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

2. Outline Introduction Potato Research in Atlantic Canada Bioinformatics
Conclusion

3. 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

4. Potato Researchers in Canada

5. 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

6. 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

7. 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

8. 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

9. Identifying important genes in Potato
Identification
Gene
Expression
Gene
Function

10. 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

11. 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)

12. BioMATS: Bioinformatics: Models, Algorithms, Tools and Systems
Computational Models
Computational Algorithms
Tools and Systems, including databases

13. Models Statistical Models Artificial Neural Networks (ANNs)
Evolving Transformation Systems
Evolutionary Computing
Prototeins - Models of Protein Folding
Database Models

14. Computational Algorithms
Microarray Analysis
Multi-dimensional Spatial Data Representation and Search
Structural Pattern Search
Parallel and Distributed Algorithms

15. Microarray Analysis Structure Analysis
Expression Analysis, including clustering
Integration of Structure and Expression
Interaction of Gene Products (e.g. DNA, proteins, and RNA)

16. 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

17. Databases Potato Genome Database Annotation of Databases
Interrelating Information from Databases
Scalable Databases and Servers

18. 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, GB Storage
Member of C3.ca Association, Inc. (

19. Conclusion Potato Genomics Proposal BioMATS Proposal
Potential Collaborations