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Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered irradiating sperm and attempting to create haploid females via gynogenesis, but I was wondering if there was a faster and easier method that could utilize gametes directly.

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Are you limited to a particular species of fish? Or can you use one of the asexually-reproducing species? – Atticus29 Feb 5 '13 at 7:57

If your aim is to isolate the two haplotypes (chromosomes) maybe you should try flow cytometry. You might read this paper by Dolezel which is leader in the field, at least for plant chromosomes. I'm pretty sure that the applicability of the method depends on the physical properties of the chromosomes you have (especially their size distribution).

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