Population Structure and Genetic Connectivity of Malabar Red Snapper (Lutjanus malabaricus) Across the South China Sea and Northern Australia: Implications for Aquaculture and Broodstock Management

Malabar red snapper (Lutjanus malabaricus) is widely farmed across Asia (e.g., China, Malaysia, Singapore, Taiwan) and is highly valued in regional markets. Despite its importance to fisheries and aquaculture, population structure and genetic connectivity between wild and farmed populations across the South China Sea remain poorly understood. We analyzed 594 individuals retained after quality filtering from an initial dataset of 930 samples, representing eight wild and farmed populations spanning north-eastern Australia (Queensland) and the South China Sea region (Hong Kong, Malaysia, Singapore, Taiwan), using 18,177 SNPs to quantify genetic diversity, population structure, and effective population size (Ne). Genetic differentiation was low but significant. Wild populations from Australia were differentiated from all other populations, indicating regional genetic isolation. In contrast, farmed populations from Malaysia and Singapore clustered closely with wild populations from Hong Kong and Singapore, indicating regional connectivity. Effective population size (Ne) in farmed populations was low (Ne = 49.1–138.6). Farmed populations from Malaysia and Singapore formed a genetically connected cluster, whereas the Taiwan farm population was genetically distinct. Low Ne was observed in farmed populations from Singapore and Taiwan. These findings support aquaculture management by identifying Australian populations as a distinct unit and enabling biosecure broodstock exchange within the Malaysia–Singapore cluster to minimize inbreeding and strengthen sustainable selective breeding programs.