The part a thing grows from, and the base form a word's variants share. Both are what the rest branches off.
Old English stefn (the stem of a tree or plant, the stock a thing grows from), from Proto-Germanic *stamniz; a word's shared base form takes the same name as the part a plant branches from.
The part a thing grows from, whether the base a stalk rises out of or the base form a word's variants share. Everything else is what branches off it.