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

Studying domestication is crucial to understanding the genetic diversity and adaptive evolution of species. Thus, the purpose of this study is to screen the selection signatures on the whole genome of rock bream (Oplegnathus fasciatus) in the history of evolution and domestication. Whole genome resequencing was performed on 75 individuals from six wild rock bream populations and one domesticated farmed group. Genetic differentiation coefficient (FST), nucleotide diversity (Pi) and the Minimum Allele Frequency (Maf) difference were applied to detect the selection signatures. Principal component analysis, population structure analysis and linkage disequilibrium decay analysis were conducted to understand the genetic differences between wild and cultured populations. The results of genetic diversity and population structure analyses indicated significant differences in genetic structure between the wild and domesticated populations, while no such differences were observed among the six wild populations. Selective signature analysis screened 80 target genes, including genes associated with behavioral traits (RCAN1, MEIS2), skeletal development and growth (CasR), immunity (CaMK4), and energy metabolism (PDK2). These findings unveil the underlying molecular genetic mechanisms responsible for domestication in rock bream and offer a vast array of genetic variation across the genome to aid in future selective breeding.