AS hens lay they use up the pigments stored in their skin, internal organs and body fat. Stored pigment is used as yolk and shell pigment. This leads to a decrease in the color intensity seen in egg shells, and sometimes yolks as well. The legs, skin and beak of good layers will fade in color the longer they have been laying. Selecting for very dark colored egg layers can sometimes lead to selecting hens that lay fewer eggs, as they do not use pigments up as fast.
While birds are laying they do not store additional pigment, so having a break - for example in the winter or while molting - provides the opportunity to build pigment stores up. Feed can have added pigments to enhance egg yolk color, marigold petals are often used for this. Some foods with lots of beta carotene, such as squash and green vegetables, provide a source of pigments as well.