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there are many different strategies that can help.
- tons of experience. like decensored said, they have seen the underlying stuff often enough. also knowledge of markers of different morphs, etc.
- super forms. if you hit a 5 gene combo and the female is a super enchi super pastels, thats 2 less genes to figure out. same with the males, he is super this, she is super that. leads to clutches where everything will have, for example, single-gene enchi + cinnamon + YB. now you have a head-start for identifying the clutch. gene complexes / "acts like a super" can also help, like in highway + extra genes to ivory + extra genes.
- careful pairing. multi-sire clutches only when it wont later interfere with identification. like when one male has super GHI, and the other male has no GHI or darkeners in it whatsoever, its fine, running them both over the same group of females wont cause identification issues. or when you have a triple gene male, and a different male that has the same 3 genes and one additional extra gene. also no problem.
- good record-keeping over multiple generations with pictures. when in doubt, see if the database can help, pictures of grandparents and clutches and such.
- using clutch results to prove out the parents, then using the now proven genetics of the parents to better identify future clutches. and if needed holding back and breeding possible new combos to prove them out.
- kinda obvious, but... numbers. large numbers of clutches, large numbers of snakes, multiple examples of the morphs in the collection.
its quite a bag of tools. i guess experience and good record keeping and proving stuff out and being smart about the pairings would be the most important ones. when a breeder keeps learning and uses some of these tools, i can see how they can get to high numbers of genes and can still be sure about it, at least most of the time.
about health, it doesnt really affect the health, unless there are issues with the individual genes that are present in the snake; these will also be present in combos containing the gene. Also you can do this stuff without inbreeding over multiple generations, and there is a way to reset bloodlines back to an inbreeding factor of zero, by outbreeding.
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