Comparative liver transcriptomics of Kadaknath and Aseel chickens reveals molecular basis of their unique nutritional and metabolic traits

1. Indigenous poultry breeds, like Kadaknath and Aseel, represent invaluable genetic resources, combining unique nutritional and cultural traits. The Kadaknath breed is famed for its black, lean, iron-rich meat with high protein and antioxidant content, while Aseel is a muscular breed prized for endurance, stress tolerance and fighting abilities. Despite their economic and nutritional value, the genetic and metabolic underpinnings of their distinct traits remain underexplored. 2. This study conducted a comparative transcriptomic analysis of liver tissue from Kadaknath and Aseel chickens using RNA sequencing (RNA-seq) to uncover the molecular mechanisms driving their phenotypic diversity. The results identified 435 differentially expressed genes (DEG) linked to key processes such as lipid metabolism, oxidative phosphorylation and stress response. 3. In Kadaknath chickens, up-regulated genes, including <i>CPT1A, PCK1</i>, <i>TXNRD3</i> and <i>PPARGC1A</i>, were associated with efficient triglyceride breakdown, strong antioxidant defence and optimised energy metabolism. This likely contributes to the characteristic lean, nutrient-rich meat with high protein and low fat content. 4. In contrast, Aseel birds showed elevated expression of stress response genes (<i>MRPL18</i> and <i>RPL11</i>) and mitochondrial genes (<i>NDUFA1, NDUFA8, NDUFB9</i> and <i>PTPMT1</i>), supporting its high energy requirements and resilience to stress, crucial for its endurance as a fighter breed. Gene co-expression network analysis highlighted critical hub genes driving these breed-specific adaptations.