What are these brown lines in my apple?
From Ask An Expert:

These symptoms are characteristic of a physiological disorder called bitter pit, which is the result of a calcium deficiency. This may be the result of inadequate calcium in the soil.



Bitter pit does not necessarily indicate low soil calcium, although consistent bitter pit for several years certainly points in that direction. Anything that results in excessive foliar growth can cause bitter pit, because calicum gets diverted to the foliar growth. Heavy pruning, excessive nitrogen fertilizer, and excessive irrigation all can lead to bitter pit.