Unleashing the potential of all-female cobia farming

Abstract

Cobia is a pelagic fish with tropical and subtropical distribution across the globe and ideal biological attributes amenable to aquaculture: growth rates of five kg per year, excellent fillets for sashimi, relative ease of juvenile production and acceptance of formulated diets. Cobia has been farmed in Asia, the Americas and Australia. However, farmed stocks remain unimproved and the genetic basis for economic important traits are still unknown as there is very limited genomic information and resources available for the species. Given cobia is a mass-spawner, whereby single pair mating or artificial fertilization techniques are either impractical or not available for full control of the reproductive output, the development of a rapid, reliable and cost-effective genotyping strategy is the first critical genetic tool for the domestication of the species without inbreeding. DNA parentage analysis would enable our understanding of broodstock contribution to mass-spawning, and the estimation of relatedness, genetic parameters and breeding values of selected candidates.
In this study, previously reported microsatellite markers were scanned for polymorphisms and nine highly informative markers were incorporated into an optimized multiplex PCR suite (PET_Rca1B-H09, PET_Rca1-A11, PET_Rca1B-F06, NED_Rca1-C04, NED_Rca1B-C06, VIC_Rca1B-E08A, VIC_Rca1-H08, FAM_Rca1-H01, FAM_Rca1B-D10), which successfully amplified 97.5% of loci typed. A total of 77 alleles were identified within broodstock, averaging 8.55 (6~11) alleles per locus, 0.753 (0.69~0.82) of polymorphic information content and 0.837 (0.59~1) of observed heterozygosity. DNA parentage analysis of offspring produced in February 2018 yielded 95% success in assignment rate (74 out of 78 tested offspring). Seven families (out of two females and four males) were identified, with one of the females mothering 80% of the offspring. Paternal contributions to the spawning were less skewed, with three males contributing to ~30% of the offspring. This reliable and cost-effective genotyping strategy enabled rapid and unambiguous DNA parentage analysis for the first time in the species, and highlighted the efficacy of broodstock management at the Bribie Island Research Centre to reliably produce larvae from multiple families. The adoption of this standard marker panel in studies of wild and farmed populations will facilitate our understanding of the species diversity and contribute to the genetic improvement of cobia worldwide.