"The rootstock cultivar makes up the lower few inches of the trunk and the tree’s roots. The scion cultivar makes up the rest of the trunk and all the branches, leaves, and fruit. Rootstocks are selected for their improved disease and nematode resistance, tolerance to adverse soil conditions, nutrient uptake, cold hardiness, and favorable influence on the performance of the scion cultivar, including tree size (dwarfing effects), fruit quality (sugar-to-acid ratio, flavor, texture, size), and productivity (yield efficiency)."

1. The point of connection between the desirable variety and the rootstock is the graft union. Refer to the illustration below.
2. Prune all growth that originates from the rootstock, i.e. below the graft union. 
   
3. If it's difficult to locate the graft junction, sometimes it's possible to identify the source by the growth pattern of the branch. If there's a difference between the growth of branches higher vs. lower on the plant, it's possible the lower growth is from the rootstock. For citrus, this sometimes results in large thorns.

Citrus graft junction

Image source: Citrus Problems — Sprouting Rootstock, Louisiana State University Extension