Ball Python DNA mapping

I am in the process of developing a system for a ball python genetic library as well as DNA mapping for morph ball pythons. The process will result in a visualization of a selected ball python's genetic markers in order to validate genetics. This will primarily serve those purchasing high end snakes that are het for a desirable breed. An example would be, you are about to purchase a Spider het pied. You can visibly confirm the snake is a Spider. What about the fact that it is het for pied? Through database comparison a person will be able to guarantee a snakes genetics when the trait is not visually apparent. The process and output will be in the form of Gel Electrophoresis. This will allow for easy position matching for genetic similarity.

I want to get a more robust idea of the potential interest this service will have in the herpecultural world and any other information you may find useful. Any input would be greatly appreciated and help further develop the process, in turn enhancing the understanding of ball python genetic variability, and grow the overall understanding of ball python mutations.

It will have to be cheap, I would love to be able to test potential het purchases, but it simply would cost too much.

Good idea in theory, most likely not a good thing in reality. Genetic tests are expensive and timely. Its alot easier and cheaper to just buy from reputable breeders. I had my DNA mapped and it cost me nearly $500 for all the tests and took around 3 months to get the results. Definately a very interesting idea, I'm sure people would be interested in the knowledge about certain genes but not for testing hets.

I have done Gel Electrophoresis before. Very interesting process.

What lab are you going with? I was considering speaking to my university's genetics lab for headway on a similar project.

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Originally Posted by Slashmaster

I have done Gel Electrophoresis before. Very interesting process.

What lab are you going with? I was considering speaking to my university's genetics lab for headway on a similar project.

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I will be performing all of the work and analysis myself. I am going to start by building a library of samples to compare to. Then move on to comparative work for individuals seeking genetic confirmation or variation analysis.

im not exactly sure what you are looking for us to say?

of course it would be awesome for someone to map the ball python genome. since you already apparently have a means to get dna into digital form, you already have one obstacle out of the way. some questions I would ask are how long does it even take to get one snakes dna into a database. just a quick look around on google is showing me humans take about 3 days. With that in mind how many normal snakes are you going to have to test before you can compare them to morphs to see where these alleles sit? I mean are we looking at a possible multi year project before you have the data you need?

It wouldn't be only testing hets, you could also end the lesser/butter debate and the cinny/black pastel debate, see what other morphs are actually the same, see what morphs lay on the same locus. Theres a lot we could get from this, but as you see above there concerns of money and also time.

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Originally Posted by OhhWatALoser

im not exactly sure what you are looking for us to say?

of course it would be awesome for someone to map the ball python genome. since you already apparently have a means to get dna into digital form, you already have one obstacle out of the way. some questions I would ask are how long does it even take to get one snakes dna into a database. just a quick look around on google is showing me humans take about 3 days. With that in mind how many normal snakes are you going to have to test before you can compare them to morphs to see where these alleles sit? I mean are we looking at a possible multi year project before you have the data you need?

It wouldn't be only testing hets, you could also end the lesser/butter debate and the cinny/black pastel debate, see what other morphs are actually the same, see what morphs lay on the same locus. Theres a lot we could get from this, but as you see above there concerns of money and also time.

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Is this a appealing service for you? Why? Why not? What else would you want out of it?

I am working on targeting a specific section of DNA, not mapping the entire genome. By targeting a specific sections, a benchmark will be generated and can be used for comparison.

I am still working on setting up trials to determine turnaround time. There are a lot of factors that influence turnaround time including, sample type (swab or blood), DNA concentration for PCR (DNA replication) and then the actual protocol for running the sample. I am estimating that given basic constraints turnaround would be 1-2 days for digital results and 7-10 days for prints. With that being said, this is still only speculative until trials have been run and the protocol has been optimized.

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Originally Posted by BPSP

Is this a appealing service for you? Why? Why not? What else would you want out of it?

I am working on targeting a specific section of DNA, not mapping the entire genome. By targeting a specific sections, a benchmark will be generated and can be used for comparison.

I am still working on setting up trials to determine turnaround time. There are a lot of factors that influence turnaround time including, sample type (swab or blood), DNA concentration for PCR (DNA replication) and then the actual protocol for running the sample. I am estimating that given basic constraints turnaround would be 1-2 days for digital results and 7-10 days for prints. With that being said, this is still only speculative until trials have been run and the protocol has been optimized.

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i obviously have no idea how any of this works, but how exactly can you target a section and know that is where you should be looking.

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Originally Posted by OhhWatALoser

i obviously have no idea how any of this works, but how exactly can you target a section and know that is where you should be looking.

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Well the short answer is Sanger Sequencing.

I will have to identify which chain terminating variant is best for comparison purposes through accumulation and analysis. Once a sample is amplified using PCR then all 4 chain terminating variants will be introduced and then the results will be run through electrophoresis and the sequence will be deduced from there.

From that point on the same chain terminating variant can be introduced and then compared to the same section in the catalog to confirm a relationship between samples.

im more referring to theory, like how do you target where the albino gene resides. is it basically get enough data from normals together and then test an albino and hope your looking in the right area? im just not understanding if you don't first map the entire genome, how do you know the albino gene doesn't actually reside in the area your not looking.

Be very careful who you get samples from. Years ago (like when het pieds where $12,000 and we didn't know about the markers) someone asked for samples to try to find the pied gene. I talked to a breeder who had pieds at the time and sent samples but he said he "mixed them up to see if he knew what he was doing". With help like that you would never get anywhere.

I personally could have used a simple paternity test as recently as last year. Sure actual gene tests would be better but a basic paternity test could answer a lot of questions and wouldn't become obsolete. I did see a post by a guy on kingsnake indicating he was looking into that so maybe that one will be covered.

most snakes aren't expensive enough to warrant people paying to make sure that it's a het however there are a few reccessives that do cost a lot clowns, candys, and toffees come to mind but not many people are buying those due to the cost.

One phrase will cover it all:
"Possible Het for Ultramel"

Yes, there will be some demand for this service. :D
I would LOVE to be able to sort out my poss hets, and sell them as guaranteed hets. It just has to be affordable.
Even if it's only worth doing for very high-end poss hets at first, if the price can be brought down over time, I can certainly see becoming common.

In cattle, similar genetics tests cost only around $25. If you can accomplish that for ball pythons, I'm on board. That's worth it, even for poss het albinos.
I'd definitely pay for this service.

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Originally Posted by BPSP

I will be performing all of the work and analysis myself. I am going to start by building a library of samples to compare to. Then move on to comparative work for individuals seeking genetic confirmation or variation analysis.

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Interesting... but you know the turnaround for something like that is gonna be years if you're doing it all yourself? I have quite a bit of experience with gel electrophoresis, but my real area of expertise is denaturing gradient gel electrophoresis, which is a quick way to actually visualize DNA variation down to (theoretically) the single base pair level... though you have to have targeted sequence first.

I know the cost and time required for whole genome sequencing has dropped drastically recently - I attended a fascinating seminar about Sanger sequencing a couple years ago too.

Anyway, I think the project is VERY interesting. Because of my background, I actually have spent a lot of time considering the genetics behind various ball python traits. Have you considered focusing some of your attention on determining the cause for detrimental traits, such as "wobbler" spiders, infertile desert balls or various lethal sable and yellow belly crosses? I'd be very interested in the wobbler info, since I own a spider myself, and if the cause could be determined then selective breeding might be able to reduce or eliminate such a problem.