It's (kind of) both. It is true that a lot of pruning and training goes into getting fruit trees to be the desired shape, but there is also a genetic component. Trees which have been bred to be short (and usually also cold tolerant & disease resistant) are used as rootstocks for a lot of fruit trees, with the above ground portion that produces the fruit being grafted onto those roots. The end result is dwarf trees that are easier to work with. True, this isn't genetic engineering, but it is a bit more than just pruning.