Potato Genomics and Bioinformatics Virendra C. Bhavsar Advanced Computational Research Laboratory Faculty of Computer Science University of New Brunswick Fredericton, NB, Canada bhavsar@unb.ca

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 UNB, NSAC, Carleton, Laval, Mtl., Moncton Atlantic Provincial Governments International Potato Centers Potato growers & processors Agriculture & Agri-food Canada - Fredericton, Charlottetown, Lethbridge Genomics companies Seed companies

Embryogenesis Potato Genome Database 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. Potato Genome Database Resistance to : Late blight scab viruses CPB etc. Molecular farming: plants as bio-factories for structural polymers pharmaceuticals; vaccines etc. Nutrient uptake efficiency and stress resistance

Identifying important genes in Potato Identification Gene Expression Gene Function

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