For plant patents, it actually involves recognizing something. If a branch of your Apple tree mutates nd produces good tasting fruit, then by law, you can patent a plant that exists in only one instance in the wild prior to you recognizing its value and propagating it. That means that you can take that branch of the apple tree and grow it into a new variety and patent it. Because the patent is on asexually reproduced plants, you now have a patent on that variety, but you couldn't get a patent on a tomato for example where it's propagated by seed (good luck gettinga greenhouse to but tomato cuttings from you). The new strain can arise accidentally in the wild (but if there is more than one plant of that variety, then its nonpatentable! It has to be a freak variation that would not persist without your recognition or intervention). Or, it could be something you created through a breeding program, or by irradiation growing shoots (very common way of making new citrus varieties). But the patent is on the end plant, not the method.

These plant patents have nothing yo do with genetic manipulation/bioengineered/"gmo" plants. There, the DNA sequence itself, not the plant, is covered by the patent, its a whole different ball game