Genome-Wide Microsatellite Development for Genetic Assessment in Takifugu obscurus Restocking Programs

The obscure pufferfish, Takifugu obscurus, is an economically important species in South Korea. It has become endangered due to overfishing and habitat degradation during the last decades. A national restocking program has been initiated to restore wild populations by releasing cultured juveniles into river systems. To ensure the success of this effort, maintaining genetic diversity and understanding population structure in both wild and aquaculture populations are critical. In this study, we successfully developed 14 polymorphic microsatellite loci for T. obscurus, demonstrating their high amplification success, strong polymorphism (PIC = 0.45–0.84), low null allele frequency, using next-generation sequencing (NGS) from three whole-genome shotgun libraries. These loci were used to assess the genetic diversity and population structure of 150 T. obscurus individuals from five populations: two wild adult populations from Busan (BAW) and Gyeonggi-do (GAW), and three aquaculture juvenile populations from Busan (BJA), Chungnam (CJA), and Gyeonggi-do (GJA). The genetic diversity analysis indicates that the two wild populations, BAW and GAW exhibit high genetic diversity, with a mean number of alleles per locus (Na) of 6.286 for both populations, mean number of effective alleles (Ne) of 3.453 and 3.478, mean observed heterozygosity (Ho) of 0.658 and 0.657, mean expected heterozygosity (He) of 0.680 and 0.677, and polymorphic information content (PIC) of 0.637 and 0.634, respectively. This high level of genetic diversity could serve as a crucial benchmark for selecting broodstock and monitoring the genetic health of restocked populations. Meanwhile, one aquaculture population, GJA showed similar genetic diversity and clustered closely with the wild populations, suggesting its suitability for restocking. In contrast, the other two, BJA and CJA displayed lower genetic diversity and significant genetic differentiation from the wild adult populations, raising concerns about their compatibility for restocking efforts. This information is vital for guiding future management actions and ensuring the long-term success and sustainability of restocking programs of T. obscurus.