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It is my experience that a misshapen apple usually has unfertilized seeds in the area of the depression. Apples of the proper shape have all of their seeds pollinated.. If a pome fruit was seedless, wouldn't it be misshapen all over, and not a full sized fruit?
It would seem to be a function of nature not to put a lot of plant resources into a fruit, or portion of a fruit, where the seeds are not pollinated (let the runts die off). I have no explanation for seedless oranges, other than if it wasn't for man, they would have died out too.
My guess would be that a fertilized seed gives off hormones in the growing fruit, that stimulates fruit flesh development around it. An unfertilized seed would not inspire fruit flesh growth and the fruit would be misshapen (or abort).
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