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This is a video of a female guppy giving birth, then attempting (possibly successfully) to eat the fry
This will explain the best characteristics to look for when choosing females to breed with.
When breeding with sepcific males (rather than community breeding) these are the main factors I believe you should take into account :
Shows standards have minumum sizes for tail and dorsal fins, so if you are breeding a specific strain those should be met with any breeding males. If you are breeding a cross then look for as full and long a dorsal fin and again a full tail. Do not breed with males that have deformed fins or ragged edges (unless it is a swallow tail)
This is based either on personal choice or strain specific guidelines. Strain specific characteristics should be looked for in breeding males, for instance with Black Moscow you look for a dark black without hints of blue or green and the body should be as fully black as possible (usually there is some silver underbelly) If you want to keep a certain colour or marking from a male, mate him to a female but remove and ignore the first drop since pairing them and grow the fry on in a separate tank (so you know which ones they are) Then mate the father to one of the female offspring and you should start to see similar makrings on the male offspring of that second mating (F2) The more generation you can do this, the more you can 'fix' a colour or set of markings
Males need to do two things in life; Show Off and Mate. You need to look for a male that has a strong caudal peduncle so it can carry his tail. A reasonable but not too deep chest and smooth body lines. As with finnage, do not breed with any male that shows a deformity as you do not know if it is hereditary or not and should not take the risk
Knowing the lineage of a fish is especially important with pure strains. I have seen many pairs of guppies sold as a strain only to see fry that have no resemblance to the parents. this can be frustrating if you are trying to breed true strains. Knowing and trusting the breeder you get your fish from is important, although not as easy when it comes to shipped fish. Store bought random guppies often look as good as pure strains, and will give lovely colours of fry but it is pot luck as to what you get.