Session 3: Agriculture & Nutrition Title : Doubling Crop Productivity And Ensuring Nutritional Security Dr. K. Harikrishna, Sime Darby

1. The Impact of Genome Technology in
the Oil Palm Industry
A presentation by
Dr. K. Harikrishna
Head of Research, Quantum Leap R&D
Sime Darby R&D Centre
October 6, 2009
for CEO’s Life Sciences Conference
hosted by Malaysian Life Science Capital Fund (MLSCF)
and Malaysia Technology Development Corporation
(MTDC)
1

2. Presentation Flow
Global Challenges: Developing Sustainable Future
Application of biotechnology in the oil palm industry
Productivity improvement in DNA synthesis and sequencing
Oil palm genome assemble statistics
Oil palm traits improvement and value creation potential
Conventional breeding vs. Marker assisted breeding
Breeding technology pipeline
End in mind: Trait stacking for higher productivity
Revolutionizing a bio-based economy
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 2

3. Developing Sustainable Future
Securing role in
agriculture
development
Global Challenges
Ensuring food Environmental
Urbanization
security conservation
Food consumption
Food production
Land and water
Nurturing
communities
Promoting innovation to solve global challenges – opportunities for R&D!
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 3

4. The Application of Biotechnology

5. Industry Goals: 2020
“It is timely for
35 MT FFB / ha Malaysia to make 25% OER
a paradigm shift to
boost oil palm
yields via
biotechnology.”
Datuk Seri Najib Razak
Prime Minister
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 5

6. Productivity Improvement in DNA Synthesis and Sequencing
Significant improvements in key technologies used to study and manipulate biological systems
at the molecular level—tools for sequencing and synthesizing DNA are opening the door to a
new era of genome engineering and design.
1st Generation 2nd Generation 3rd Generation
Sanger-Based Cyclic-Array Method Single Molecule
Sequencing Sequencing Sequencing
Information Capacity
100’s 10,000,000’s 1,000,000,000’s
(reads per experiment)
Scalability of Sample Hundreds at a time
A few at a time
Prep Easily automated
No amplification
Amplification Required True direct DNA
measurement
Analog Analog Digital
Sequencing Accuracy Resolves copied DNA of Averages data from Single DNA molecule
varying lengths amplified DNA copies resolution
USD1,000,000’s USD100,000’s USD10,000’s to
Cost per Human Genome
USD1,000’s
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 6

7. Oil Palm Genome Assembly Statistics
• This is the world’s first project that only used read generated from so called “next generation”
sequencers as the data input for de novo assembly of the oil palm genome
• Sime Darby has sequenced the oil palm genome (30 fold coverage – 60 billion base pairs) – the oil
palm genome is approximately 1.7 billion base pairs in size
• It is the largest genome in world history assembled using 100% latest-generation sequence reads
as data input
Over 60% Repeats
Makes Assembly
Very Challenging
Estimated coverage • 93.8%
Estimated size of genome • 1.7 billion base pairs
Assembled genome size • 1.594 billion base pairs
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 7

8. Largest 454 Genome Sequencing Project in the World
DNA Base Pairs
66,205,000,000
Number of contigs
Reads
238,151,400
Coverage
93.8%
Assembly stage
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 8

9. Other Plant Genome Projects
Genome Size of
Approach Time Taken Assembly
Sequencing Genome Team
Used (months) Coverage %
Project (millions bp)
10 global
Rice 464 Sanger 86 77%
institutions
5 institutes in
Sanger WGS,
Papaya 372 38 China and 101%
Sanger BACs
Hawaii
DOE + 33
Sanger WGS,
Poplar 480 48 other global 98%
Sanger BACs
institutions
454 BACs and
Cucumber 370 NA 2 companies 54%
WGS
Sime Darby’s
454 BACs and Sime Darby
Oil Palm 1700 15 93.8%
WGS and Synamatix
genome
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 9

10. Value Creation Potential
Identification of genetic markers for oil palm traits improvement/control

11. Oil Palm Traits Improvement
High High Iodine Disease Height
Oil yield Long stalk
carotene Value resistance reduction
Screening Oil Palm Populations for Desired traits
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 11

12. End in Mind: Higher Productivity
Stacking exponentially
increases value
Oil yield
Trait retail
Iodine Value value added
per hectare
Height reduction
1
Double Triple
Trait stacking or pyramiding
stack stack
1 = Indexed value of single trait
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 12

13. Conventional Breeding vs. Marker Assisted Breeding
Conventional Breeding Marker Assisted Breeding
Steps Procedures Duration (years)
Duration
Steps Procedures
(years) DxD / TxT&TxP
1 year
fingerprints
DxD / TxT Growing of
trials in the ~10 years Selection of selected dura
5 years
Selection of field dura/tenera & and
dura/tenera pisifera tenera/pisifera
and pisifera
Progeny DxT/P
trials of DxT, ~10 years fingerprints
6-7 years
DxP & field
confirmation
Using results 2 years after Using results
Seed 1
from DxD, completion Seed from DxP
production maximum after
TxT/P trials of trials production confirmation
confirmation
trials
TOTAL ~22 years TOTAL 14 years
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 13

14. Breeding Technology Pipeline
Currently, we are
developing reagents for
breeding and mapping of
SSR’s and SNP’s.
Source: A. R. Fernie and N. Schauer , Metabolomics-assisted breeding: A viable option for crop improvement?
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 14

15. Revolutionizing a Bio-based Economy
Seeds of Wealth Green Fingers Futuristic Diet
• Raw materials • Premium agriculture • Breeding by design
for food, land create novel crops
biofuels and • Raw material produce • Offer balanced
biomaterials will invigorate the nutritional value
• Gate keeper of industry
the economy • Preserving biodiversity
Consumer Plant-made
Connoisseurs Right Chemistry Pharmaceuticals
• Choice of food with • Emergence of green • Tailored oil palm to
good shelf life, chemical, address specific
taste and texture biodegradable needs
• Able to consume biopolymers & • Tackle major
organic, cisgenics biofuels disease today and
or conventional future
palm oil
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 15

16. Re-cap
By 2020, the industry targets to achieve yields of 35 MT FFB/hectare and with 25% OER
Elements of biotechnology are currently used in the oil palm industry such as biogas from
POME, clonal production for elite palms and molecular marker
Significant improvements in tools for sequencing and synthesizing DNA are opening the
door to a new era of genome engineering and design
Sime Darby has sequenced the oil palm genome (30 fold coverage – 60 billion base pairs) –
the oil palm genome is approximately 1.7 billion base pairs in size with over 90% coverage
Identification of genetic markers through genetic marker assisted selection & conventional
crossing and recombinant DNA technology will contribute to oil palm traits improvement
and control
Trait stacking will exponentially increase the retail value added per hectare
We are able to shift towards a green sustainable economy largely based on renewable
resources or known as the “bio-based” economy
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 16

17. For more information on the oil palm genome:-
Dr. K. Harikrishna
Chief Executive Officer
Sime Darby Genomics Sdn. Bhd.
No. 2, Jalan Tandang,
46050 Petaling Jaya, Selangor.
Phone : 03 - 7787 8900
Fax : 03 - 7781 0298
E-mail : collaboration@simedarbygenomics.com
Web : http://plantation.simedarby.com/genomics
The Impact of Genome Technology in the Oil Palm Industry |© 2009 Sime Darby Research Sdn Bhd 17

18. Thank you