Differences between conventional plant breeding and GM
Crossing the species barrier
The biggest difference between conventional plant breeding and GM methods is that GM allows genes to cross the species barrier. Geneticists can insert into plants any gene from any living thing, such as a fish or an insect, or more usually, a benign bacterium. This allows for the creation of plant characteristics that would be impossible to do by traditional methods. In conventional plant breeding, genes can only cross within the same or closely related species.
Opponents believe that we cannot know what will happen once we have 'tampered with nature' in this way. And once it is done, it is permanent and cannot ever be reversed in that particular variety. However, since the new variety still behaves like any other plant, it would be possible to select out an unwanted genes by conventional techniques.
The fear is that the proteins produced by these foreign genes might be dangerous, either because the protein itself is poisonous, or because it might alter the chemistry of the plant, so that the plant becomes toxic. However, at the time of writing there have been no known cases of poisoning from commercially grown GM crops. The issue of toxicity is dealt with in more detail here.