This study investigates the genomic differentiation between wild common carp from the Caspian Sea and farmed common carp from various regions of Iran. DNA was extracted from 49 individuals’ tail fin samples. Genomic libraries were prepared using 2bRAD-Seq. 64,645 SNP markers passed the final quality control. The FST analysis was done using R software to determine genetic divergence between wild and farmed populations, northern and southern farmed populations, and carp with normal scale patterns against those with different scale pattern (line and mirror). FST investigation of farmed and wild common carp revealed several interesting genes close to outlier loci, including birc6, cleavage stimulation factor subunit 2-like, mucolipin-1-like and cytochrome c oxidase subunit gene 5 A. These genes were linked to biological pathways such as ubiquitin-mediated proteolysis, mRNA surveillance, oxidative phosphorylation, metabolism, and cardiac muscle contraction.The grm3 gene, which is implicated in the biological process of the neuroactive ligand-receptor interaction pathway, was identified by comparing southern (Shahid Maleki) and northern (Silver Carp and Taavoni12) farmed populations. Key genes such as 5- hydroxytryptamine receptor 1E, WAS/WASL-interacting protein family member 1-like and protein kinase C eta typelike, were finally identified through comparison of farmed carp with line and mirror against normal scale patterns. These genes are involved in pathways linked to neuroactive ligand-receptor interaction, endocytosis and vascular smooth muscle contraction. Overall, this study represents a foundational step in understanding genomic differentiation between wild and farmed common carp in Iran, offering valuable insights into the genetic basis of traits such as scale pattern variation in this species.
