Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens

Feather pecking (FP) is a repetitive behavior in chickens, influenced by genetic, epigenetic, and environmental factors, similar to behaviors seen in human developmental disorders (e.g., hyperactivity, autism). This study examines genetic and neuro-epigenetic factors in the thalamus of chickens from lines selected for seven generations for high or low FP behavior (HFP or LFP). We integrate data on DMRs, SNPs, and CNVs in this controlled artificial selection process. Significant differences in behavior, immunology, and neurology have been reported in these lines. We identified 710 new SNPs related to FP, and found that CNVs was the omic level most affected during selection. The largest CNVs found were in RIC3 (gain in HFP) and SH3RF2 (gain in LFP) genes, linked to nicotinic acetylcholine receptor regulation and human oncogenesis, respectively. Our study also suggests that promoters and introns are hotspots for CpG depletion. The overlapping of the omic levels investigated here with data from a public FP QTL database revealed novel candidate genes for understanding repetitive behaviors, such as RTKN2, associated with Alzheimer’s disease in humans. This study suggests CNVs as a crucial initial step for genomic diversification, potentially more impactful than SNPs.