Last month's Supreme Court decision against patentability of normally-existing human genes should also inform this discussion. Discovery does not make anything patentable. Only newly-created genes can be patented.
In the case of these patented fruit tree varieties, only the entire combination of genes, the hybrid, taken inseparably as a whole, can be patented; the individual genes cannot be rightfully patented. Any new combination, such as a seed resulting from open pollination, or a seed resulting from purposeful breeding with another plant, is not correctly included under patent protection.
Any claim to the contrary is over-reaching, and challengeable.
NO VEGETATIVE PROPAGATION (i.e. Cloning) may legally be done of a patented plant without documented permission--- not even one in your yard. Doing so would constitute thieving of royalties.