Potato Genomics and Bioinformatics

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Potato Genomics and Bioinformatics

• Virendra C. Bhavsar
• Advanced Computational Research Laboratory
• Faculty of Computer Science
• University of New Brunswick
• Fredericton, NB, Canada
• bhavsar_at_unb.ca

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Outline

• Introduction
• Potato Research in Atlantic Canada
• Bioinformatics
• Conclusion

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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

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Potato Researchers in Canada
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Superior Industrial Infrastructure

• NB Intl headquarters for the worlds largest
  producer of frozen french fries
• Processing plants in 11 countries
• 5.5 billion in sales, employing 12,000
  world-wide
• NB intl headquarters for variety testing
• Intl conduit for varieties developed here

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Superior Industrial Infrastructure

• Atlantic Region is home to
• several other processors incl. Cavendish,
  Smallfry/ Humpty-Dumpty, CANUSA.
• Canadian arm of the worlds largest seed potato
  company
• Atlantic region (incl. Maine) is 2nd largest
  potato growing region in North America

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

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
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Identifying important genes in Potato
Gene Identification
Gene Expression
Gene Function
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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

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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)

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BioMATS Bioinformatics Models, Algorithms,
Tools and Systems

• Computational Models
• Computational Algorithms
• Tools and Systems, including databases

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Models

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

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Computational Algorithms

• Microarray Analysis
• Multi-dimensional Spatial Data Representation and
  Search
• Structural Pattern Search
• Parallel and Distributed Algorithms

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Microarray Analysis

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

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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

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Databases

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

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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)

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Conclusion

• Potato Genomics Proposal
• BioMATS Proposal
• Potential Collaborations