Canadian Potato Genome Project (CPGP)

(Molecular Determination of Tuber Health and Quality in the Potato)

Barry FlinnSGII/BioAtlantech

(Fredericton)

Sharon ReganCarleton University

(Ottawa)

Co-Lead PI’s:Co-Lead PI’s:

CPGP - Rationale

Importance Of The Potato

• Integral part of the diet of a large proportion of the world’s population; daily staple of over 1 billion people• Supplies at least 12 essential vitamins and minerals

• Fourth most important crop worldwide

• Utility derived from the tuber; contains 22% dry matter, primarily starch • Commercial varieties are tetraploid (2n=4x=48)• Regulatory mechanisms governing tuber development require elaboration

CPGP - Rationale

• 46% of national potato production $1 Billion/year

ATLANTIC CANADA

• Solanum Genomics International Inc.

• Potato Research Center of AAFC

• Home of McCain Foods Ltd. $5.5 billion/year

CPGP - Rationale

• AAFC Potato Research Centre:• Over 50 years of potato breeding history• Shepody potato an example of improved tuber quality• Large germplasm collection with desirable qualities for tuber health and tuber quality traits• Expertise in potato physiology, trait mapping, tissue culture & transformation, molecular plant biology and pathology

Potato Expertise in Atlantic Canada

CPGP - Rationale

• Solanum Genomics International:• Staff with significant genomics experience (Genesis R & D, Auckland, NZ)• Project on foliar late blight resistance ongoing• Database containing several thousand foliar ESTs

Potato Expertise in Atlantic Canada

CPGP - Rationale• Solanum Genomics International:

• Expression profiling via microarray to identify genes associated with enhanced field resistance

ANDLBRLF02345HTF.01

ANDLBRLF01256HTF.01

ANDLBRLF02041HTF.01

• Further elaboration of expression patterns, followed by testing of gene constructs in plants

S R

World-Wide Solanaceae genomics

TIGR & NSF~60,000 potato ESTs

TIGR & NSF~120,000 tomato ESTs

SCRI & SGII~10,000 potato ESTs

8,222 mixed species assemblies

Only 2,108 potato specific assemblies*Much less than the ~25,000 genes expected in plants

* David Marshall, SCRI

CPGP - Rationale

Increasing The Genetic Resources Of The Potato

CPGP – Project Description

• Integrated project team comprising researchers from:• SGII/BioAtlantech (Flinn)

• Carleton University (Regan)

• AAFC Potato Research Centre (Audy, Goyer, Li, DeKoeyer)

• University of New Brunswick (Bhavsar, Evans, Culver, Siebrasse)

• Nova Scotia Agricultural College (Wang-Pruski)

• Targeting genes associated with tuber health and tuber quality:

• Tuber Health – Late Blight and Common Scab• Tuber Quality – Stable dry matter accumulation, cold sweetening and after-cooking darkening

CPGP – Project Description

Research Areas

• Genomics Operations:• cDNA library construction• EST sequence generation• Bioinformatic analysis and research

• Expression Analysis:• Microarray profiling

• Potato Mutant Generation:• Activation tagged lines

• GEELS

CPGP – Project Description

Research Areas

• cDNA Library Construction (SGII):• Tuber developmental series using the Shepody variety• Controlled growth and storage environment for the collection of 4 developmental stages and 2 cold storage stages

CPGP – Project Description

Research Areas

• EST Sequence Generation (SGII; NRC)• Sequencing outsourced to NRC Halifax platform• 10,000+ EST’s to be sequenced• Virtual subtraction methods to ensure sequencing of less abundant transcripts

CPGP – Project Description

Research Areas

• Bioinformatic Analysis (SGII; AAFC; CBR):• Access to resources via CBR membership/node status• Raw sequence processing and analysis by Fredericton bioinformatics group (Vector trimming, base calling, clustering, contig assembly, BLAST, annotations)

• Relational database management system of CPGP to link NRC (sequencing), CBR and researchers• In silico assignment of gene function• Microarray data

CPGP – Project Description

Research Areas

• Bioinformatic Research To Suit Project Needs (UNB):• Autonomous agent development to automatically update sequence annotations• Enhancement of bioinformatic algorithm performance with parallel computing• Algorithm development using annotation information to enhance sequence searching• The application of clustering and learning techniques to the analysis of expression data

CPGP – Project Description

Research Areas

• Microarray Profiling (SGII, AAFC, NSAC, UNB, OCI):• Preparation of approx. 10,000 unigenes for arraying• Array preparation outsourced to Ontario Cancer Institute Microarray Centre• Array experiments designed using probes from unique germplasm backgrounds with resistance/susceptibility for traits under study

CPGP – Project Description

Research Areas

• Activation Tagged Mutants: (Carleton University, NSAC, AAFC):

• Use of strong promoter construct and Agrobacterium• Insertion results in activation of genes adjacent to the integrated promoter construct• Overexpression of the gene leads to gain-of-function mutant• Kennebec variety to be used with pSK1074 vector• Generation of 20,000 mutant lines desired• Global resource for potato researchers

Research Areas

• GEELS (UNB):• Small, self-contained project with a direct relationship to potato biotechnology• Intellectual property issues:

• Appropriateness of patents vs Plant Breeders Rights Act • Prevention of biopiracy• Judicial

• Regulatory/enforcement issues:• Enforcement of IP rights

CPGP – Project Description

The CPGP Will Increase World-Wide Potato Resources:

• Enhance EST sequence information• Identify key genes associated with tuber quality and health traits• Generate array and mutant population resources for potato researchers world-wide• Enrich GEELS knowledge relating to unique questions regarding IP and regulatory/enforcement issues

CPGP – Wrap Up