The Plant Patent Act excludes "sexual and tuber-propagated plants" - basically, pretty much all the crops you have to replant each season aren't covered, though it does restrict the propagation of fruit trees and the like. Prior to GMOs, sexually-propagated crops like corn were covered by the Plant Variety Protection Act, which is much less restrictive than the utility patents on GMOs - for example, it allows farmers to save and replant seeds, which is illegal with GMOs.
To cut a long story short, plants were ineligible for utility patents (in the US at least) because they were considered "products of nature". However, the US Supreme Court decided that because GMOs existed, plants now count as something made by man rather than a product of nature and could be patented - including non-GMO ones produced using traditional breeding techniques that were previously not patentable. It's a strange decision and I'm not sure I follow their logic, but it's the law now.
