Whole-genome Resequencing Reveals the Sex Determination System and Develops a Sex-specific Marker in Fat Greenling (Hexagrammos otakii)

Teleost fishes display remarkable diversity in sex determination mechanisms, yet this aspect remains uninvestigated in the family Hexagrammidae. In this study, we performed whole-genome resequencing of Hexagrammos otakii to characterize its sex determination system. Genome-wide association studies and population differentiation index analysis identified chromosome 9 as the sex chromosome, supporting a male heterogametic (XY) system. A 3.11 Mb sex-determining region (SDR) was delineated, containing the potential candidate gene gdf6a. Comparative genomic analysis revealed that the H. otakii sex chromosome is non-homologous to those reported in other Cottioidei species, suggesting an independent origin and a dynamic evolutionary trajectory. In addition, we identified a 99 bp male-specific deletion within the SDR and developed a PCR-based marker that successfully differentiates sex with 100% accuracy. This study provides the first characterization of a sex chromosome in Hexagrammidae and offers a practical tool for sex-controlled breeding and germplasm management in H. otakii.