Trachinotus carolinus Genome sequencing

The United States can meet the demand for sustainable seafood products by expanding the commercial aquaculture industry in federal waters and land-based recirculating systems. Growth in domestic production would reduce the reliance on global imports, lower the trade deficit, and mitigate environmental impacts. However, vertical integration for small fish farms is economically and technologically challenging. Substantial production output, specialized equipment, and skilled personnel are required to maintain broodstock (adults for controlled spawning) and seedstock (juveniles for grow-out) farming operations. Multidisciplinary research can assist fish farmers with selective breeding schemes to optimize seedstock for maximum performance and production efficiency in various aquaculture systems. Here, we introduce the genetics research component of a long-term project (USDA-ARS Agreement No. 59-6034-9-007) to ensure year-round availability of high-quality seedstock to support the development of the U.S. warm water marine finfish aquaculture industry. This ongoing study focuses on improving the genetic quality of fish stocks for optimal performance and sustainable commercial production via DNA marker-assisted selection (MAS), or molecular breeding. Our model species for genetic improvement is the Florida pompano (Trachinotus carolinus) due to its consumer popularity, market value, and known capacity to spawn in captivity. We use whole-genome sequencing and bioinformatics tools to discover single nucleotide polymorphisms (SNPs) on genes linked to superior phenotypes and determine the applicability of these genetic variants as DNA markers for selection. Our research will contribute to designing a sustainable selective breeding program for T. carolinus aquaculture by achieving the following objectives. 1) Identifying genome-wide DNA markers associated with desirable phenotypic traits, including faster growth and sexual maturity; 2) analyzing a subset of the markers to genotype fish stocks for quality control and pedigree validation; and 3) developing a high-throughput DNA microarray to rapidly detect hundreds of markers for selection, measure differences in genetic diversity among individuals or cohorts, and track changes in family lines over generations.