Genomic Analysis Reveals Pleiotropic Alleles at EDN3 and BMP7 Involved in Chicken Comb Color and Egg Production

Dongxiang blue-shelled chicken, an indigenous chicken breed in China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The recent selection has also resulted in a significant difference in egg production. The red comb line (RCL) chicken produces significantly higher number of eggs than that by the dark comb line (DCL) chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. We performed genome-wide association study to identify candidate genes associated with chicken comb color using SNP array data, and we conducted selective sweep analysis to identify putative regions of selection harboring pleiotropic genes affecting both comb color and egg production. Affymetrix Axiom 600 K Chicken Genotyping Array were performed according to the manufacturer's directions on DNA extracted from brachial veins of chickens. A total of 178 female chickens were used in the study.