Genetic Differentiation and Adaptive Evolution Mechanisms of Cultured and Wild Spotted Sea Bass (Lateolabrax maculatus) Populations Based on a 40K SNP Liquid Array

The spotted sea bass (Lateolabrax maculatus) is a key aquaculture species in China. However, issues, such as farmed fish escape, closed-cycle farming, and nonstandardized breeding, have intensified inbreeding depression and germplasm degradation, necessitating an evaluation of escapement-induced genetic introgression and diversity loss in wild populations. We genotyped two cultured (Fujian [FJ] and Zhejiang [ZHJ]) and four wild (Qingdao [QD], Wendeng [WD], Yantai [YT], and Tianjin [TJ]) populations along China’s coast using a 40K SNP liquid array, obtaining 31,421 high-quality SNPs. Population genetic structure analysis revealed that all samples could be classified into three categories, with relatively distant genetic distances between groups. Genetic diversity assessment showed that all populations were moderately polymorphic, with observed heterozygosity (H_o) and expected heterozygosity (H_e) being relatively close, conforming to Hardy–Weinberg equilibrium (HWE). Notably, wild populations exhibited slightly higher genetic diversity than cultured populations. Population dynamic parameters—inter-population fixation index (Fst) ranging from 0.005 to 0.007, nucleotide diversity (π) from 2.108 × 10⁻⁵ to 2.177 × 10⁻⁵, and Tajima’s D from 2.172 to 2.207—collectively indicated that the populations have experienced genetic bottleneck effects or selective pressures, resulting in a small effective population size. Selective sweep analysis identified 57 core candidate genes from regions under positive selection. Functional enrichment analysis indicated that these genes are primarily involved in nervous system function, substance metabolism, cellular processes, and immune regulation. However, their expression patterns differed among populations, revealing that cultured and wild populations have developed distinct genetic regulatory mechanisms during adaptation to their respective environments. Based on genome-wide selection signature analysis, this study provides new insights for elucidating the germplasm characteristics and genetic evolutionary patterns of spotted sea bass in China.