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Another clever biotechnical trick is to confine patented genes to the small genomes of chloroplasts (subcellular mechanisms that use sunlight to make sugars in plants). Pollen doesn't generally contain chloroplasts and so could not transfer patented genes to neighboring farmers.
And one other technique that might be useful is a technology that turns on patented genes in a crop by treating them with certain chemicals that can be purchased from the patent holder. Thus if a farmer saved his seed, he could decide whether he wanted to take advantage of the patented genes in any given year simply by deciding to buy the relevant treatments or not. These patented genes might be transferred via pollen, but they would have no effect on their neighbors' crops.
The fact of the matter is that worrying about farmers infringing on patented genes may just be a transitory problem since U.S. farmers and farmers in other countries with sensible biotech regulations are rapidly adopting genetically enhanced crops. Increasingly, they are finding that the advantages offered them by biotech crops outweigh any costs associated with licensing agreements and the requirement to purchase new seed every year.