Differential Transcript Expression Associated with Pigmentation Variation in Cultured Takifugu Rubripes

Accurate molecular authentication of edible pufferfish is essential for ensuring food safety and regulatory compliance. However, morphological similarity among Takifugu rubripes, T. chinensis, and T. pseudommus complicates their taxonomic distinction and labeling accuracy. This study investigated whether differential transcript expression contributes to the phenotypic variation underlying current classification ambiguity. Eight transcripts associated with large genomic deletions previously identified were analyzed using quantitative real-time PCR in dorsal skin and anal fin tissues from six aquacultured T. rubripes specimens showing distinct anal fin coloration. Three transcripts (ENSTRUG30845, GPD2, and ENSTRUG28536) were significantly upregulated (1.3–2.8 fold) in individuals with mixed pink-and-black anal fins compared with those exhibiting uniformly pink fins. Enhanced expression of GPD2, a mitochondrial enzyme regulating redox balance, indicates that variation in pigmentation is associated with metabolic and post-transcriptional regulation rather than genomic divergence. The remaining transcripts showed no significant differential expression. These results suggest that phenotypic plasticity, driven by environmental and developmental modulation of transcript activity, underlies the observed morphological diversity.