Perhaps breeding wasn't the right word. Many varieties vary by way of mutation when I single branch on a given tree has fruit of a significantly different quality. This is called a sport.
Changes in a cultivar through vegetative "sports" where say a branch after a
certain point on the branch bears perceptibly different but similar fruits, are thought
to be due to single-gene mutations which occurred during the growth of the plant, and
are considered to be the same cultivar. A mutation which decreases or increases
russeting, or red colour, may affect a lot of other things including flavour.
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