The book/movie, "The Martian", by Andy Weir essentially deals with this exact question, but on the surface of Mars.
Scientists need to consider the gravity of growing plants and the materials required to stay together and not fall apart and float (gravity chamber). An addition, astronauts can only take so much with them into space. This means, for long journeys in space, self independent energy generation is important, or another way to store lots of energy. Mutations that would help not just plants, but many other organisms as well in space would include g-force and pressure resistance, as well as surviving with varying amounts of nutrients (i.e. light, water, oxygen, etc.)
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Answer:
Some of the challenges that scientists might face in space when growing plants would be the fact that plants must have carbon dioxide to carry out their process, which is why they are grown in special chambers. It is true that the astronauts would put off some carbon dioxide, but perhaps not enough. You would also be trying to grow plants in a zero gravity environment, which they aren't accustomed to.
The astronauts would have to be able to provide an extremely large amount of food in order to meet their nutrition needs. There would have to be enough room to grow an adequate amount of food aboard the ship. The plants would also need to be able to produce more than one crop per growing.
If scientists could genetically modify plants to help them grow better in space, they would need to make them able to thrive in a low gravity setting. They would also need to try and engineer them to need less water to survive. They would need to be strong enough to survive the lift off when going into space. The plants would also need to be able to regenerate and produce vast quantities of food.
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