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I have asked this question of maybe three indigo breeders, and the concensus from this small group is that the color phases are random. There are no recognized subspecies within eastern indigos, so I do not see how you would be bastardizing the species. My largest male is a red throat and his parents were both black throats!
I have really come to favor the black throats, but when I first got involved with this species I wanted the more colorful red-throats. But in my very small sample size, I have only two black throats. They are both really great snakes, and are the fastest growers I have.
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