Development of sex-specific markers for Tachysurus vachellii using whole-genome resequencing

The darkbarbel catfish ( Tachysurus vachellii ) is an economically important species in China. Due to pronounced sexual dimorphism in growth, all-male breeding of T. vachellii is highly valuable for aquaculture. However, the lack of reliable sex-specific markers remains a major bottleneck for early sex identification. In this study, all experimental fish were collected from the Huaihe River basin. Whole-genome resequencing was performed on a full-sib family consisting of 32 offspring and their parents. Using a genome-wide association analysis (GWAS), we identified five sex-specific markers located within the previously reported sex-determining region (SDR) on chromosome 3. Notably, an InDel marker, characterized by a 52-bp deletion on the Y chromosome, was validated in a set of 32 offspring and 27 mixed-population individuals from different farms. Genotyping results were fully consistent with phenotypic sex determined by gonadal observation. This study provides an effective tool for sex identification in Huaihe River populations of T. vachellii .