Barry Flinn SGII/BioAtlantech (Fredericton)

Canadian Potato Genome Project (CPGP)(Molecular Determination of Tuber Health and Quality in the Potato) Co-Lead PI’s: Barry Flinn SGII/BioAtlantech (Fredericton) Sharon Regan Carleton University (Ottawa)

CPGP - Rationale Importance Of The Potato • Fourth most important crop worldwide • 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 • 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 ATLANTIC CANADA • 46% of national • potato production • $1 Billion/year • Home of McCain • Foods Ltd. • $5.5 billion/year • Potato Research • Center of AAFC • Solanum Genomics • International Inc.

CPGP - Rationale Potato Expertise in Atlantic Canada • 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

S R ANDLBRLF02345HTF.01 ANDLBRLF01256HTF.01 • Further elaboration of expression patterns, followed by • testing of gene constructs in plants ANDLBRLF02041HTF.01 CPGP - Rationale • Solanum Genomics International: • Expression profiling via microarray to identify genes • associated with enhanced field resistance

CPGP - Rationale World-Wide Solanaceae genomics TIGR & NSF ~60,000 potato ESTs SCRI & SGII ~10,000 potato ESTs TIGR & NSF ~120,000 tomato 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 – Project Description Increasing The Genetic Resources Of The Potato • 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

CPGP – Project Description 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 – Wrap Up 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

Barry Flinn SGII/BioAtlantech (Fredericton)