Genetic Basis of Egg Production in Baicheng-You Chickens: A Genome-Wide Association Study

The Baicheng-You chicken is a valuable local breed in Xinjiang, China, known for its strong disease and stress resistance and excellent meat quality. However, it has not been scientifically bred or protected, leading to low production performance, particularly in reproductive traits. This study collected phenotypic and whole-genome resequencing data from 742 individuals at an average coverage of -5×, constructing a comprehensive variation map for the first time. Heritability estimates for egg-laying traits were moderate to high, ranging from 0.382 to 0.592. Through genome-wide association analysis, 19 SNPs and 120 candidate genes potentially associated with egg-laying traits were identified, with NCAPG, FAM184B, and the HOXA family playing crucial roles in regulating reproductive performance. These findings enable marker-assisted selection for higher egg yield, offering a targeted strategy to enhance productivity while preserving the genetic diversity and adaptive traits of this local breed.