PROPOSAL Project Leads: Paul Bentzen, Sharen Bowman, Daniel Ruzzante - PowerPoint PPT Presentation

GENOMIC TOOLS FOR TRACEABILITY AND SUSTAINABILITY OF LOBSTER ( AND SOME OTHER SPECIES … ) : A RESEARCH PROPOSAL Project Leads: Paul Bentzen, Sharen Bowman, Daniel Ruzzante October 5, 2010 Traceability and Certification of the Lobster Industry, Cheticamp, NS

WHO WE ARE Dr. Paul Bentzen Dr. Daniel Ruzzante Dr. Sharen Bowman Professor, Professor, Adjunct Professor, Dept. of Biology Dept. of Biology Dept. of Biology Dalhousie University Dalhousie University Memorial University Population genetics of Population genetics of Co-leader of Cod marine organisms marine organisms Genomics & Aquaculture Conservation Biology Project 225+ scientific publications

WHAT WE WANT TO DO Develop DNA-based methods of identifying the geographic origin of individual lobsters. Would work on any small bit of fresh, frozen or cooked lobster. Application submitted to ACOA (Atlantic Innovation Fund) to develop traceability markers for lobster , cod, haddock and shortnose sturgeon.

WHY WE WANT TO DO IT Market traceability [fishery ‘branding’, eco -labeling]. To better understand lobster biology: how stocks are structured, how far lobster move. Study the genetics of local adaptation (for example, how genes vary with sea temperature). Begin study of how lobster may respond to climate change.

HOW WE INTEND TO DO IT Use latest technology to sequence the genomes (DNA) of many lobsters from different areas. Use computer based methods to look for differences in DNA sequence (‘genetic code’) between lobsters from different regions. Develop data bases (‘genetic profiles’) for each region. Develop efficient tests to quickly identify geographic origins of lobsters.

Genetic markers for traceability: Single Nucleotide Polymorphisms (SNPs)

Why genomic approach to traceability? ‘Conventional’ genetic studies have revealed some differences among regions, but lacked resolution needed for full traceability. Sequencing of multiple genomes (billions of DNA bases) across populations will allow us to identify and target those parts of the genome that vary among populations.

WHY NOW? Need is not new, but (affordable) technology is. (Virtually) impossible ~10 years ago, much too expensive 5 years ago. 1 lobster genome = 200 Encyclopaedia Britannica DNA sequencing will continue to get cheaper, but with diminishing returns: Now at point where sequencing costs are less than cost of human resources needed to get job done.

Proof of concept: Atlantic cod & the Cod Genomics Project (CGP) Genomic sequencing done primarily for aquacultural objectives. 160,000 sequences  3072 SNPs (genetic variations). Only a few of the ‘best’ SNPs sufficient to distinguish NS from Nfld cod (also from Iceland, Ireland & Norway cod).

QUESTIONS?

Increasing need for traceability of fish/shellfish/seafood Sustainable fisheries of vital importance to Atlantic Canada Many fisheries already depleted: e.g. Atlantic cod production in Atlantic Canada currently 1/20 th of maximum sustainable yield for well managed populations. Tools to identify stock structure needed. Increasingly, consumers want to know where their seafood comes from, and whether it is sustainably harvested.

MSC is leading organization that certifies fisheries and seafood as sustainable. Over 2,000 seafood products, and over 2,500 tonnes certified. Fisheries pay for cost of certification, and pay royalty for use of MSC logo on seafoods. MSC-certified products command market premiums, and are required for access to some markets, particularly in Europe. Many N.A. retailers (e.g., Loblaws, WalMart, WholeFoods, McDonalds) have expressed commitments to sourcing seafood from sustainable sources. In Atlantic Canada, Northern Shrimp, Offshore Lobster, Sea Scallop and Scotia-Fundy Haddock either have or are in process of attaining MSC certification.

MSC recognizes importance of traceability Rupert Howes, MSC chief executive, said: “As the momentum behind the MSC programme increases and market demand for MSC-certified products grows, so too does the incentive for fraudulent use of the MSC ecolabel. DNA testing helps build public confidence in product sourcing and labelling claims. Traceability is an essential business requirement and the MSC will continue to develop systems that help protect our partners’ investment, markets and reputation .” http://www.msc.org/newsroom/news/forensic-techniques-boost-msc- traceability-programme?fromsearch=1&isnewssearch=1

First steps towards DNA- based traceability of MSC- certified seafood “One -third of fish on sale in the US is not the species it is sold as” “one -quarter of cod and haddock sold in Ireland is neither of these” “ The study was able to differentiate between species such as farmed Atlantic salmon the more expensive but sustainable Alaska salmon ” “This opens the possibility of telling apart sustainable and unsustainable fisheries of the same species. Ogden (Royal Zoological Society of Scotland) now plans to develop tests to distinguish between different populations of cod, herring and hoki.”

Workflow for development of SNP-based traceability toolkits Populations A B C 1. Collect specimens from each relevant population. ~100 ~100 ~100 individuals individuals individuals 2. Pool DNA from each population. Sequence each population separately. Genome coverage: 30-40x (lobster), >50x (cod, haddock). 3. ‘Assemble’ & ‘BLAST’ (identify genes). 4. Identify informative SNPs (population specific; geographic variation; temperature-related). 5. Design 1536 SNP assay (Golden Gate).Screen SNPs in each population. 6. Select ‘best’ SNPs for traceability. Small panels of B C A ~100 SNPs. Confirm with more genotyping.

Target species: lobster , haddock, cod, shortnose sturgeon Export value ~$1Billion 45,000-50,000 tonnes ‘Offshore’ lobster ( Clearwater; 720 tonnes) is MSC certified. Competes with non-certified American lobster and European lobster in Europe. Are ‘offshore’ lobster different stock from inshore? Management/enforcement: different seasons, lower size limits. ‘Canners’ trucked to Gulf ?

Target species: lobster, haddock, cod , shortnose sturgeon Fishery in crisis : COSEWIC assessed all cod populations from Nfld south to the U.S. border as ‘Endangered’ in April 2010. Predicted extinction of Southern Gulf of St. Lawrence stock. CGP developed genetic markers for only 2 Atlantic Canada populations. Used older sequencing technology ( more costly, less powerful ). Insufficient resolution. New markers will allow greater resolution of fine-scale stock structure.

Target species: lobster, haddock , cod, shortnose sturgeon Scotia-Fundy haddock fishery about to gain MSC certification. Only remaining major groundfish stock in Atlantic Canada in good condition. Landed value 2003: $28.1 million. However, Eastern Scotian Shelf (ESS) haddock may have undergone fishery induced evolution: ESS haddock now referred to by fishermen as ‘pygmy haddock’. SNP markers will provide evidence of genetic changes associated with change to ‘pygmy’ form.

Target species: lobster, haddock, cod, shortnose sturgeon • Increasing scarcity/endangered status of wild sturgeon fuelling demand for aquaculturally produced caviar. • NB company, Supreme Sturgeon and Caviar, produces 2000kg of caviar/yr (~$2million). • Currently in receivership, because can’t export to largest market in US. • Need to be able to prove their product is not from wild stock. • Propose to sequence maternally inherited mitochondrial DNA in SS&C captive stock, and wild populations across range to provide tools to genetically discriminate SS&C products.

Atlantic Innovation Fund: Key aspects Parameters Criteria Projects $1-3M ACOA funding. Scientifically and/or technically At least 20% co-funding. sound; Objectives Significant economic benefits Increase R&D carried out in Atlantic Canada for Atlantic Canada; leading to the launch of new products, Commercialization potential of processes and services. project; Improve region’s capacity to commercialize New or improved technologies R&D. or new applications of Strengthen region’s innovation system by technologies; supporting R&D and commercialization Support one or more strategic partnerships and alliances among private sectors or technologies. sector enterprises, universities, research institutions and other organizations in Atlantic Canada; and enhance region’s ability to access national R&D programs.