Cobia is a popular recreational fishery, and the species gathers in large numbers in high-salinity estuaries on the Atlantic coast and the Gulf of Mexico to spawn, including Port Royal Sound in South Carolina. Heavy fishing pressure in inshore waters has reduced the population in the past two decades, prompting harvest restrictions and seasonal closures of the fishery.
S.C. Department of Natural Resources grows hatchery broodstock for a cobia stock enhancement program.
This project aims to improve the success of stock enhancement by determining the sex ratio of wild populations through a non-lethal and minimally invasive identification tool. The research goal is to use next generation sequencing to develop a sex-linked DNA marker for cobia and use that information to assess the genetic health and hatchery contribution to cobia in South Carolina.
Project Findings
Using whole-genome sequencing of individual samples, researchers successfully identified a region in the cobia genome that includes sex-specific genetic variation. Successful primer design and optimization, coupled with access to archived known-sex genetic cobia samples, resulted in a new validated molecular marker for cobia. The genotypic sex corresponded to phenotypic sex in 99% of the tested samples, indicating that this novel molecular tool can confidently provide sex identification for cobia.
While previous methods of sex determination were expensive, time-consuming, and required invasive biopsy or lethal dissection of gonads, this new method can be done rapidly and non-invasively, maintaining the wellbeing of the tested individuals and expanding the potential testable season outside of harvest closures. The development of this new method enables resource managers to more efficiently assess the success of stock enhancement programs and better ensure the long-term sustainability of the cobia fishery and helps hatchery managers optimize broodstock sex ratios in aquaculture tanks to maximize genetic diversity and production.