Molecular characterization and expression profiling of the Pax9 gene in bighead carp ( Hypophthalmichthys nobilis )

Bighead carp ( Hypophthalmichthys nobilis ) is one of the most important freshwater food fish in China, with its head as the main edible part of high commercial value. The Pax9 gene encodes a transcription factor essential for craniofacial and skeletal development, yet its role in growth regulation of this economically important species remains poorly understood. In this study, the HynPax9 gene was characterized in bighead carp, and its expression was examined in individuals exhibiting extreme growth phenotypes. The full-length HynPax9 cDNA is 2,018 bp in length, containing a 1,032 bp open reading frame that encodes a 343-amino-acid protein with a highly conserved paired box domain. Phylogenetic analysis placed HynPax9 within the cyprinid clade, with the closest relationship to zebrafish Pax9. Quantitative real PCR revealed that HynPax9 was expressed in all five tissues examined, with the highest expression in the brain. Notably, expression levels in the brain were significantly higher in fast growing individuals than in slow growing individuals (approximately 2.3 fold, FDR adjusted P < 0.01). In muscle, expression was also significantly higher in the fast-growing group (approximately 1.4-fold, FDR-adjusted P < 0.05). These findings suggest that HynPax9 expression is associated with growth phenotypes in bighead carp, providing a preliminary candidate for further validation in marker-assisted selection programs.