Analysis of population structure and selection signatures for artificial domestication of rock bream (Oplegnathus fasciatus) in coastal China

Domestication represents a powerful model for exploring genetic differentiation and the evolutionary dynamics of adaptation. In this study, we investigated selection signatures across the whole genome of rock bream ( Oplegnathus fasciatus ) to explore its evolutionary and domestication history. Whole-genome resequencing was performed on 75 individuals from six wild populations and one domesticated group. Selection signatures were identified using genetic differentiation coefficient ( F st ), nucleotide diversity (Pi), and minimum allele frequency difference (Maf). Principal component analysis, population structure analysis, and linkage disequilibrium decay analysis were conducted to assess genetic divergence between wild and cultured populations. The analyses revealed indicated significant differences in genetic structure between the wild and domesticated populations, while no such differences were observed among the six wild populations. A total of 80 candidate genes under selection were identified, including those associated with behavior ( rcan1 , meis2 ), skeletal development and growth ( casr ), immunity ( camk4 ), and energy metabolism ( pdk2 ). These findings shed light on the molecular mechanisms underlying rock bream domestication and provide valuable genomic resources for future selective breeding programs.