I read somewhere that you can manipulate the yolk color through different types of feed, but I'm not sure if that's true or not. I used to raise a bunch of hens and yeah... nothing beats eggs from healthy ones. I "did" however get sick of eggs for a while... they're almost too productive! I finally built a network of neighbors who were gladly willing to take them off my hands.
That is 100% the determining factor in yolk color. It comes down to carotenoid content of feed.
Also, in reference to the original comment, there is no difference between GMO and non-GMO feed either.
Some may claim that high carotenoid feed results in more nutritious eggs. That's debatable. Even super-cheap eggs are packed with nutrients. It's an egg, after all. However, the nutritional difference in conventional eggs vs backyard eggs is practically irrelevant. The differential nutrient contents are not significant and come in higher quantities in other foods that we all have cheap access to.
