How do you know it was not a mutation to a gene controller/
If the gene is present, but not switched on, you can detect the presence of the gene by Southern blotting. Basically you make a probe which will "stick" specifically to a sequence of the gene in question. You then take the DNA of the organism in question, seperate it out on an agarose gel then apply your labelled probe and see if it sticks. That detects the presence of the gene.
Alternatively you can use specific primers and attempt to amplify the gene in question using PCR. If the gene isn't present, there's no template for PCR to copy from so you get no product at the end.
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