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I frequently buy batches of mangoes to sun-ripen. 5% of these mangoes retain yellow flesh (and do not darken to orange) even as the fruit ripens (and becomes tasty). Why does this happen?

Is this simply due to genetic variability in mango offspring?

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It depends on the cultivar (genetic traits) and on the amount of exposure to light. You can't reliably judge a mango's ripeness by color.

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