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Potato Genomics and Bioinformatics

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Title: Potato Genomics and Bioinformatics


1
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

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 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

6
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

7
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
8
  • 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
9
Identifying important genes in Potato
Gene 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,
    181.2 GB Storage
  • Member of C3.ca Association, Inc.
    (http//www.c3.ca)

19
Conclusion
  • Potato Genomics Proposal
  • BioMATS Proposal
  • Potential Collaborations
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