Genomic analysis reflects recent domestication of farmed red sea bream Pagrus major

Red sea bream Pagrus major is a cultured fish species in Japan, but the genetic architecture of farmed populations is unclear. We identified genome-wide single-nucleotide polymorphisms (SNPs) using the genotyping by random amplicon sequence-direct (GRAS-Di) technique and a novel chromosome-scale reference genome to analyze the genomic structure of five farmed red sea bream populations, comparing them to a wild population. The red sea bream genome contained 24 chromosomes (786.0 Mbp) with 98.6% of the identified gene set contained in the BUSCO Actinopterygii database. The farmed populations showed significantly lower genomic diversity than did wild fish, as indicated by minor allele frequency, linkage disequilibrium decay, and effective population size. One cultured population, which was developed via marker-assisted selection, exhibited exceptionally low genomic diversity. Population cluster analyses revealed four genetic clusters within the five farmed populations. Nineteen chromosomes displayed positive selection in the farmed populations, with a selective sweep on chromosome 2 evident in all. While several growth- and immune-related genes were found in the selective sweep regions, no common chromosomal region was detected. These findings illustrate the genetic underpinnings of economically valuable traits in red sea bream, offering significant insights for broodstock management.