The Innovators
The Innovators: August 27, Seattle
Intelli-GEN-Design: Fruit of the Future
Amit Dhingra, Ph.D. Assistant Professor of Horticultural Genomics and Biotechnology College of Agricultural, Human, and Natural Resource Sciences
No GMOs
No Transgenics
Genetically Modified Organism No Frankenfoods
No Nien αριθ 不 Non
Intelli-GEN-Design: Fruit of the Future Human genome and beyond
Apple genome sequencing
How does it impact us?
Inside a Living Cell Life alphabet 4 letters A, T, G, C
English alphabet 26 letters
Structure Static
Function Dynamic
Function Dynamic
Cost: ~ $3 billion Time: 13 years
http://www.life.uiuc.edu/ib/494/images/genome.jpg www.sciencemag.org
Impact of the Human Genome Sequence Genome-wide scan uncovers two genes involved in osteoporosis risk Richards JB et al. Lancet 2008:1505-12.
New Clues to type 2 diabetes. Six new genes discovered that play a role in development of type 2 diabetes Zeggini E et al. Nature Genetics 2008:
Identification of the key genetic mutations involved in up to 50 types of cancer International Cancer Genome Consortium 2008
Identification of genes for several important diseases
Cost: ~ $3 billion Time: 13 years Do we have the time and the money?
Innovation in Technology
Technological Advancement
Technological Advancement in Sequencing
10,000 base pairs per day
1 million base pairs per day
100 - 500 million base pairs per day
2007 One Human Genome $1million J. D. Watson Co-discoverer of DNA structure
Apple Genome Project at WSU
General Facts Golden Delicious Apple Innovative Approach – Genetically simpler double haploid apple Downstream assembly expected to be simpler
Diploid vs. Double Haploid Apple Chromosome pair in a diploid cell
1
2
1 2 Genes on the chromosomes are different at the sequence level
Genome assembly becomes extremely difficult
Method being used by our collaborators in Italy
Diploid vs. Double Haploid Apple Chromosome pair in a double haploid cell
1
1
1 1 Genes on the chromosomes are same at the sequence level
Extremely amenable to genome assembly
WSU apple genome project
Apple Genome Project at WSU
Funding from Washington Tree Fruit Research Commission, April 2008
Collaboration with Roger Bumgarner at UW and seed funding from WSU-ARC, January 2008
Funding from USDA – NRI, August 2008
Need to cover this distance ~ 20 times – 15,000 miles Covered only 1500 so far Ananth Kalyanaraman
Roger Bumgarner
Assembly and annotation ongoing
Each machine run covers 100 to 500 miles – 100 to 500 million base pairs 750-mile highway – 750 million base pairs
Apple Genome
Ways to go…
Ananth Kalyanaraman
Assembly and annotation ongoing Roger Bumgarner
1.6 billion base pairs generated
Apple Genome
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
The Hub for Rosaceae Genomics
The Global Consortium for Rosaceae Genomics INRA Group, France
Riccardo Velasco, Italy
Jasper Reese, South Africa HortResearch, New Zealand
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
The Pixie Grape Vine to Wine in 4 months Vineyard Grapes – 3-4 years Pixie flowers in 4 months 4 crops in a year
Genomics, Genetics, and Breeding at WSU Producers
Kate Evans Apple breeding program Matthew Whiting Stone fruit physiologist Consumers Cameron Peace Molecular geneticist
Processors
Nnadozie Oraguzie Sweet cherry breeding program Markus Keller Grape physiologist Packers Dorrie Main Bioinformatics
Amit Dhingra Genomics and biotechnology Retailers
Shippers
From cell to consumer
How does it impact us?
Why Sequence the Apple Genome? Producer
Environment Labor Technology
Fresh Market
Shelf life Quality Consumer
Processing
Nutritional value Shelf life Flavor/characteristics Value-added traits
Desirable Trait Wish-list Targeted Nutrition
Anti-cholesterol
Mechanical Harvesting
Mechanical harvester for cherries at WSU Photo courtesy: Dr. Matthew Whiting
Anti-cancer
Sustainable
Flavor / longer shelf life
Organic Production Phase out pesticides and herbicides
How?
Generate new varieties that are resistant to pests and pathogens via breeding and mutation or sports
Natural Mutations
(sports)
Crop Varieties Generated through Induced Mutations
Untapped area for fruits
Honey Crisp Apple Journey of an apple •Crosses made in 1960s •Selected in 1974 •Released in 1991 •Most prized commercial variety – Now
Computing Challenges An opportunity for innovation
T T T
T T T
T
T T T
TT T T
T T
T
High-compute power computers
T
T
T
T
T
New algorithms
Mountain of sequence data
This is just the start…
Educational Challenges •Train next generation
of teachers and students
•Started the process
with Partners in Science Murdock Grant
•Much needs to be done
Personalized Medicine
Genotype
Genotype
The right apple a day keeps the doctor away.
Funding
This image cannot currently be displayed.
Acknowledgements Undergraduate Students Danielle Druffel - CE Dustin DeMars – ME Christina Duncan – CE Farooq – EE Jake Able - Physics Mahlet - Neuroscience Kathie Nicholson – V&E Tyler Armour – V&E Shane Moore – V&E Dane Scarimbolo – V&E Salma Tariq - Microbiology Maureen McFerson – Food Sci Fantahun Tedla - Microbiology Justine Poff - Hort Christine Tong - Microbiology High School Tina DaVault - Teacher Paige Druffel Harshini Jayaram Hannah Old
Graduate Students Scott Schaeffer Tyson Koepke Derick Jiwan Lisa Taylor Vandhana Krishnan Andy Wu Ananth Kalyanaraman, Computer Scientist WSU Roger Bumgarner, Professor of Microbiology UW Trevor King Jessica Vick
Roche/454
Kathy Bantle Angie Lackey Jamie Jett Tim Harkins
The best way to predict the future is to invent it. Alan Kay Discoverer of object-oriented programming and windowing graphical user interface.
Questions?
Coming Up The Innovators lecture series Fall 2008
The Innovators: October 9, Seattle
Strategies for Tomorrow: Re-engineering for a Sustainable Built Environment
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
The Innovators: November 13, Seattle
Biofuels: Natural Solutions to the Energy Crisis
Norman G. Lewis, Ph.D. Regents Professor, Molecular Plant Sciences Director, Institute of Biological Chemistry College of Agricultural, Human, and Natural Resource Sciences
The Innovators: December 4, Seattle
Saving Lives Worldwide: The Animal-Human Health Connection 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
For more information: www.theinnovators.wsu.edu Toll free 877-978-3868
Intelli-GEN-Design: Fruit of the Future
Amit Dhingra, Ph.D. Assistant Professor of Horticultural Genomics and Biotechnology College of Agricultural, Human, and Natural Resource Sciences
No GMOs
No Transgenics
Genetically Modified Organism No Frankenfoods
No Nien αριθ 不 Non
Intelli-GEN-Design: Fruit of the Future Human genome and beyond
Apple genome sequencing
How does it impact us?
Inside a Living Cell Life alphabet 4 letters A, T, G, C
English alphabet 26 letters
Structure Static
Function Dynamic
Function Dynamic
Cost: ~ $3 billion Time: 13 years
http://www.life.uiuc.edu/ib/494/images/genome.jpg www.sciencemag.org
Impact of the Human Genome Sequence Genome-wide scan uncovers two genes involved in osteoporosis risk Richards JB et al. Lancet 2008:1505-12.
New Clues to type 2 diabetes. Six new genes discovered that play a role in development of type 2 diabetes Zeggini E et al. Nature Genetics 2008:
Identification of the key genetic mutations involved in up to 50 types of cancer International Cancer Genome Consortium 2008
Identification of genes for several important diseases
Cost: ~ $3 billion Time: 13 years Do we have the time and the money?
Innovation in Technology
Technological Advancement
Technological Advancement in Sequencing
10,000 base pairs per day
1 million base pairs per day
100 - 500 million base pairs per day
2007 One Human Genome $1million J. D. Watson Co-discoverer of DNA structure
Apple Genome Project at WSU
General Facts Golden Delicious Apple Innovative Approach – Genetically simpler double haploid apple Downstream assembly expected to be simpler
Diploid vs. Double Haploid Apple Chromosome pair in a diploid cell
1
2
1 2 Genes on the chromosomes are different at the sequence level
Genome assembly becomes extremely difficult
Method being used by our collaborators in Italy
Diploid vs. Double Haploid Apple Chromosome pair in a double haploid cell
1
1
1 1 Genes on the chromosomes are same at the sequence level
Extremely amenable to genome assembly
WSU apple genome project
Apple Genome Project at WSU
Funding from Washington Tree Fruit Research Commission, April 2008
Collaboration with Roger Bumgarner at UW and seed funding from WSU-ARC, January 2008
Funding from USDA – NRI, August 2008
Need to cover this distance ~ 20 times – 15,000 miles Covered only 1500 so far Ananth Kalyanaraman
Roger Bumgarner
Assembly and annotation ongoing
Each machine run covers 100 to 500 miles – 100 to 500 million base pairs 750-mile highway – 750 million base pairs
Apple Genome
Ways to go…
Ananth Kalyanaraman
Assembly and annotation ongoing Roger Bumgarner
1.6 billion base pairs generated
Apple Genome
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
The Hub for Rosaceae Genomics
The Global Consortium for Rosaceae Genomics INRA Group, France
Riccardo Velasco, Italy
Jasper Reese, South Africa HortResearch, New Zealand
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
The Pixie Grape Vine to Wine in 4 months Vineyard Grapes – 3-4 years Pixie flowers in 4 months 4 crops in a year
Genomics, Genetics, and Breeding at WSU Producers
Kate Evans Apple breeding program Matthew Whiting Stone fruit physiologist Consumers Cameron Peace Molecular geneticist
Processors
Nnadozie Oraguzie Sweet cherry breeding program Markus Keller Grape physiologist Packers Dorrie Main Bioinformatics
Amit Dhingra Genomics and biotechnology Retailers
Shippers
From cell to consumer
How does it impact us?
Why Sequence the Apple Genome? Producer
Environment Labor Technology
Fresh Market
Shelf life Quality Consumer
Processing
Nutritional value Shelf life Flavor/characteristics Value-added traits
Desirable Trait Wish-list Targeted Nutrition
Anti-cholesterol
Mechanical Harvesting
Mechanical harvester for cherries at WSU Photo courtesy: Dr. Matthew Whiting
Anti-cancer
Sustainable
Flavor / longer shelf life
Organic Production Phase out pesticides and herbicides
How?
Generate new varieties that are resistant to pests and pathogens via breeding and mutation or sports
Natural Mutations
(sports)
Crop Varieties Generated through Induced Mutations
Untapped area for fruits
Honey Crisp Apple Journey of an apple •Crosses made in 1960s •Selected in 1974 •Released in 1991 •Most prized commercial variety – Now
Computing Challenges An opportunity for innovation
T T T
T T T
T
T T T
TT T T
T T
T
High-compute power computers
T
T
T
T
T
New algorithms
Mountain of sequence data
This is just the start…
Educational Challenges •Train next generation
of teachers and students
•Started the process
with Partners in Science Murdock Grant
•Much needs to be done
Personalized Medicine
Genotype
Genotype
The right apple a day keeps the doctor away.
Funding
This image cannot currently be displayed.
Acknowledgements Undergraduate Students Danielle Druffel - CE Dustin DeMars – ME Christina Duncan – CE Farooq – EE Jake Able - Physics Mahlet - Neuroscience Kathie Nicholson – V&E Tyler Armour – V&E Shane Moore – V&E Dane Scarimbolo – V&E Salma Tariq - Microbiology Maureen McFerson – Food Sci Fantahun Tedla - Microbiology Justine Poff - Hort Christine Tong - Microbiology High School Tina DaVault - Teacher Paige Druffel Harshini Jayaram Hannah Old
Graduate Students Scott Schaeffer Tyson Koepke Derick Jiwan Lisa Taylor Vandhana Krishnan Andy Wu Ananth Kalyanaraman, Computer Scientist WSU Roger Bumgarner, Professor of Microbiology UW Trevor King Jessica Vick
Roche/454
Kathy Bantle Angie Lackey Jamie Jett Tim Harkins
The best way to predict the future is to invent it. Alan Kay Discoverer of object-oriented programming and windowing graphical user interface.
Questions?
Coming Up The Innovators lecture series Fall 2008
The Innovators: October 9, Seattle
Strategies for Tomorrow: Re-engineering for a Sustainable Built Environment
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
The Innovators: November 13, Seattle
Biofuels: Natural Solutions to the Energy Crisis
Norman G. Lewis, Ph.D. Regents Professor, Molecular Plant Sciences Director, Institute of Biological Chemistry College of Agricultural, Human, and Natural Resource Sciences
The Innovators: December 4, Seattle
Saving Lives Worldwide: The Animal-Human Health Connection 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
For more information: www.theinnovators.wsu.edu Toll free 877-978-3868
