In terms of optimization, here are some:
1. What is the optimal time for getting a lettuce plant until harvest without juicing it up with nitrates?
2. What parameters could double the functional components of my mint (think about essential oils) and basil plants just by proper timing in stress and nutrition. These are already questions that botany departments have worked on- I want to bring them out in commercial setting (and may be a bit better).
3. Does back-radiation i.e. reflected light from plant leaves help in measuring plant well-being?
4. What's the right grow medium
5. In general, I BELIEVE, that there is a sub-optimal application (as in wastage) of light (which is roughly 20-30% of indoor farm expense), sub-optimal production in terms of the harvest we get. An improvement in harvest timing by a day would still be a very big volume once you scale it to bigger grow area; more importantly, I believe plant experts are good (even though very rare and expensive), but a DeepFarmer might be able to do better (and this is my main bet), both in terms of scaling and expertise.
Aqua- and Hydroponics have been successfully used to grow food for a very long time now.
If you have any evidence of food grown this way lacking any nutrients, please provide it.
Jokes aside, from a biology perspective why the aversion to GMO? From an ML perspective, what are you optimizing for - maximized growth rate?