Mapping the Ball Python "Morph" Genome?

Hello everyone. I am very new to the whole world of Ball Pythons and reptile breeding for the purpose of selecting specific colorations and patterns. I don’t even own a snake…yet.

I have been browsing through a lot of sites, forums, youtube videos and other sources to find out if anyone has tried to collect enough breeding data to put together a rough map of the morph genome, a “morphome” map if you will.

The reason I ask is because I have only found 2-3 threads that address the subject of recombination here and on other forums. While no youtuber or blogger I can find ever discusses the subject in relation to Python regius. I’ve read a couple genetics papers on snakes, but they aren’t very helpful on this front.

I would think that such a map would be immensely helpful to breeders attempting to hedge their odds.

Is it the case that every single identified gene thus far found to affect morph segregates exactly according to Mendelian ratios? I’d think that breeders who have been at it for a long time might have noticed deviances from the predicted ratio when it comes to certain combinations. Certainly if breeding results were pooled from a large number of breeders, a low certainty map could be obtained.

Of course I can see an issue with confidentiality of trade secrets in such a scenario, I would like to know if anyone has ever attempted it?

Also, it seems that the likely candidate category of gene that is mutated in certain alleles to produce the various morphs are transcription factors. Since both neurodevelopmental (eye size, head wobble/orientation), and color/pattern are affected in a few, a series of transcriptions factors seem likely since they regulate a number of other genes and can affect phenotype in multiple ways.

If I choose to engage in the hobby (something I’d like to do once I gain the requisite keeping experience and monetary means), building a rough map would be something I’d be highly interested in doing.

Thoughts?

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This might answer some of your questions:

The whole thread is pretty good actually

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Thank you t_h_wyman. It is good to know the idea of sequencing has been brought up. I was given to understand that Raregenetics Inc was working towards that goal. Ultimately whole genome sequencing and acquisition of enough data, plus all the clustering and refinement required is probably a ways off, not to mention costly. You’d probably have to sample wild populations as well. Although, much cheaper these days. In the end, it will definitely be some PCR based method that will be implemented to confirm the combination of genes within an organism (although, that sometimes has artefacts like all assays).

However, merely from best guesses from morphology of offspring from combination reptiles, a crude map could be constructed, in the old way. Furthermore, this crude map could be used as a guide for genomic searches later. Also, while sequencing, SNP analysis and clustering will most definitely determine the exact loci of the different genes, it may not give a functional mapping of the genome, actual distance on the genome doesn’t always translate into recombination frequency. That is, just because two genes are located close to one another, doesn’t necessarily mean that they will recombine more frequently and vice versa.

For breeders, I’d think a more functional map, derived from empirical data they themselves have collected would have the greatest utility in predicting non-Mendelian odds of certain combinations. What I’m saying, is that if breeders are keeping good records of the snakes they are producing (something I am given to believe they do fastidiously), even with best guesses, they should be able to cobble together a rough map that has predictive power as to how certain genes will be more likely or less likely to be co-inherited. Especially since some have produced hundreds if not thousands of snakes, which should be a large enough sample size to make this sort of map.

However, this sort of assumes that some have observed deviances from Mendelian ratios and favourings towards certain combination morphs over others given particular pairings.

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I’d be more incline to think they aren’t in most cases. While there are a handful of morphs that lead to other abnormalities (wobble in spiders, sables, etc, smaller eyes in super butter/lesser, and kinking in super cinnamon, super spider lethality) most of the morphs seem to do just fine in the homozygous form. Mutations in transcription factors affect a ton of pathways and in many cases lead to pretty severe developmental phenotypes and cancers.

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To quote directly from the thread Travis provided -

Thank you for the response chesterhf. That is a major flaw in the hypothesis. Thanks for pointing it out. I suppose it was this paper which caused me to consider the possibility as somewhat likely: https://www.hindawi.com/journals/abi/2016/1286510/
I’m sure it probably made the rounds here when it was published. I’ll have to delve a bit deeper into the older threads. It isn’t the greatest source of evidence, that is for sure.
There are other possibilities of course, such as promotor mutations for pigmentation genes.

Yes I saw that. I’ll probably be looking at it later, although there isn’t much one can derive without some high end computation…maybe I can negotiate with a colleague at work.

Nah, there are enough WT produced in captivity that you can use those without need of going to wild samples.
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Ummmm… Actually this is a fundamental factor of genetics - linkage. The closer any two loci are to one another, the higher the likelihood that they will travel as a single unit.
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This is the thing I feel is potentially going to trip you up, your assumption completely misses things like BlackPastel and Enchi which, despite having been around for close to two decades and was being bred by numerous of the big breeders during that time, are only just now being recognized as being allelic. Ditto Chocolate and Spotnose. Also add in the whole ambiguity around the Spider complex and how probably half of the hobby still refuses to accept that the SuperSpider is a lethal phenotype… I just think there is both a myopia and a willful obtuseness within the hobby that will hinder you.

Re: transcription factors. I agree with Hilary that TF mutations are unlikely, but TF binding sites are a possibility.

I was not immediately familiar with this paper but having read it I have to question their understanding of genetics/morphs:
Pied breeding

:rofl: :rofl: :rofl:

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Good points. Surprising that the hobby has some myopia about known issues, that would confound data fundamentally.

I was always told to treat linkage as a useful observation and the “distances” calculated in forming a map from it shouldn’t always be assumed to be proportional in all cases to the actual genomic distances. They often are, at least roughly, but I was warned about that assumption long ago in undergrad, though I’ll admit, I’m not a hard core geneticist. Maybe my prof from back then just had a bad experience once upon a time, and made a research error. Either way I’ll yield to your expertise.

My practical application of genetics usually begins and ends with finding interesting disease mutations in homologous recombination genes. Human ones too, which makes my expertise of little merit.

I said it wasn’t the best evidence…paper’s got some issues.

Thanks for the responses everybody. It seems that the reason no-one (as far as I can tell, correct me if I’m wrong) has gone through the trouble to discuss recombination and linkage extensively in this community is because the waters are either just too muddy or it wouldn’t be helpful. Good to know. Again thank you!

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It is not a one-for-one, that much is true. There are situations where it absolutely does not apply. But it is still a good rule of thumb. The way you had phrased it, or maybe the way I read it (internet sucks that way sometimes) was that it was a totally worthless correlation.
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Was not trying to say it would not be helpful, it might indeed. I just think that relying on the hobby and big breeders for your info would likely be setting you up for a lot of pain - as you noted, things are pretty muddy.

Pain is an ugly bedfellow of science, along with existential dread, obsession and imposter syndrome :woozy_face:. I’ve never had a research project that wasn’t laden with a sizable number of difficulties and pitfalls. I’d say bring it on!

That being said, I do need to make sure I have the time to parse the data. Maybe in a year or two, once I get a better idea of what seems to be currently known. The entire realm is really fascinating, and I feel a bit sheepish that I’m so late to such an amazing scientific party.

P.S. Just sort of realized that I can start with just the data on Morph Market itself. It’ll be a heavy load for sure, also very biased towards certain gene combinations, and I don’t have an automated way of collating the data since each snake has to be examined separately to see if parentage information is present, but even if only a few thousand meet data criteria, it could be a starting point.

Well yeah… Running a marathon is a challenge too, but why intentionally make it more difficult by throwing out landmines and bear traps and caltrops on to the course and strapping thirty pound weights to your legs?? :rofl:

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