Online Direct Field-to-Researcher Phenomics
At the Forefront of Plant Genomics
October 20121 1
AGENDA
Introduction to Evogene
The CROP system concept
Current status & future directions
Summary
At the Forefront of Plant Genomics
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The Challenge & the Opportunity Modern agriculture The Challenge : Provide More with Less -
Need to double (!) agri output by 2050
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Yield needs to grow faster to close gap
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ONLY 10% of world land is arable
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Climate change & deforestation amount of arable land being reduced every year
The Solution: Improved Plants
Yield & Abiotic
Biotic & Other
Increase yield
Resistance to insects
Secure yield stability
Disease control
Improve drought tolerance
Herbicide tolerance
Enhance fertilizer utilization
Enhance quality characteristics
The Opportunity: Utilize Plant Genomics to Improve Plants At the Forefront of Plant Genomics
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Evogene’s Mission
To be the world leader in applying Plant Genomics for improving plant performance to address the global demand for food, feed, fiber & fuel
At the Forefront of Plant Genomics
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Evogene’s Role in Plant Improvement Application Pathways
Improved Plants
Biotechnology
Plant Genomics
Advanced Breeding
Ag-Chemicals
Unique Science & Technology aaaaaaaa
Major Ag-Companies
Partnerships for Products Development
At the Forefront of Plant Genomics
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Overview Trait Discovery Process
Science Plant expertise & know-how Product Definition
Product Understanding
Multi-Year Work Plan
On-going programs: Discovery rounds
Data Public & proprietary Infrastructure Development Computational Technology
Validation Technology Plant POC
At the Forefront of Plant Genomics
Product Development
Product Definition
Experimental Genomics
At the Forefront of Plant Genomics
Multi-Year Work Plan
On-going programs: Discovery rounds
Product Development
Infrastructur e Developmen t
Process
Experiment design
Product Understanding
Growth
Data production
Phenotypic Data
Expression
Metabolome
Genome
Transcriptome
Gene to gene interactions
GWAS
QTL
Pathways
Data integration
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AGENDA
Introduction to Evogene
The CROP system concept Requirements & objective System overview
Current status & future directions
Summary
At the Forefront of Plant Genomics
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CROPs - Required Features
What are the challenges of the Experimental Genomic process?
Reliability of data Response times Throughput and costs
What is required from a phenotyping system?
Comprehensive Reliable & rapid data transfer Enable data standardization Provide quality control
Cost-effective High capacity
CROPs: Comprehensive Remote Online Phenotyping system
At the Forefront of Plant Genomics
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CROPs - Objective To facilitate generation of comprehensive and reliable data from field trials and enable their rapid transfer for QA and analysis
At the Forefront of Plant Genomics
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AGENDA
Introduction to Evogene
The CROP system concept Requirements & objective System overview
Current status & future directions
Summary
At the Forefront of Plant Genomics
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CROPs - Overview
Station One
Standardized 1. terminology
Phenotypic 4. repository and data analysis platform
At the Forefront of Plant Genomics
Communication 2. channel
data acquisition and 3. QA
1. Book of traits & Trait Ontology Main Application: standardization
At the Forefront of Plant Genomics
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2. Station One Main Application: data acquisition and on line data transfer
Field Office
At the Forefront of Plant Genomics
3. Acquisition & Rapid QA Main Application: data collection & QA
Raw
Processed
Final
1 Technical QA
Data ranges Units Missing values
2
3
Scientific QA
Normalization
Outliers Treatment effects
Station One At the Forefront of Plant Genomics
Spatial effects
4. eTrait Main Application: data QA, storage and analysis
Target To assess, store and analyze phenotypic data in order to gain understanding of traits of interest under various conditions Overview and Key features Trait-centric data repository Integration of data from many fields Methodology of QA and analysis Analysis of measurable phenotypic traits Flexible visual reports
At the Forefront of Plant Genomics
Trait1
Trait2
Trait3
Study1 Per study
Study2 single trait
Per study multi-traits
Study3
Study4
Cross studies single trait
Cross studies multi-traits
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CONFIDENTIAL
AGENDA
Introduction to Evogene
The CROP system concept
Current status & future directions
Summary
At the Forefront of Plant Genomics
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Current Status- Available CROP Features Comprehensive- a variety of phenotypic data sources used. Book-Of-Traits management, Plant Ontology definitions Secure remote communication to Evogene's R&D facilities Built-in data QA mechanisms Metadata recording for every measurement (user, timestamp, station, etc.) Unlimited number of experiments / plots / traits
At the Forefront of Plant Genomics
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Example – Wheat Data generation & transfer by CROPs
Field size: 5.5 ha.
3000 Plots
Phenomics data 32 measured phenotypic parameters per plot More than 1M data points
Other Data types: Genomic Expression Ionome
Reliability and timing: 90% of the Phenomic data stored and assessed within 3 wks after harvest
At the Forefront of Plant Genomics
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Data generated & transferred by CROPS to date Years Data Type
2008
2009
2010
2011
2012
Non-coding RNA Proteomic Ionomic Metabolomics Genomic Transcriptome Expression
Phenomics 1
3
8
10
20
28
17
7
6
4
3
3
‌
Crop / species (example) Total number of trials: over 100 At the Forefront of Plant Genomics
CONFIDENTIAL
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Future Directions - The Phenomics Vision Imaging for structural & physiological parameters
Aerial phenotyping
RGB
Crops
Root phenotyping
Considerations
At the Forefront of Plant Genomics
I.R
Relevance Precision Standardization Throughput Cost
Plant indexes
Hyperspecral
AGENDA
Introduction to Evogene
The CROP system concept
Current status & future directions
Summary
At the Forefront of Plant Genomics
22
Summary
Evogene is a world-leader in trait discovery for improving plant trait performance.
Trait discovery is achieved by combining cross-location, cross-trial comprehensive, accurate OMIC data; Phenomics data is key to the process.
CROPs has been developed for obtaining large amounts of high resolution, accurate, standardized phenomic data from field trials, enabling rapid data transfer and providing quality control.
Forecast: Integration of technologies and processes, focusing on
Increasing capacity and accuracy Reducing costs and time Extending phenotypic characteristics (e.g. additional organs, physiology characteristic, other)
At the Forefront of Plant Genomics
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Development of an Online Direct Field-to-Researcher Phenomics System at Evogene System at At the Forefront of Plant Genomics
October 2012
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