Unveiling conserved and breed-specific RNA expression signatures underlying hepatic homoeostasis across genetically diverse chicken breeds

1. The liver plays a key role in lipid metabolism, immune regulation and energy balance. To better understand the fundamental molecular mechanisms that support liver function, this study investigated hepatic transcriptomes from four genetically diverse chicken breeds: Kadaknath, Aseel, Punjab Brown or commercial broilers.2. The RNA sequencing revealed 11938 genes that were commonly expressed across all breeds. From these, the top 1000 most abundantly expressed genes were analysed in depth. In addition, breed-specific genes were identified, including 53 in Kadaknath, 63 in Aseel, 498 in broiler and 45 in Punjab Brown chickens.3. The GO enrichment analysis revealed that the conserved hepatic genes were mainly involved in haemostasis, immune response, lipid metabolism, amino acid metabolism, oxidative stress regulation and protein quality control. Pathway analysis highlighted key pathways including PPAR signalling, unsaturated fatty acid biosynthesis, complement and coagulation cascades, ER-associated degradation, glutathione metabolism and iron homoeostasis, reflecting core liver functions.4. Functional interpretation of the identified hepatic genes indicated associations with pigmentation and muscle-related functions in Kadaknath, neuroendocrine and behaviour-associated functions in Aseel, growth and muscle development functions in broilers and reproduction-related functions in Punjab Brown birds. This highlighted distinct genetic architectures underlying breed-specific phenotypes.5. This study defined a conserved hepatic transcriptional landscape shared across chicken breeds, alongside breed-specific gene expression patterns, providing a foundation for future functional studies.