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I asked this same question a week or so ago and Coda told me that the genetics would not be affected. I will be keeping some bonsai mothers under 2 42 cfls for space and electricity concerns and then I'll use a 400w HPS whenever I want to grow some more bud.
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I've never kept a mother using a hydro setup (or soil! I'm pretty new to growing), but I don't see why you wouldn't be able to. Root trimming might be a little easier, but transporting her would be a bit of a hassle(I think). I plan to use soil for my mothers(bonsai), just because it's less expensive to maintain and if I have to move anywhere I can easily transport them.