Hello Galina, 

Thanks for reaching out. When you say "clear" do you mean normal white flesh or more clear/glassy patches? Apples with these clear sections have what we call water core that can progress to what you are seeing now. Here's an article on water core (Microsoft Word - WatercoreinApples.docx (msu.edu)). 

If not, I am also curious about how you stored these apples. Apples are living structures that will continue to age and rot over time unless their temperature, moisture, oxygen, and carbon dioxide are carefully managed to limit cellular respiration. While they can be successfully stored for about a year in commercial settings, it is expected that apples will exhibit decay and rot in storage. Even when these factors are carefully managed, a percentage will almost always rot earlier. 

Great! Watercore isn't initially an issue. The clear areas are higher in sugar! But it will reduce the storage capacity of the impacted fruits. 

Best,