When it comes to genetic modification, the most mentioned type is one that is mostly used in laboratories known as transgenics. This type has it's own risks as well as benefits. While most risks remain unknown on the long term, benefits are known already. On the course of evolution, most things are unknown.
Let's not forget about one subject to think about, there are natural influences on organisms themselves, even if they are GMO. Not limited to background radiation (patterns), mutagenic chemicals and spontanious mutations.
What genes would change if plants are GMO? And how would they change in the long term without any involvement of synthetic modification of genes?