Prioritization of Variants and Genes for Egg Production Traits in Indigenous Chickens Using Multi-Trait Fine-Mapping

Egg production traits are major breeding targets, but their genetic architecture remains poorly characterized in indigenous chickens. In this study, seven egg production traits were measured in the WG chicken line: age at first egg (AFE), egg number at 21–25 (EN21–25W), 26–30 (EN26–30W), 31–35 (EN31–35W), and 36–43 weeks of age (EN36–43W), total egg number from 21 to 43 weeks of age (TEN), and average clutch length (ACL). Heritability and genetic correlations among seven egg production traits were estimated. Genome-wide association studies (GWASs) were performed using mixed linear model (MLM) and FarmCPU, followed by multiple trait fine-mapping with mvSuSiE. Variants were prioritized based on posterior inclusion probability (PIP) and proportion of phenotypic variance explained (PVE), and genes were prioritized for further investigation based on their positions within linkage disequilibrium-defined QTL intervals. Heritability estimates ranged from 0.19 (EN26–30W) to 0.74 (EN36–43W). AFE was moderately to strongly negatively correlated with other traits (rg = −0.37 to −0.93), whereas genetic correlations between egg numbers across laying stages were strongly positively correlated. GWASs identified 26 significant SNPs within 24 independent regions across 14 chromosomes. Multi-trait fine-mapping prioritized 25 SNPs, among which rs732088229 showed the strongest evidence of pleiotropic effects. Seven genes (NHLH2, MAFB, SYNDIG1, BNC1, TFPI2, EDNRB, and GSS) were prioritized for further investigation based on QTL delimitation and functional annotation. These findings provide potential markers for improving egg production and support the application of multiple trait fine-mapping to reproductive traits in poultry.