Genetic diversity and population structure in cultured families of Marsupenaeus japonicus using microsatellite markers

The kuruma shrimp (Marsupenaeus japonicus) is a highly fecund marine aquaculture species with substantial variance in reproductive success. These traits may lead to genetic diversity loss and inbreeding, particularly under mass selection programs. In this study, we assessed genetic diversity levels and effective population size across 18 M. japonicus families using 10 microsatellite markers. The results demonstrated that the cultured families of M. japonicus exhibited lower heterozygosity. Pairwise comparisons of genetic differentiation coefficients revealed moderate to high differentiation among the families. Phylogenetic, structural, and discriminant analyses of principal components identified two distinct genetic clusters within the sampled families. Low effective population size estimates and genetic bottleneck signatures were observed, likely due to incomplete or skewed parental contributions to offspring. Therefore, we recommend implementing mating schemes involving genetically distant brooders. These findings provide critical insights for population level genetic studies and breeding strategy optimization in M. japonicus.