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Apples...like a lot of other fruit...ripen from the inside. The core is the brain of the fruit. Everything the apple brings in comes through the stem into the core and then out into the meat of the fruit. You never know until you bite into it.
I don't what causes it but I know how to avoid it. Just add a little bit of lemon to the cut apples and they won't go brown. Also works with bananas. The acid stops teh fruit oxidasing and it won't go brown.
"Brown Core" is a low temperature storage disease
See : http://postharvest.tfrec.wsu.edu/marketdiseases/browncore.html