What causes the difference in colour of egg yolks?

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YOLK colour does not affect the flavour, nutritive value or quality of an egg. However, to some people who are concerned about their egg yolk coming out pale or white, be rest assured that it is just an indicator of the kind of diet provided to the layer. For example, pasture-raised hens produced eggs with more yellow/orange yolk because their
feed (plants) contain a pigment called xanthophyll.

Xanthophylls are natural yellow pigments found in plants, pastures, cereal corns, and flowers. This pigment is stored in the shanks and beaks of laying hens, they accumulate in the egg yolk, thus the yellow/orange colour.