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

Professor,

Dept. of Biology

Dalhousie University

Population genetics of

marine organisms

Conservation Biology

Dr. Daniel Ruzzante

Professor,

Dept. of Biology

Dalhousie University

Population genetics of

marine organisms

Dr. Sharen Bowman

Adjunct Professor,

Dept. of Biology

Memorial University

Co-leader of Cod

Genomics & Aquaculture

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 1/20th 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

2. Pool DNA from each population. Sequence each population

separately. Genome coverage: 30-40x (lobster), >50x (cod, haddock).

1. Collect specimens from each relevant population.

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.

Populations

~100individuals

A

A

~100individuals

B

B

~100individuals

C

C6. Select ‘best’ SNPs for traceability. Small panels of

~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

Projects $1-3M ACOA funding.

At least 20% co-funding.

Objectives

Increase R&D carried out in Atlantic Canada

leading to the launch of new products,

processes and services.

Improve region’s capacity to commercialize

R&D.

Strengthen region’s innovation system by

supporting R&D and commercialization

partnerships and alliances among private

sector enterprises, universities, research

institutions and other organizations in

Atlantic Canada; and

enhance region’s ability to access national

R&D programs.

CriteriaScientifically and/or technically

sound;

Significant economic benefits

for Atlantic Canada;

Commercialization potential of

project;

New or improved technologies

or new applications of

technologies;

Support one or more strategic

sectors or technologies.