Choosing the best dwarfing rootstock for your orchard will depend on multiple factors. Probably one of the most important is the cultivar that will be propagated on the rootstock. Cultivars vary greatly in vigor, with some being very weak growing (‘Honeycrisp’) compared to others that are very vigorous (‘Cripps Pink’/’Pink Lady’). You should select the cultivar/rootstock combination that will give you the desired tree size for your desired tree density, support system, soil, and management system.
The disease sensitivity of the cultivar may also determine what rootstock you should select. If fire blight is an issue in your region and for the cultivar you are planting, select a rootstock that has some degree of tolerance to fire blight (ex. Bud. 9).
Another factor to consider is the cold or heat tolerance of the rootstock in your environment. When growing in lighter soils and in a warmer environment, a rootstock with a little more vigor may be required. If planting in more northern and colder regions, make sure that the cultivar/rootstock combination will tolerate the coldest temperatures.
If the orchard is being planted where apple trees were previously planted (a replant site), consider selecting a rootstock with some tolerance to replant issues.
Answer provided by Dr. Michael Parker, North Carolina State University.