IntelliGENDesign: Fruit of the Future

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Intelli-GEN-Design Fruit of the Future
The Innovators August 27, Seattle

• Amit Dhingra, Ph.D.
• Assistant Professor of Horticultural Genomics
  and Biotechnology
• College of Agricultural, Human, and Natural
  Resource Sciences

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No GMOs
No Transgenics
No Nien a??? ? Non
No Frankenfoods
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Intelli-GEN-Design Fruit of the Future
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Inside a Living Cell
Structure Static
Function Dynamic
Function Dynamic
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Cost 3 billion Time 13 years
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Impact of the Human Genome Sequence
Personalized Medicine
New Cures
Identification of genes for several important
diseases
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Cost 3 billion Time 13 years
Innovation in Technology
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Technological Advancement
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Technological Advancement in Sequencing
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2007 One Human Genome 1million
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Apple Genome Project at WSU
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General Facts
Golden Delicious Apple
Innovative Approach Genetically simpler double
haploid apple
Downstream assembly expected to be simpler
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Diploid vs. Double Haploid Apple
Chromosome pair in a diploid cell
Genome assembly becomes extremely difficult
Method being used by our collaborators in Italy
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Diploid vs. Double Haploid Apple
Chromosome pair in a double haploid cell
Extremely amenableto genome assembly
WSU apple genome project
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Apple Genome Project at WSU
Funding from USDA NRI, August 2008
Funding from Washington Tree Fruit Research
Commission, April 2008
Collaboration with Roger Bumgarner at UW and seed
funding from WSU-ARC, January 2008
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Need to cover this distance 20 times 15,000
miles Covered only 1500 so far
Each machine run covers 100 to 500 miles 100 to
500 million base pairs
750-mile highway 750 million base pairs
Apple Genome
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Ways to go
1.6 billion base pairs generated
Apple Genome
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Novel Genomic Data Fueling Innovation
Challenge De novo assembly of a large, complex
plant genome
No dearth of determination, ideas, and effort
Need big computers with high compute power
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The Hubfor Rosaceae Genomics
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The Global Consortiumfor Rosaceae Genomics
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The Consortium
14 X coverage of Golden Delicious
Solexa Sequencing of DH Material
Discussions ongoing Full length cDNAs? Funding?
DH Material and Genotyping
4X Shotgun sequencing Assembly and annotation
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The Pixie GrapeVine to Wine in 4 months
Vineyard Grapes 3-4 years
Pixie flowers in 4 months
4 crops in a year
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Genomics, Genetics, and Breeding at WSU
Amit Dhingra Genomics and biotechnology
From cell to consumer
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How does it impact us?
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Why Sequence the Apple Genome?
Environment Labor Technology
Producer
Shelf life Quality Consumer
Consumer
Fresh Market
Processing
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Desirable Trait Wish-list
Targeted Nutrition
Anti-cholesterol
Anti-cancer
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Organic Production
Phase out pesticides and herbicides How?
Generate new varieties that are resistant to
pests and pathogensvia breeding and mutation or
sports
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Natural Mutations (sports)
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Crop Varieties Generatedthrough Induced Mutations
Untapped area for fruits
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Honey Crisp Apple
Journey of an apple

• Crosses made in 1960s
• Selected in 1974
• Released in 1991
• Most prized commercial variety Now

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Computing Challenges
An opportunity for innovation
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Educational Challenges

• Train next generationof teachers and students
• Started the processwith Partners in Science
  Murdock Grant
• Much needs to be done

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Personalized Medicine
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The right apple a day keeps the doctor away.
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Funding
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Acknowledgements
Undergraduate Students Danielle Druffel -
CE Dustin DeMars ME Christina Duncan
CE Farooq EE Jake Able - Physics Mahlet -
Neuroscience Kathie Nicholson VE Tyler Armour
VE Shane Moore VE Dane Scarimbolo
VE Salma Tariq - Microbiology Maureen McFerson
Food Sci Fantahun Tedla - Microbiology Justine
Poff - Hort Christine Tong - Microbiology
Graduate Students Scott Schaeffer Tyson
Koepke Derick Jiwan Lisa Taylor Vandhana
Krishnan Andy Wu
Roche/454 Kathy Bantle Angie Lackey Jamie
Jett Tim Harkins
Ananth Kalyanaraman,Computer Scientist WSU
Roger Bumgarner,Professor of Microbiology UWTrev
or King Jessica Vick
High School Tina DaVault - Teacher Paige
Druffel Harshini Jayaram Hannah Old
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The best way to predict the future is to invent
it.
Alan Kay Discoverer of object-oriented
programming and windowing graphical user
interface.
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Questions?

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• Coming Up
• The Innovators lecture series
• Fall 2008

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Strategies for Tomorrow Re-engineering for
a Sustainable Built Environment
The Innovators October 9, Seattle

• Michael Wolcott, Ph.D.
• Director, Institute for Sustainable Design
• Louisiana-Pacific Distinguished Professor of
  Wood Materials and Engineering
• Civil and Environmental Engineering
• College of Engineering and Architecture

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Biofuels Natural Solutions to the Energy Crisis
The Innovators November 13, Seattle

• Norman G. Lewis, Ph.D.
• Regents Professor, Molecular Plant Sciences
• Director, Institute of Biological Chemistry
• College of Agricultural, Human, and Natural
  Resource Sciences

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Saving Lives Worldwide The Animal-Human Health
Connection
The Innovators December 4, Seattle

• Wendy C. Brown, M.P.H., Ph.D.
• Professor of Immunology
• Department of Veterinary Microbiology and
  Pathology
• School for Global Animal Health
• College of Veterinary Medicine

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• For more information
• www.theinnovators.wsu.edu
• Toll free 877-978-3868

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