I have planted well over a thousand trees and shrubs on my permaculture site. I have tried bare root, potted, long tap root pots, and seedlings. The problem with all of these options for plant material is that it is not the same as a tree that is planted from seed and is never moved. A tree that is seeded in place has a huge advantage in that it has its taproot intact, and it never had to go through transplant shock. The negative is that for certain seed like apples and pears, you will not get a true to type plant. If you plant a seed from a Gala Apple, the apple tree will not be a Gala.

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