Genome-wide association study in the Baicheng-You chickens highlights candidate variants for egg quality traits

The Baicheng-You chicken is an indigenous Chinese breed known for its superior egg quality and stress resistance, yet the genetic basis of these traits is not fully understood. This study investigated the genomic architecture of 10 egg quality traits in 1 002 Baicheng-You chickens using whole-genome resequencing. The estimated genomic heritabilities for these traits ranged from 0.30 to 0.83. Genome-wide association studies identified 30 single nucleotide polymorphisms reaching genome-wide significant or suggestive association thresholds, which were mapped to 386 candidate genes, including ALAS1, LCORL, and CTNNBL1. Functional enrichment analysis indicated these genes are primarily involved in developmental patterning and embryonic skeletal system morphogenesis. To prioritise candidate variants, statistical fine-mapping using the Sum of Single Effects method (SuSiE) was integrated with epigenomic data (H3K27ac and ATAC-seq). Furthermore, the activity-by-contact model prioritised putative regulatory variants within enhancer regions on chromosomes 20 and 6 that may contribute to the regulation of eggshell colour and thickness, respectively. These findings improve our understanding of the molecular mechanisms regulating egg quality and provide potential genetic markers for breeding programmes in indigenous poultry.