Yes, both economically (sterile seeds sold at a premium) and ecologically (accidentally affecting wild strains in unintended ways). But, with the latter, I guess the same could be said of selective breeding.
Yeah the two biggest issue seem to be proprietary plant DNA and the potential to introduce genes into wild plants unintentionally through hybridization or horizontal gen transfer.
It can be said of the former as well, with highly prized hybrid strains of, say, tomatoes with strictly controlled patented seed supplies; the plants do not bear true (being hybrids) so trying to harvest seeds from the fruit itself doesn't help.
For example, I like the kumatoes from the grocery store, but I can't grow any myself, and probably never will: https://en.wikipedia.org/wiki/Kumato
Like all technologies there is the possibility of abuse (i.e. Monsanto), but there is also high potential for good as well. The majority of people don't discuss the possibilities of growing food in unsuitable climates, or introducing different nutrients into other foods. Feeding the less fortunate, helping those with allergies, making it easier for people with deficiencies with Iron or Vitamin D. Many different problems can be solved with genetic modification.
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