There are two separate concepts here. Patents are sought to protect intellectual property and have been available on seeds and plants since the 1930s. These patents reflect the novel use of plant breeding, including genetic engineering techniques. They do not indicate that the food produced from those plants is somehow different from other varieties of the plant. FDA looks at the safety, nutrition and composition of a GM seed or crop, as compared with that of a non-GM seed or crop. FDA and food safety regulatory authorities around the world have determined that foods made with GM crops are as safe and nutritious as foods made with non-GM ingredients and are not significantly different in terms of their composition.
If you’d like to know more about plant patents, check out this detailed response from law professor Drew Kershen.