Potato Genomics and Bioinformatics
Virendra C. BhavsarAdvanced Computational Research Laboratory
Faculty of Computer Science
University of New Brunswick
Fredericton, NB, Canada
Outline
• Introduction
• Potato Research in Atlantic Canada
• Bioinformatics
• Conclusion
Potato Genomics in Atlantic Canada
• Superlative research infrastructure
• Superior industrial infrastructure
• World-class expertise in potato variety development
• An industry completely connected to global markets
• Canadian repository of potato germ plasm
Potato Researchers in Canada
Superior Industrial Infrastructure
• NB = Int’l headquarters for the world’s largest producer of frozen french fries
• Processing plants in 11 countries
• $5.5 billion in sales, employing 12,000 world-wide
• NB = int’l headquarters for variety testing
• Int’l conduit for varieties developed here
Superior Industrial Infrastructure
• Atlantic Region is home to :– several other processors: incl. Cavendish,
Smallfry/ Humpty-Dumpty, CANUSA.– Canadian arm of the world’s largest seed potato
company
• Atlantic region (incl. Maine) is 2nd largest potato growing region in North America
BioAtlantech
Genomics companies
Potato growers& processors
International Potato Centers
Atlantic Provincial Governments
Seed companies
Agriculture &Agri-food Canada - Fredericton, Charlottetown,Lethbridge
UNB, NSAC,Carleton, Laval, Mtl., Moncton
Embryogenesis• seeds vs. tubers:• 2 tons of tubers versus 100 g seed
Tuber quality traits:• sugar content• dry matter content• after-cooking darkening• sprouting/dormancy• etc. Resistance to :
• Late blight• scab• viruses• CPB• etc. Molecular farming:
• plants as bio-factories for• structural polymers• pharmaceuticals; vaccines• etc.
Potato GenomeDatabase
Nutrient uptake efficiency and stressresistance
Identifying important genes in Potato
Gene Identification
Gene Expression
GeneFunction
Bioinformatics
• Coordinated by Dr. Virendra Bhavsar, UNB
• Potato Genome Database
• Identify better ways to organize and mine genomic data
• Improve existing bioinformatic tools to meet the needs of potato researchers
Bioinformatics Group
• Eric Aubanel• Virendra Bhavsar• David Bremner• Weichang Du• Patricia Evans• Ali Ghorbani
• Lev Goldfarb• Claudia Iturriaga• Steve Marsh (NRC)• Bradford Nickerson• Rachael Ritchie (RPC)• Todd Wareham
(MUN)
BioMATS: Bioinformatics: Models, Algorithms, Tools and
Systems
• Computational Models
• Computational Algorithms
• Tools and Systems, including databases
Models
• Statistical Models
• Artificial Neural Networks (ANNs)
• Evolving Transformation Systems
• Evolutionary Computing
• Prototeins - Models of Protein Folding
• Database Models
Computational Algorithms
• Microarray Analysis
• Multi-dimensional Spatial Data Representation and Search
• Structural Pattern Search
• Parallel and Distributed Algorithms
Microarray Analysis
• Structure Analysis
• Expression Analysis, including clustering
• Integration of Structure and Expression
• Interaction of Gene Products (e.g. DNA, proteins, and RNA)
Tools• Gene Expression Analysis Tool
• Multi-Agent System for Automatic Annotation based on ACORN
• Data Mining Tools (e.g. IBM Intelligent Data Miner)
• Homology Modeling Tools
• Interactive Visualization Tools
• Web-based Data Access and Mgmt. Tools
Databases
• Potato Genome Database
• Annotation of Databases
• Interrelating Information from Databases
• Scalable Databases and Servers
Advanced Computational Research Laboratory
• High Performance Computational Problem-Solving and Visualization Environment
• Computational Experiments in multiple disciplines: CS, Science and Eng.
• 16-Processor IBM SP with 24 GFLOPS performance, 181.2 GB Storage
• Member of C3.ca Association, Inc. (http://www.c3.ca)
Conclusion
• Potato Genomics Proposal
• BioMATS Proposal
• Potential Collaborations