Transcript No Slide Title - University of New Brunswick

Canadian Potato Genome Project
(CPGP)
(Molecular Determination of Tuber Health and Quality in the Potato)
Co-Lead PI’s:
Barry Flinn
Sharon Regan
SGII/BioAtlantech
(Fredericton)
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
CPGP - Rationale
Potato Expertise in Atlantic Canada
• 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
CPGP - Rationale
• Solanum Genomics International:
• Expression profiling via microarray to identify genes
associated with enhanced field resistance
S
R
ANDLBRLF02345HTF.01
ANDLBRLF01256HTF.01
ANDLBRLF02041HTF.01
• Further elaboration of expression patterns, followed by
testing of gene constructs in plants
CPGP - Rationale
World-Wide
Solanaceae genomics
TIGR & NSF
SCRI & SGII
~60,000 potato ESTs ~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