Detection of quantitative trait loci and genetic correlations of lipid reserves and production traits in aging laying hens

Maintaining laying performance at advanced ages requires a better understanding of the genetic regulation of lipid metabolism, a process central to egg production through yolk formation, hormone synthesis, and energy balance. Abdominal fat weight (AFW) and yolk percentage (YP) are important indicators of lipid partitioning in layers, reflecting lipid storage and allocation to the egg, respectively. Despite their important role, their genetic architecture remains poorly characterized particularly during late laying stages. This study investigated the genomic architecture of AFW and YP, and their genetic relationships with egg weight (EW) and laying rate (LR) in hens at 90 weeks of age. Liver weight (LW) was also analyzed at the same age, given its central role in lipid synthesis as well as blood glycaemia (GLY) and ketonemia (KET) as metabolic indicators of energy balance. Analyses were performed in an experimental population of 7000 Rhode Island Red hens genotyped with a 60k SNP array and imputed to 600k. Genome-wide association studies (GWAS) were combined with linkage disequilibrium (LD)-based QTL refinement, and the resulting signals were integrated with liver expression quantitative trait loci (eQTLs) derived from age-matched gene expression data. Heritability estimates for AFW and YP were high (0.50 and 0.51), indicating that genetic factors explain a substantial proportion of phenotypic variation at advanced ages. AFW also exhibited markedly greater phenotypic variability than most of the other traits, consistent with a larger magnitude of genetic variation. Positive genetic correlations of AFW and YP with LR (0.26 and 0.27) suggest that lipid reserves are also associated with laying persistence, whereas negative correlations with EW (-0.15 and -0.54) point to potential trade-offs between lipid allocation and egg mass. KET, reflecting circulating ketone body levels, was negatively correlated with LR (-0.32) and LW (-0.29), KET can be interpreted as a marker of metabolic stress, which may compromise laying performance. Finally, the strong genetic correlation between LW and YP (0.48) supports a shared genetic architecture between hepatic lipid synthesis and yolk formation. GWAS identified several suggestive QTLs for lipid-related traits. LD-based refinement and liver eQTLs integration allowed to drastically reduce the number of candidate genes and highlight positional and regulatory candidates. Overall, these findings establish a basis for future functional investigations and for breeding programs designed to improve metabolic efficiency and sustain reproductive performance over time.