Why are there spots on my apple?

A new study suggests late season surface water is to blame for the spots that appear on many varieties of apples. The skin spots in question are not the large brown spots that appear when an apple has developed a rotten spot as the result of a bruise or pest; instead they are small brownish specks that appear concentrated on an apple's skin.
Researchers say these spots -- a cosmetic issue more than anything else -- can diminish an apple's value at the market. The spots are caused by the death of individual epidermal and hypodermal cells. These cellular deaths result in microcracks on the fruit's cuticle, which in turn leads to the formation of small brown spots.
In experiments in Germany, researchers showed that water on an apples surface late in the growing season encouraged the brown spotting. Apples that were kept dry throughout the growing period showed the least spotting, while surface water early in the growing period had little effect on spotting.
"Previous report have suggested that apples are particularly susceptible to skin spot if they are poorly colored, from dense canopies, grown in wet years, or harvested late," study co-author Moritz Knoche, an agricultural researcher at Germany's Hannover University, explained in a recent press release.
Instead, the new evidence shows, rainy days late in the growing season are most to blame for excessive skin spots. The study was published in the journal HortScience.