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A BASF Plant Science Company
The Challenges of [high-throughput] Phenotyping
Mount Hood - sept 2008 Topics
° Introducing BASF Plant Science
° Phenotyping, for what purposes?
° What are the challenges?
° High-throughput phenotyping Ù The TraitMill example
° What is the output? Ù Some lead examples
° Future developments BASF Plant Science BASF Plant Science: a Global Technology Platform
BASF Plant Science North Carolina
BASF Plant Science BASF Plant Science BASF Plant Science Ames Iowa Ludwigshafen BASF Plant Science Global R&D Platform
Plant Science Sweden CropDesign DNA LandMarks Metanomics SunGene ExSeed Genetics Limburgerhof
North Carolina
¢ Founded in 1998 ¢ 700 employees in R&D ¢ Coops with universities, biotech start-ups and major AgBio players BASF Plant Science Units ¢ Partnerships with seed External Cooperations companies CropDesign at a Glance
° Headquartered in Gent, Belgium; 90 employees
° Founded in 1998 as a spin-off from VIB, acquired in June 2006 by BASF Plant Science
° Focus on the development of high productivity traits by operating a unique rice-based trait discovery platform
° Focus on rice as a commercial crop opportunity and as a model for corn BASF Plant Science The BASF approach to gene discovery: unique technology platform
Crop yield improvement
Look Look
at plant inside 0 6.008.0010.0102.0104.0106.0108.0200.0202.0204.00
BASF Plant Science
CropDesign metanomics
Unique and synergistic platform for gene function discovery Combines visual plant screening & metabolic profiling for gene function analysis High throughput at 5,000 to 10,000 genes tested per year ° Introducing BASF Plant Science
° Phenotyping, for what purposes?
° What are the challenges?
° High-throughput phenotyping The TraitMill example
° What is the output? Some lead examples
° Future developments BASF Plant Science Trends driving demand for agricultural products
Food & Feed ¢ UN estimate* on word population: 9.2 billion people for 2050 ¢ Rising social standards drive global demand for more processed foodM (AmReKaEtT cPoOnTsEuNmTIApLtion in Asia)
Biofuels** ¢ Worldwide: Programs to support bio-fuel projects ¢ EU biofuel target: 10% of total transportation fuel by 2020: ‰ 55% of total agricultural land needed to reach the target (in canola)
u To meet the demand we have to double productivity within the next 20 years
*Published in May 2007 by the UN; ** EU-Directive, March 2007 BASF Plant Science Our Projects
Crops
wheat rice corn soybean canola Traits Novel Agronomic Enhanced feed Specialty food Industrial specialty traits traits traits traits
- Yield - NutriDense - PUFAs - Modified starch - Stress tolerance - Phytate reduction - Increased Oil - Fungal resistance - Amino acid - Biofuels enhancement Basic Technologies Enabling Genomics Bioinformatics ° Introducing BASF Plant Science
° Phenotyping, for what purposes?
° What are the challenges?
° High-throughput phenotyping The TraitMill example
° What is the output? Some lead examples
° Future developments What are the challenges?
° High Throughput ‹ Efficient logistics ° Low costs ‹ Automation
° Early discovery ‹ Model plants ‹ Screening strategy ° Predictability ‹ Traits
° Organize the data flow ‹ LIMS ‹ Productivity tools Key traits
Established field crop markets Rice Bioenergy crops (corn, soybean,...) (sugarcane, switchgrass,..)
• Seed yield • Seed yield • Leafy biomass • Seed number • Seed number • Plant height • Grain filling rate • Grain filling rate • Development rate • 1000 seed weight • 1000 seed weight • Oil content • Harvest index • Harvest index • Rooty biomass • Heading time • Heading time • Root thickness • Development rate • Development rate • Root shoot ratio • Root biomass • Root biomass • Root shoot ratio • Root shoot ratio ° Introducing BASF Plant Science
° Phenotyping, for what purposes?
° What are the challenges?
° High-throughput phenotyping: Ù The TraitMill example ° What is the output? Some lead examples
° Future developments TraitMillTM : Trait Development for Different High-Value Opportunities
Productivity traits for Rice with Productivity established field improved yield traits for crops bioenergy crops
Annual Product leads throughput
Patent filing >60 validated leads
Data mgt & analysis 10s of terrabytes
Plant phenotyping 140,000 plants Molecular analysis 300,000 PCRs
Plant transformation >75,000 transformants
Vector construction 1300 constructs Gene selection 2,000 genes Genes The TraitMill pipeline
VECTOR PLANT MOLECULAR PLANT SEED LEAD CONSTRUCTION TRANSFORMATION ANALYSIS EVALUATION EVALUATION IDENTIFICATION
LIMS and DATA MANAGEMENT PLANNING FACILITIES
Myriam Van Quickenborne_June 13th 2007 HTP plant evaluation Evaluation set up
T0 generation
T1 generation
Evaluation
Statistical data analysis Green biomass Green biomass
Leaf area Early vigour Max leaf area After drought Height Maximum Gravity centre Green biomass
Leaf area Early vigour Max leaf area After drought Height Maximum Gravity centre
Greenness index Before flowering After drought Green biomass
Leaf area Early vigour Max leaf area After drought Height Maximum Gravity centre
Greenness index Before flowering After drought
Days to flowering Root biomass Root biomass Root biomass
Ù Area
Ù Length Ù Thickness Ù Branching
ÙShoot/Root Yield components
Number of panicles Yield components
Number of panicles
Total number of seeds Flowers per panicle
Number of filled seeds Fertility (—fill rate“)
TKW
Total seed yield Harvest index Yield components
Number of panicles
Total number of seeds Flowers per panicle
Number of filled seeds Fertility (—fill rate“)
TKW
Total seed yield Harvest index
Seed dimensions Width Length Area Materials tracking
LIMS Dbase over 50 manyears of development Screening strategies
Optimal regime Salt stress regime
Drought stress regime Nitrogen limitation regime
Dro- ught ° Introducing BASF Plant Science
° Phenotyping, for what purposes?
° What are the challenges?
° High-throughput phenotyping The TraitMill example
° What is the output? Ù Some lead examples ° Future developments Gene selection targets different yield components
Biomass components Plant height Root Biomass Green biomass
Development Number of panicles time 50 Time to Flower 100 150
Flowers per panicle Yield Total weight seeds Filling rate Yield components 1000 kernel weight A “Phenotype tool kit”
J L J L + biomass - biomass L J + flowers - flowers + seeds - seeds
J L J L L L
J L J + biomass + flowering + panicles - biomass + seeds - flowers - seeds L J L A “Phenotype tool kit”
+ flowers L + seed size + seeds - panicles = yield J J K J
J + fertility + biomass + yield + seed size J + yield J J J Family stories..
NAC genes Yield stability..
Lead “C” Normal
Drought Salt Low N And in the field..
Wild type -/- +/+
+ 15 % yield
LeaCdD E“ D”
+ 26 % yield increase Null line Event 4 Field Validated Leads
°°BByy eenndd ooff 22000066,, 5566 LLeeaaddss tteesstteedd inin aatt leleaasstt 11 ffieieldld ttrriaiall °°FFieieldld ccoonnffirirmmaattioionn rraattee cclolossee ttoo 5500 %%
25 Lead confirmed in field: 25 positive phenotype observed in TraitMillTM 20 23 confirmed in 2 field trials Lead not confirmed in 15 field: positive phenotype observed in TraitMillTM not 10 confirmed in 2 field trials Pending: 8 1 field trial result or 5 conflicting results after 2 trials 0 Confirmed Not Pending Confirmed ° Introducing BASF Plant Science
° Phenotyping, for what purposes?
° What are the challenges?
° High-throughput phenotyping The TraitMill example
° What is the output? Some lead examples
° Future developments BASF Plant Science Integration of Phenotyping & Metabolic Profiling Create Unique Opportunities
Analyze phenotype Metabolic profiling
¢ Identify important pathways + ¢ Characterize mode of action
+ ¢ Rational identification of new lead genes based on pathway knowledge
¢ Increased efficiency & efficacy of gene Determine yield Expression profile discovery BASF Plant Science R&D Commercialization Collaboration with Monsanto
¢ Trait: High yield and abiotic stress tolerance
ò Independent gene discovery programs
ò Joint research pipeline
ò Commercialization through Monsanto
¢ Crops: corn, soybean, cotton, canola
¢ Revenue sharing: 60/40 (Mon/BASF)
¢ Additional coop: Soybean cyst nematode BASF Plant Science Monsanto Collaboration From Discovery through Commercialization
Focus: Structure:
¢ Establishment of licensed brands a joint technology & Monsanto commercialization discovery regional brands collaboration program BASF ¢ Combination of discovery mational brands BASF and Monsanto program expertise ¢ R&D-pipeline for yield and stress DDiissccoovveerryy DDeevveellooppmmeenntt CCoommmmeerrcciiaalliizzaattiioonn ¢ ¢ ¢ tolerance traits Maintenance Funding at 50-50 Emerging products of independent cost sharing distributed by ¢ Corn, soybean, discovery programs ¢Potential Monsanto across in each company overall budget its three existing canola, cotton ¢Nomination of 1.2 billion/ commercial channels of projects $1.5 billion ¢Value sharing at for development through all phases 60% for Monsanto to jointly of development and 40% for BASF managed board Conclusions
TraitMill: result of continuous ° Example of cost-effective, highly improvements automated platform for screening yield- enhancement genes
° Large effects (>20%) on yield
° Different yield components: opportunities for trait stacking
° In some cases, increased yield stability 2000 2002 2008 ° Phenotypes in the greenhouse confirm Know-How & Expertise under field conditions
° Transferability of transgenic traits to other crops is ongoing