The planting depth is critical, especially for trees on dwarf or semi-dwarf rootstocks. When planting, dig the hole deep enough to allow the tree to be planted with the graft union 2 to 3 inches above the ground. If the tree is planted too deep and the graft union is below the ground level, the scion variety will form roots and the tree will become a standard-sized tree. Also, if the graft union is buried, the tree may send up shoots from the roots. Planting trees with the graft union higher than 3 inches above the ground can be a way to reduce vigor. However, planting too high above the ground can lead to burrknot formation on the aboveground portion of the rootstock creating potential feeding sites for insect larvae and dogwood borer. Burrknot cracks can also be entry points for fire blight.
Interstem apple trees should be planted with the interstem piece at least partially buried. This will tend to decrease the amount of root suckering, lead to better trunk development, and better cropping efficiency. Remember that the soil and/or tree may settle, so be sure to revisit the planting to ensure the graft union is at the correct height.
Answer provided by Jon Clements, University of Massachusetts, Amherst.