Literally all of the problems you mentioned existed before GMO was a thing. Companies have been patenting varietals since the 1930's. Patent trolling in agriculture is also quite old. E.g. the yellow bean patent debacle:

https://www.nature.com/news/2008/080507/full/453145b.html

GMO is tangentially related but few of the biggest overreaches in agricultural IP are directly tied to them.