that I know of that do DNA testing on dogs to determine what breed(s) are in their make-up. One has a smaller breed "range" than the other, and there is a price difference between them as well. One of the breeders that comes to our clinic had one of his pure-bred dachshunds tested, just for kicks. The results came back saying his dog was a Border Collie X Cocker Spaniel mix. :shrugs:

 

[zwyatt]

For instance, a quick google turns up this gentleman (http://www.life.uiuc.edu/pjw/snake.htm) who is using "DNA-based genetic markers for determining kinship and characterizing population structure" in snakes, and is studying a bunch of rat snake species, too, judging from his publications.

Hey! I learned Animal Behavior from him! He was the prof when I took that course a couple years ago at U. of Illinois.

That just looks like he's using genetics to moniter population size and diversity...that can either be done by measuring the size and change in certain regions of non-coding DNA between individuals, generally not by finding out where the gene actually lies in the genome.

It does depend on what you want to know. If you want a database for determining parentage and relatedness using microsatellites is a very straightforward and reliable approach. It can be time consuming to optimize the microsats, but once done it can be well worth it.
There are also a myriad of other techniques for generating very high numbers of genetic markers in any organism. Restriction site associated DNA markers are one option. Additionally, there are often times already many markers available for organisms due to previous phylogenetic work, which is often done for many species. In order to construct evolutionary histories based on genetics there must be some genetic markers used. The most simple method rather than trying to find new markers is to just use the ones that have already been used in previous phylogenetic research.

If you are looking genetic testing that can be used for testing for certain traits, then it likely would take a bit more time and maybe more money...but not always. An entire genome sequence is not needed to locate informative genetic information within an organism.
Furthermore, you don't even have to sequence the exact gene that causes a disease. All that has to be done is to find some marker that is linked to the gene. It can be upstream, downstream or in a completely different place in the genome. As long as it is linked, it can be informative about the specific gene of interest.
Even if you have an entire genome sequenced you still have to have known sequences from other species to compare it to. Otherwise, how can you tell that a particular stretch of DNA is the gene for amelanism? You wouldn't know unless you could compare it to a gene for amelanism in another previously sequenced species. And if you already have an amelanism gene sequence from another species, you don't need to sequence the whole genome. You just design PCR primers based on the gene from the other species and use those primers to amplify the gene in your species.
This is often the approached used because many gene sequences are often quite conserved across taxa (groups of organisms). If you want to locate the gene for trait "X" in cornsnakes, you can search sequence databases for the sequence for "X" in other organisms. Then you can design primers that will amplify that sequence in cornsnakes. There are things called "degenerate" primers that allow for the fact that the sequence may not be exactly the same between cornsnakes and the other organism you used to design your primers. The degenerate primers allow you to sucessfully amplify the sequence even if it is slightly different between cornsnakes and other other species.

So doing genetic testing doesn't have to involve nearly as much work as it used to and it doesn't require mapping an entire genome or targeting the specific gene sequence for the trait of interest.

I still don't see genetic testing for cornsnakes in the pet trade becoming a popular thing anytime soon. However, the arrival of traits like "stargazer" and other traits that may pop up over the years, makes cornsnakes more and more viable as study organisms. Who knows, stargazer may be related to some disease in humans, which could make it a very lucrative thing to research. The first step wouldn't be to run out and try to sequence the whole cornsnake genome, but to try to identify traits that may be related in other organisms and try to find genes/sequences for those traits using the genetic databases full of sequences from thousands of other species that can be used to probe the cornsnake genome.

To actually map out the whole snake genome and find out where certain genes are would cost several (probably hundreds of) million dollars...what kind of breeder/herper is going to want to put money in that? It's not an investment, its an interest.

Most non-human related research is done just for interest. And the cost would not be hundreds of millions of dollars...not even tens of millions. Besides, that is what grant funding is for. People get grants all the time to conduct research like this. The professor I worked with as an undergraduate is working on putting together a project to produce genome sequences for several species of fish. If there wasn't funding for it, she would never be doing it. I'm not suggesting there is funding right now for a cornsnake genome project, but you never know what could happen in the future.

 

[Intravenous]

It does depend on what you want to know. If you want a database for determining parentage and relatedness using microsatellites is a very straightforward and reliable approach.

Yup...that could be done right now with little difficulty and it wouldn't be that bad cost wise (I don't know about over there but here it would probably only be a few hundred £).

As you said, it does just depend on what the original person meant by "DNA testing"...I don't know if they just meant parentage, or if they were actually taking about sequencing the whole genome.

In order to construct evolutionary histories based on genetics there must be some genetic markers used. The most simple method rather than trying to find new markers is to just use the ones that have already been used in previous phylogenetic research.

What I meant here was that these kind of techniques do tell you about the evolution and distribution of animals but not that much about specific genes...microsatellites repear numbers aren't going to be of much use to the average person who keeps snakes as a hobby, its much more useful for looking at a species as a whole.

An entire genome sequence is not needed to locate informative genetic information within an organism. Furthermore, you don't even have to sequence the exact gene that causes a disease. All that has to be done is to find some marker that is linked to the gene. It can be upstream, downstream or in a completely different place in the genome. As long as it is linked, it can be informative about the specific gene of interest.
Even if you have an entire genome sequenced you still have to have known sequences from other species to compare it to. Otherwise, how can you tell that a particular stretch of DNA is the gene for amelanism? You wouldn't know unless you could compare it to a gene for amelanism in another previously sequenced species. And if you already have an amelanism gene sequence from another species, you don't need to sequence the whole genome. You just design PCR primers based on the gene from the other species and use those primers to amplify the gene in your species.
This is often the approached used because many gene sequences are often quite conserved across taxa (groups of organisms). If you want to locate the gene for trait "X" in cornsnakes, you can search sequence databases for the sequence for "X" in other organisms. Then you can design primers that will amplify that sequence in cornsnakes. There are things called "degenerate" primers that allow for the fact that the sequence may not be exactly the same between cornsnakes and the other organism you used to design your primers. The degenerate primers allow you to sucessfully amplify the sequence even if it is slightly different between cornsnakes and other other species.

Yup, that is all possible but it has a few problems: i.e. I know plenty of genes are highly conserved across across species but I would have thought the amel gene "just for example in snakes is probably pretty different from regular albanism in mammals. So are there any snakes which have already been screened for the amel gene that we can compare with?

I can see it being considered as research in the future though, and its good to know that people are willing to give grants for things like this (I was suprised to see that the guy in the above link had managed to get so far doing research just on snakes).

 

[zwyatt]

Yup, that is all possible but it has a few problems: i.e. I know plenty of genes are highly conserved across across species but I would have thought the amel gene "just for example in snakes is probably pretty different from regular albanism in mammals. So are there any snakes which have already been screened for the amel gene that we can compare with?

I don't how highly conserved specific genes would be. Certain genes or regions of the genome evolve at faster rates. However, even if the two sequences have changed somewhat, that's where degenerate primers can be handy. If you have an amel allele sequence from one species (species 1) you can design degenerate primers that can be used in your species of interest. Degenerate primers are still capable of amplifying the sequence in your species even if it has diverged somewhat from the original sequence in species 1. If there's been a lot of divergence, then degenerate primers may not be enough to get the job done.

It would also require some database searching to find out what the most closely related species is that has a related gene sequenced. There's no guarantee that a mammal would be the closest species with a known sequence. I'm not very familiar with herp-related literature, so I don't know how much genetic work has been done.