Sex identification of fishes is critical for understanding life histories, developing successful management strategies of wild stocks, and for aquaculture industry applications. For some large species without obvious phenotypic sexual dimorphism, sex can sometimes only be confirmed via dissection or invasive gonad biopsies, which prompts significant interest for the development of non-lethal and less invasive approaches. Cobia (Rachycentron canadum) has become a species of concern in South Carolina due to heavy fishing pressure on an inshore spawning aggregation over the last two decades. This distinct population segment’s (DPS) numbers have declined to levels of conservation concern and the State of South Carolina has implemented management actions, including harvest reduction and stock enhancement within inshore waters. To maintain an efficient, effective, and responsible marine stock enhancement program, determining the sex of broodstock, hatchery produced fish, and the wild population is therefore imperative.
The goal of this project was to develop and test a non-lethal and minimally invasive sex identification tool for Cobia. Here, we used whole genomic and molecular approaches to identify and validate sex-specific genetic fragments. Using long-read sequencing (Pacbio) to generate reference genomes and re-sequencing data (Illumina) from male and female Cobia, we designed primers for PCR assays that target sex-specific genetic regions and tested them on tissues from known-sex individuals. Results showed that males are consistently heterozygous at those regions, whereas females are homozygous (Figure 1) supporting a genetic-based sex identification and putative sex determination system in Cobia. These markers are currently being incorporated into our multiplexed PCR panels used for genetic tagging of hatchery fish and population genetics.