NGS-Based Identification and Validation of Polymorphic Microsatellite Markers in Takifugu obscurus

This study aims to optimize an NGS-based approach for detecting highly polymorphic microsatellite loci in Takifugu obscurus prior to experimental validation. Using bioinformatics tools, we identified polymorphic loci from three whole-genome resequencing libraries derived from populations in Busan (BAW), Gyeonggi-do (GAW), and Chungnam (CJA), South Korea. A total of 67,980,814, 82,764,911, and 77,500,391 raw paired-end reads (Q30 > 93%) were generated, yielding 783,029 potential microsatellite loci for primer design. Fourteen highly polymorphic loci were selected and validated using 150 individuals from five populations, including two wild populations (BAW, GAW) and three aquaculture populations (BJA, CJA, GJA). These markers provide valuable genetic tools for future conservation management and restocking programs for T. obscurus.