Potato Genomics and Bioinformatics

Virendra C. BhavsarAdvanced 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

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