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Simple Summary: n-3 PUFA, selenium and lutein cannot be synthesized in the human body, but these substances are very important for human health. Consuming functional eggs enriched with nutrients can increase the body's intake of these substances. To efficiently produce functional eggs, selecting breeds that can deposit higher levels of these nutrients is necessary. Therefore, we investigated the types, dosages, and cycles of additives used in the production of functional eggs. In Trial 1, we investigated the differences in n-3 PUFA deposition among five breeds of eggs. The results showed significant variations in the ability of different breeds to deposit n-3 PUFA in eggs, with Dwarf Layer demonstrating a significant advantage. In Trial 2, we investigated the difference of n-3 PUFA, selenium and lutein deposition in eggs from two reeds in terms of their ability to deposit selenium and lutein in eggs. Additionally, the n-3 PUFA content in eggs from the two breeds was similar to the findings in Trial 1. Therefore, this experiment provides valuable insights for selecting different breeds in the production of functional eggs, ultimately improving the quality and economic benefits of the production process. The purpose of this study was to compare the differences in the content of functional nutrients in eggs, performance parameters, and egg quality parameters of different chicken breeds. In Trial 1, 150 41-week-old hens of each breed, including the Dwarf Layer, White Leghorn, Silky fowl, Beijing-you chicken, and Shouguang chicken, were randomly assigned to the control (CON) and 2.5% flaxseed oil (FSO) groups to compare the difference in n-3 polyunsaturated fatty acid (PUFA) content in eggs. The contents of α-linolenic acid (ALA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and total n-3 PUFA in eggs were increased (p < 0.05) in the FSO groups. The ALA (4.28%), DHA (2.03%), and total n-3 PUFA (6.46%) contents in eggs of Dwarf Layer were the highest among the five breeds (p < 0.05). To further verify if other functional nutrients also have such differences, 600 24-week-old White Leghorn and Dwarf Layer were allocated to four groups: CON, FSO, 0.02% selenium-enriched yeast (SEY), and 0.20% marigold flower extract (MFE), in Trial 2. The content of functional nutrients in eggs was significantly increased (p < 0.05) after feeding these additions. After feeding FSO, the eggs of the Dwarf Layer had a higher n-3 PUFA content than the White Leghorn (p < 0.05). However, no significant differences were found in selenium and lutein content in different breeds. Performance and egg quality were not negatively impacted by FSO, SEY, or MFE. [ABSTRACT FROM AUTHOR]