Development and Application of Next Generation Genomics Technology for Improved Management of Marine Populations and Ecosystems

Description

This research is expected to benefit the work of the Department in five ways:

1. to help manage endangered and threatened populations and ecosystems;
2. to assist in determining the consequences of interactions between wild and cultured salmon;
3. to help assess the spread of aquatic invasive species in coastal habitats;
4. to provide data on possible adaptive responses of marine species to climate change; and
5. to increase Canada’s genomic and bio-informatics expertise and capability.

This work at the Aquatic Biotechnology Lab fosters and supports the use of genomic approaches within the Atlantic zone.

Mapping genomic variation is central to understanding the function of genes, their distribution in individuals, and biogeography. The most abundant genetic marker, single nucleotide polymorphisms (SNPs) are ideal for mapping and gene discovery, yet the development process can be lengthy and costly. This research project used next-generation sequencing of RAD (Restriction-site Associated DNA) tags in conjunction with laboratory culturing experiments to identify and screen thousands of SNPs in one fish (Atlantic salmon, Salmo salar) and two marine invertebrate species (Atlantic sea scallop, Placopecten magellanicus and European green crab, Carcinus maenas).

Although whole genome sequencing is possible, RAD sequencing enables sampling at restriction sites across target genomes, delivering population-scale genetic data across many individuals in species with little or no previous genetic data available, all at a faster rate and reduced cost. These genome scans and laboratory experiments identified regions of the genome and traits involved with climate associated adaptations thought critical to fishery stability, species persistence, and the establishment and spread of aquatic invasive species. Moreover, in Atlantic salmon, using regional fish (both wild and captive) maximized the ability to evaluate the amount of gene exchange that has taken place between farmed and wild salmon.

Results: This project has proven to be a great success. The description (sequencing) of RAD libraries and SNP identification has been completed for all three species. Processing and analysis, which includes analysis of SNPS in all species for the identification of the genomic and geographic scale of adaptation, has also been completed for the RAD sequencing data. Specifically:

• 17 samples of Atlantic salmon, including wild salmon from southern Newfoundland and representatives of aquaculture lines, were examined using RAD-sequencing SNPs. All analyses have been completed and several genetic markers have been identified and tested.
• Analysis of Atlantic salmon stock structure using RAD-sequencing derived SNPs has identified an unexpected diversity in southern Newfoundland, resulting in a revision of the conservation units in the region, and a manuscript describing this study has been published in Molecular Ecology .
• Data analysis to explore differences among farmed and wild Atlantic salmon has been completed. This analysis indicates very accurate identification of farmed escape salmon and hybrids. The SNPs identified in this project are now being used as the basis for new Genomics Research and Development Initiative (GRDI) research projects currently underway.
• Data analysis has been completed on the results from the fourteen scallop RAD-sequencing libraries. Population genetic analysis evaluating RAD-sequencing data in comparison to oceanographic and biological factors has been completed.
• Analyses revealed a major split between (i) Newfoundland and Gulf of St. Lawrence scallop stocks and (ii) southern Scotian Shelf, Bay of Fundy/Gulf of Maine and mid-Atlantic Bight stocks. Further analysis of Newfoundland and Gulf of St. Lawrence scallop populations also showed differences in their population structure, indicating that different processes may be influencing different levels of population structuring within the region.
• Green crab sequencing of RAD libraries is now complete and SNP identification is also complete.
• Analysis revealed population structuring consistent with the presence of two separate green crab invasions into eastern North America. Preliminary evidence has also shown interbreeding in regions where they co-exist. The analysis has identified a group of genetic markers that can be used to identify these two invasions. These markers are being further developed as a tool for monitoring and invasion tracking.

The scientific title for this project:

Rapid SNP discovery and genetic mapping using next-generation RAD sequencing: fostering the tools and expertise for genomic based management in model and non-model marine organisms

Program Name

Genomics Research and Development Initiative (GRDI)

Year(s)

2011 - 2014

Principal Investigator(s)

Dr. Ian Bradbury

Dr. Claudio DiBacco
leads

Lorraine Hamilton
Fisheries and Oceans Canada