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Their diet like your diet affects health, (you ARE what you eat)

Well @Shamo Hybrid , remember store bought eggs for the most part are fed the cheapest available diet in order to maintain peak laying; your chickens are likely fed MUCH better thus better quality eggs - that shows in your yolks!

There are other things that darken yolks, much of those they obtain when free ranged or in large outdoor runs . Even them getting some corn will cause a darker yolk than a layer mash only fed chicken for example.