A recent study has mapped the regulatory genetic landscape of complex traits in chickens, utilizing an advanced intercross line (AIL) population that has been maintained for 15 years, established from reciprocal crosses between Huiyang Bearded chicken and the High-Quality Chicken Line A.

Researchers collected a total of 4,671 samples across 16 generations, allowing for comprehensive genome sequencing and in-depth analysis of phenotypic traits related to growth and development.

The study identified 682 quantitative trait loci (QTLs) across 75 phenotypes, with 43 of these exhibiting significant associations in genome-wide association studies (GWAS).

By integrating GWAS with expression quantitative trait loci (eQTL) and functional annotation from ChickenFAANG, the research revealed that many QTLs are linked to multiple genes and traits, enhancing our understanding of gene-phenotype associations.

The QTLs demonstrated a stable genetic diversity in the AIL population, with minimal genetic drift and a rapid decline in linkage disequilibrium across generations, which improved the resolution of gene mapping.

Significant findings included the identification of numerous regulatory variants, with over half of the significant SNPs located in intronic regions, underscoring the importance of regulatory mechanisms in influencing growth traits.

Specific genes such as HOXB8 and SOX10 were implicated in growth traits, alongside new candidate genes identified for traits like alkaline phosphatase regulation, which is linked to feed intake and gut function.

The research also highlighted evolutionary patterns, indicating that a significant proportion of chicken growth-related genes have human orthologs, suggesting shared genetic mechanisms that influence growth traits in both species.

This study emphasizes the utility of chickens as a model organism for understanding complex traits and their genetic underpinnings, which could have important implications for poultry breeding and human health research.