Transcriptome Differentiation of Wild and Hatchery‐Reared Gibelion catla Fish in Bangladesh

ABSTRACT Transcriptome differences between wild and hatchery‐reared Gibelion catla collected from Halda (HL) and Padma River (PD) as wild and a hatchery (HR) population in Bangladesh were identified in this study. A total of 6780 differentially expressed genes (DEGs) in HL compared to HR indicated significant variations in gene expression consistent with habitat‐ambitious transcriptional divergence. Gene ontology and KEGG pathway revealed that HL was characterized by enhanced growth and energy‐related processes, including ribosome pathways, ATP biosynthesis, cell cycle regulation, and oxidative phosphorylation compared to HR and PD. Conversely, PD showed enrichment in the nucleotide, cofactor and carbohydrate metabolism pathways, suggesting higher metabolic efficiency under natural environmental conditions. In contrast to wild populations, HR was enriched by endocrine, immune and stress‐related pathways, including ATPase regulatory molecular function and pathogen‐associated signalling, suggesting elevated physiological stress in the hatchery environment. Overall, wild populations showed enhanced metabolic efficiency and growth, while the hatchery population displayed reduced metabolic performance and heightened stress responses. These findings showed habitat fragmentation influenced the growth, metabolism and stress response in both wild and hatchery population, where the different environmental factors shape the population's genetics and different biological pathways, which made the wild population unique and more suitable for improving breeding programs, boosting aquaculture productivity and ensuring the aquaculture sustainability of this important fish species in Bangladesh.