A genomic approach to the genetic management of aquaculture and stock enhancement in emerging marine species

End Date: 08/31/14


The objective of this project is to demonstrate the value of a new high throughput genomic approach (simultaneous discovery and genotyping of Single Nucleotide Polymorphisms (SNP) from RAD-tag libraries sequences) to characterize genetically wild and cultured populations. The method will be deployed in an emerging species that has a high potential for U.S. marine aquaculture (the red snapper, Lutjanus campechanus) in order to address the immediate question of spatial management of stock enhancement. Occurrence of local genetic adaptation and potential for outbreeding depression will be assessed by comparing the Mississippi-Alabama population targeted by the current stock enhancement program, to neighboring populations in Louisiana and West-Florida. The analysis of the obtained data is expected to provide a robust assessment of adaptive divergence in regions where red snapper differ in phenotype or are predicted to show limited connectivity through larval dispersal. This will allow providing reliable recommendation on the genetic origin of red snapper to be reared or released in each region. Mapping of the developed loci along with microsatellites will strengthen understanding of the magnitude and strength of local adaptation and will provide a powerful tool (genetic linkage map) for further development of domestication breeding programs in the species. The work will demonstrate the capacity to acquire high resolution genetic tools and deploy them to manage sustainably genetic resources in aquaculture programs for emerging species. The information that will be obtained during the project (i.e. within a few months) would have taken years of efforts at prohibitive costs with previously available technologies.


A large panel of single nucleotide polymorphism will be simultaneously developed and genotyped in red snapper samples from three localities along the north central Gulf of Mexico using the RAD-tag methodology. Sixty individuals from each of two year classes (120 total) will be assayed from Mississippi, Louisiana (West of Fourchon), and West Florida (Cape San Blas) respectively. Single Nucleotide Polymorphisms will be discovered and genotyped simultaneously from the obtained sequence data. One thousand to 10,000 SNPs are expected to be usable for genetic characterization of populations. Data analysis will focus on assessing baseline divergence among populations using the overall set of SNPs and microsatellites, and detecting and characterizing loci potentially under selection if there are some. The loci will be mapped in a second project component using controlled crosses implemented at the University of Southern Mississippi Thad Cochran Marine Aquaculture Center. Highly informative microsatellites (70-100) will be included in the mapping effort to facilitate mapping of SNPs. Microsatellites will include currently available homologous loci for red snapper and heterologous loci developed in closely related lutjanids. Additional loci will be developed de-novo loci from a draft genome sequence currently being assembled in our group for the red snapper.


Efficient and sustainable development of aquaculture projects for emerging marine species is limited by the absence of adequate genomic resources. An immediate issue lies in the spatial management of aquaculture programs susceptible of releasing fish in the environment. Currently, it is cost prohibitive to assess with confidence whether geographic populations have selected unique local genetic adaptations in new marine species. Knowledge of such genetic adaptation is however essential in order to avoid genetic impact of aquaculture releases on local populations if fish of inadequate genetic background are released in the environment. A reliable assessment of local genetic adaptation is therefore essential in order to manage appropriately releases geographically in the case of stock enhancement. The recent development of next generation sequencing and the RAD-tag methodology offer a new perspective to address these issues in that high resolution genome scans can be deployed for reasonable costs and within a short time frame. Deployment of these tools would provide immediate benefit to the spatial management of stock enhancement programs and would also have medium term benefits for the development of domestication and selective breeding programs in new species by allowing the rapid development of high resolution linkage maps.