Transcriptome changes provide genetic insights into the effects of rearing systems on chicken welfare and product quality.

Farm animals raised under free-range (FR) systems are assumed to have improved welfare and higher-quality products that are better to eat than intensively reared animals. However, the modulations are limited in scientific investigations. In this study, we compared 2 rearing systems (FR and cage) and their effects on chickens, including production performance, product quality, body condition, physiological indicators, and gene expression. By using a match-mismatch design in which each treatment was transferred to the other treatment during the last period of the experiment, we aimed to understand the influence of current and former rearing conditions and the ability of individuals to adapt to the current environment. The results indicated that the FR system led to better chicken welfare (e.g., gait score, feather condition, and physiological indicators, P < 0.05) and contributed to higher product quality (P < 0.05), although it resulted in poorer production performance (P < 0.05) and foot pad condition (P < 0.05) than that of the cage rearing system. Additionally, the FR system triggered a series of inner changes and genetic responses in chickens, such as the upregulation of calcium and GnRH signaling, actin and cytoskeleton regulations, immune functions, and developmental processes, and the downregulation of pathological regulations (q-value < 0.05 for all gene ontology terms and P < 0.05 for all Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways). In conclusion, rearing systems alter chicken gene expression patterns, which provide a genetic basis for the adaptability to rearing environments and ultimately affects chicken welfare and products.