The Board of Appeal of the European Patent Office apparently decided in oral proceedings in examination that the amended Rules 27 and 28 are in conflict with Art. 53(b) of the EPC. The outcome would be that plants produced by essentially biological products (such as breeding) are still patentable, in line with the decisions of the Enlarged Board of Appeal in G2/07 and G2/08 that originate from before the Rule amendments.
All this boils down to the interpretation of Art. 53(b) that excludes essentially biological processes (but perhaps not the products derived from it) from patentability and of the EU Biotech Directive. Although the detailed decision has not been published yet, the current decision seems to be the culmination of the non-legally binding Notice from the European Commission on the interpretation of the EU Biotech Directive and a, perhaps rushed, amendment of the Implementing Regulations of the European Patent Convention.
Whether you are for or against the patentability of plants produced by breeding, the current situation results in significant legal uncertainty. If the EU/EPC member states really want to exclude such products from patentability, it is to be hoped that this will be done in a quick and clear manner, such as through amendment of Art. 53(b) itself or of the EU Biotech Directive.
For the time being, plants produced by biological processes seem to be patentable. There is little doubt that the full decision will be an interesting read.
Picture by Theo Crazzolara (https://flic.kr/p/KfPgP2)