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Transcript of Michael Csukai
BioDundee
Sustainably growing more with less: fungal control solutions and technology gaps
Classification: PUBLIC
2
Issues!Gaps!
Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
3
Increasing demand for food
● World population growth- 7.0 billion today- 9.3 billion by 2050
• Large error bars!
● Increasing wealth driving increased demand for animal products- Significant effect on primary crop demand- 80% of agricultural land is used for animal production
● Bottom line: food demand in 2050 will be 70% higher than in 2006- Ignoring impacts of climate change, biofuels and the additional
production required to eliminate hunger
Classification: PUBLIC
4
Pressures on existing global farmland
● Pressures on farmland from urbanisation
● Reduction in soil fertility due to poor agronomic practices
Classification: PUBLIC
● Pressures to satisfy demand for non-food crops
- Food, feed, fibre, fuel, feedstocks, fine chemicals
- 40% of the US corn crop in 2011 was used to produce biofuels
● It would be an ecological disaster to convert wild lands to farmland on a significant scale
● Bottom line: Large increases in global farmed area are unlikely
- Indeed we may struggle to retain the amount of farmland we currently have!
5
● Evolution of resistance in existing pests- Weed resistance to glyphosate
● Evolution of new pests- Soybean rust, Ug-99
● Hopelessly unscientific pesticide legislation!- Hazard-based cut-offs- Preferential treatment of natural
products
● Bottom line: Agricultural pests are evolving to become more virulent- The political situation is making things
worse
Pressures from pests
Classification: PUBLIC
6
Pressures on farming inputs
● Fertiliser- Nitrogen prices are linked to the price of oil- Phosphorus supplies are concentrated in
North Africa (> 75%)● Water
- 70% of the world’s fresh water is used by agriculture
- Already 25% of the world’s rivers do not reliably reach the sea!
● Economic inputs & infrastructure- Credit and insurance are increasingly difficult
to obtain
● Bottom line: Current practices are unsustainable
Classification: PUBLIC
7
Uncertainties around climate change
● Crop yields- Probably already being impacted
● Global farmed area- Shifts in cropping regions- Sea level rise
● Extreme weather events● Economic, social and political stability
● Bottom line: There are significant uncertainties about the degree of impact of climate change on agriculture, and the timescale of impact- But it could well be “profoundly negative” and “soon”!
Science 9 January 2009: vol. 323 no. 5911 240-244
Classification: PUBLIC
8
How to produce more food? New and better technologies
- Understanding and mitigating against abiotic stresses• Drought, heat stress, cold stress, nutrient deficiency
- New and better crop protection technologies• More effective, resistance management, new MOA
Classification: PUBLIC
Actual yield
Pests
Stresses
Current Future?
Cro
p yi
eld
● Three strategies
- Increase intrinsic yield potential• Convert annual to
perennial crops• C3 to C4 photosynthesis
• Understanding and de-bottlenecking yield
9
It is not necessarily all about yield....
● Technologies to reduce agricultural inputs and impacts
- “Precision” technologies
- Water & nutrient use efficiency • Crops producing their own nitrogen
- Technologies to reduce GHG emissions• Increase soil carbon
● Technologies to produce “better” food
- More nutritious, better tasting, more “appealing”
Classification: PUBLIC
10
Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
11
Helping the world grow more from less
World
Our ambition:To bring greater food security in an environmentally sustainable way to an increasingly populous world by creating a worldwide step-change in farm productivity.
8Mlarge-scale
farms>100 Ha
450Msmallholder
farms~1.0 Ha
Classification: INTERNAL USE ONLY
12
Market overview 2010
Classification: PUBLIC
Global market: ~ $75 bn
Source: Syngenta Analysis, Philips McDougall
25%
16%
8%
51%
Chart Title Conventional Seeds(~ $17 bn)
Crop Protection* (~ $40 bn)
GM Seeds(~ $12 bn)
Non-Crop Chemicals (~ $6 bn)
*Includes Seed Treatment
13
Competitors in 2010
Classification: PUBLIC
Syngen
ta
Monsa
nto
Bayer
DuPont
BASFDow
0
2000
4000
6000
8000
10000
12000
14000
CP Seeds/Traits L&G
$ m
ill.
sa
les
Sources: Companies Annual/Quarterly reports, Phillips McDougall, Agreworld, Syngenta Analysis
14
Syngenta sales 2010: $ 11.6 bn
Classification: PUBLIC
Crop Protection Seeds
$ 8.8 bn (77%)
$ 2.8 bn(23%)
Selective Herbicides (26%)
Fungicides (30%)
Insecticides (17%)
Non-selective Herbicides (11%)
Crop Protection Seeds
Seed Care (9%)
Professional Products (5%)
Other (2%)
Corn & Soybean (58%)
Vegetables (10%)
Diverse Field Crops (23%)
Flowers (9%)
15
Syngenta R&D
Over 5000 Syngenta employees
work in Research and Development
We spent around $1 billion in
2010 on R&D
Classification: PUBLIC
16
Major R&D sites located on three continents
Other sites
● Marker-assisted and seed breeding capabilities
● Global field station network
Global R&D capabilities
Classification: PUBLIC
GREENSBOROFormulationEnvironmental Science
SBIBiotechnology
R&D
JEALOTT’S HILLChemical DiscoveryWeed ControlFormulationBioscienceEnvironmental Science
STEINFungicides, Insecticides &Professional Products
GOAChemistry
BEIJINGBiotechnologyR&D
17 Classification: PUBLIC
18
Lawn & Garden*
Flowers
Growing Media**
Chemical Controls**
Turf & Ornamentals**
Syngenta was focused three businesses
Classification: PUBLIC
Crop Protection
Selective herbicides
Non-selective herbicides
Fungicides
Insecticides
Seed care
Seeds
Corn & Soybean
Diverse Field Crops
Vegetables
* Newly established in 2008 - Financial reporting for product lines in 2008 under Crop Protection and Seeds respectively** Reported as Professional Products under Crop Protection
19
New Syngenta strategy is crop focused
Classification: PUBLIC
RiceSpecialty
Divers Field CropsCerealsSugar caneSoybeanVegetablesCorn
20
Integrated solutions addressing growers’ needs comprehensively
Weedcontrol
Insectcontrol
Diseasecontrol
Nematodecontrol
Yield potential
Nitrogen efficiency
Drought Quality traits
Labor shortage
Post harvest
Breeding
Native traits
GM traits
Seed care
Crop protection
Nutrients, water
Machinery
Biological solutions
Chemical solutions
Growers’ needs
Technology
Classification: PUBLIC
Services
Innovating across technologies to transform the way crops are grown
21
Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
22 Classification: PUBLIC
Why look for novel fungicides
● Likely to remain the mechanism to deliver fungal control of disease complexes in many crops
● Looking for novel Modes of Action (MoA)- resistance management- cleaner toxicological & environmental profile- broader antifungal spectrum
● New products sell better than old products
23 Classification: PUBLIC
Screening up to 300,000 compounds a year
24 Classification: PUBLIC
Discovery pipeline
Activity?
Activity Profile
Hits leads
Performance Profile
Research Development
Tox Profile
launch
Financial profile
candidates
Registration requirements
25 Classification: PUBLIC
Discovery pipeline
Activity?
Activity Profile
Hits leads
Research Development launch
Financial profile
candidates
Registration requirements
Performance ProfileTox IssuesRegulatory issues
26
Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
27 Classification: PUBLIC
MoA impact on AI pipeline
● MoA determination:
- Intrinsic potency measurement
- Structure based design strategies
- Valuable for Tox and resistance risk assessment
28 Classification: PUBLIC
Early projects
Collect and review information on “physiological effects”“symptomology”Haploinsufficiency / OERSpectrumPhys Chem
KnownMoA
UnknownMoAMoA1
Tools will generallybe available.Use external collaborationfor speed, in-house capabilityfor SAR support
Mode of action diagnosis
29 Classification: PUBLIC
Target site elucidation
M
M
M
More than 25 assays
Identify activity at known target sites (+/-)
Identify hits with interesting activity or symptomology
30 Classification: PUBLIC
Early projects
Collect and review information on “physiological effects”“symptomology”Haploinsufficiency / OERSpectrumPhys Chem
KnownMoA
UnknownMoAMoA1
Tools will generallybe available.Use external collaborationfor speed, in-house capabilityfor SAR support
Mode of action diagnosis
Structure Activity Relationships (SAR)plant pathogen vs mammalian intrinsic potency
31 Classification: PUBLIC
Haploinsufficiency and over-expression induced resistance both exploit gene dosage methods
Haploinsufficiency and over-expression induced resistance
32 Classification: PUBLIC
Basis of the assays
OverexpressingLess sensitive to 25ppm
Haploinsufficient More sensitive to 25ppm
IC50 25ppmNormal cell Target protein
33 Classification: PUBLIC
Chemical Target identified
Haploinsufficiency OEIR
Tunicamycin
F-2003-035
Cerulenin
Rapamycin
Oxytriazine ND
Flutriafol
Fenpropimorph
Soraphen
Eupolauridine
Haploinsufficiency and OEIR are complementary
34 Classification: PUBLIC
How do we utilise Haploinsufficiency and OER data
• Data and literature review
• Express proteins and determine if small molecule interact
• Mutate genes and determine if resistant clone can be produced
Typically a small gene group is identified. Which is target?
Could a data integration approach improve this process?Would like to have the ability to do OER in appropriate plant pathogens
35 Classification: PUBLIC
Early projects
Collect and review information on “physiological effects”“symptomology”Haploinsufficiency / OERSpectrumPhys Chem
KnownMoA
UnknownMoAMoA1
Tools will generallybe available.Use external collaborationfor speed, in-house capabilityfor SAR support
Testable, quality MoA hypothesis?
Sustained interestin Chemistry?
Test using reverse geneticsS. cerevisiaeM. graminicola P. InfestansEtc.
yes
yesReverse Genetics
Mode of action diagnosis
36 Classification: PUBLIC
Early projects
Collect and review information on “physiological effects”“symptomology”Haploinsufficiency / OERSpectrumPhys Chem
KnownMoA
UnknownMoAMoA1
Tools will generallybe available.Use external collaborationfor speed, in-house capabilityfor SAR support
Generate resistant strain S. cerevisiae M. graminicolaP. infestans,M. grisea
Identify mutant gene
no
successful Forward Genetics
Testable, quality MoA hypothesis?
Sustained interestin Chemistry?
Test using reverse geneticsS. cerevisiaeM. graminicola P. InfestansEtc
yes
yesReverse Genetics
Mode of action diagnosis
Collaboration with researchers at the
James Hutton Institute & Dundee University
instrumental to Phytophthora infestans work
37 Classification: PUBLIC
Early projects
Collect and review information on “physiological effects”“symptomology”Haploinsufficiency / OERSpectrumPhys Chem
KnownMoA
UnknownMoAMoA1
Tools will generallybe available.Use external collaborationfor speed, in-house capabilityfor SAR support
Generate resistant strain S. cerevisiae M. graminicolaP. infestans,M. grisea
no
Testable, quality MoA hypothesis?
Sustained interestin Chemistry?
Test using reverse geneticsS. cerevisiaeM. graminicola P. InfestansEtc
yes
yesReverse Genetics
Mode of action diagnosis
Develop affinity assay
Embark on protein purificationdirected by affinity assay or affinity chromatographysupported by proteomics
successful
Generate SAR and correlate to biology
Affinity Based
unsuccessful Forward Genetics
38 Classification: PUBLIC
Plant pathogen platform for MoA Discovery
Efficient transformation method
Good homologous recombination efficiency
– for reverse genetics construct generation
Inducible/titratible promoter
– for protein expression, overexpression induced resistance screens and lethal KO determination
Good predicted protein database
– for peptide mass fingerprinting in affinity purification studies
Ability to map resistant mutants
– direct identification of target protein by forward genetics
39 Classification: PUBLIC
M. graminicola, the most important cereal disease in northern European countries
● ~17% of cultivated land is planted with wheat (worldwide)
● Estimated annual yield loss between 30 and 50% during an outbreak
- It represents loss of >9 millions tons worldwide
● Ascomycete (Dothedomycete, like : Alternaria, Pyrenophora, Stagnospora)
● Pathogen is semi-biotrophic with a stealth growth
● Infection and spread via ascospores (airborne) and conidiospores (water splash)
- Germ tube hyphae penetrate the leaves via stomata
- First phase: biotrophic almost no growth, no symptoms for ~1 to 2 weeks
- Second phase: necrotrophic, mediate PCD in plants, fast growth
Treated
Photo: GHJ Kema, Wageningen Univerisity and Research Centre, Plant Research International B.V., Wageningen, The Netherlands.
Non treated
No 1 pathogen in No1 fungicide market!
40 Classification: PUBLIC
M. graminicola plant pathogen platform
Efficient transformation method
Good homologous recombination efficiency
Inducible/titratible promoter
– inducible promoter still needed
Good predicted protein database
Ability to map resistant mutants
41 Internal use only
Published – methods and tools to stimulate external research
42
Outline
● Global food security challenges
● Syngenta
● Syngenta seeds and R genes
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
43
What they do …
spray droplet characteristics and behaviour (microscopy)
leaf surface redistribution
foliar spray retention, uptake, rainfastness, uv photo-stability
vapour movement
xylem and phloem systemicity and movement to new growth
metabolism in model systems and target organisms
(maize cell culture, SEPTTR cell culture – looking to expand these to wheat and oomycete)
biokinetics in the lab, glasshouse, field, and on the farm
The study of all processes which occur following initial contact between a pesticide and a target crop / fungus and delivery of the toxophore to the target site
Biokinetics and Microscopy
Classification: PUBLIC
44
What they do …
spray droplet characteristics and behaviour (microscopy)
leaf surface redistribution
foliar spray retention, uptake, rainfastness, uv photo-stability
vapour movement
xylem and phloem systemicity and movement to new growth
metabolism in model systems and target organisms
(maize cell culture, SEPTTR cell culture – looking to expand these to wheat and oomycete)
biokinetics in the lab, glasshouse, field, and on the farm
The study of all processes which occur following initial contact between a pesticide and a target crop / fungus and delivery of the toxophore to the target site
Biokinetics and Microscopy
Classification: PUBLIC
45 Classification: PUBLIC
Biokinetic issues
● Gaps
- Ability to follow movement of compounds within cell!
- Range of efflux reporter strains in a plant pathogen
- Range of metabolism reporter strains in a plant pathogen
- Understanding metabolic capacity of plant pathogens
46
Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
47 Classification: PUBLIC
Resistance assessment
● Frequently asked to address if a new compound have a high or low resistance risk?
● UV mutagenesis and selection – but limited numbers are covered compared to the field.
Gap:Tools for better quality resistance assessment
48 Classification: PUBLIC
Guide selection of chemical inputs
Historically driven by diverse inputs (Combi-chem approaches)
Can we be smarter at identifying biologically relevant chemical space?
● Target based screening still not popular concept !● Stronger focus on hypothesis driven starting point
- including relevant Pharma targets & chemistry as starting points
49
Outline
● Global food security challenges
● Syngenta
● Syngenta seeds and R genes
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
Classification: PUBLIC
50
Major gaps in fundamental understanding of Fungal Biology
Classification: PUBLIC
Neurospora crassa S. cerevisiae
Systematic KO projects show similar numbers of lethal genes
~ 1200~ 1200
51
Major gaps in fundamental understanding of Fungal Biology
Classification: PUBLIC
• Crude calculations, BlastP, 25% identity cut-off so very permissive• Rounded numbers!
Neurospora crassa S. cerevisiae
500
Overlap is surprisingly poor!!!
52
Major gaps in fundamental understanding of Fungal Biology
Classification: PUBLIC
• Crude calculations, BlastP, 25% identity cut-off so very permissive• Rounded numbers!
Neurospora crassa S. cerevisiae
350
Compare Lethals to M. graminicola1000/1200 Neurospora lethal are in M. graminicola
850/1200 Yeast lethal are in M. graminicolaOverlap = 350
53
Major gaps in fundamental understanding of Fungal Biology
Classification: PUBLIC
• Crude calculations, BlastP, 25% identity cut-off so very permissive• Rounded numbers!
Neurospora crassa S. cerevisiae
350
750500
150
1000/1200 Neurospora lethal are in M. graminicola850/1200 Yeast lethal are in M. graminicola
M. graminicola
54 Classification: PUBLIC
A significantly better understanding
of genetics/biochemistryof plant pathogens!!!!
55
General areas of interest for Syngenta Biological Sciences
● Weed, insect and fungal resistance (including mathematical modelling)
● Metabolism in fungi, plants, nematodes and insects (including modelling and prediction)
● Predictive toxicology and selectivity between pest and non-target organisms
● Chemical biology approaches to agricultural science
● Systems and synthetic biology in agriculture
● Assay development and target identification
● Microscopy – micro-localisation of chemicals in plant, fungal and insect tissues
● In-vitro assay to whole organism translation
● Plant phenotyping
● Movement of chemicals in soil and uptake into roots
● Genetics - translation into pests from models & marker identification
● Protecting seeds from insect and fungal attack
● Plants and abiotic stress
Classification: PUBLIC
56 Classification: PUBLIC
A web portal to submit innovative ideas - opportunities and collaboration www.syngentathoughtseeders.com
57 Classification: PUBLIC
Questions?
58 Classification: Confidential
Key pathogens (no particular order)
● Mycosphaerella graminicola (Zymoseptoria tritici) ● Fusarium graminearum, oxysporum & verticillioides ● Botrytis cinerea● Blumeria graminis tritici● Puccinia graminis tritici● Alternaria● Cercospora● Magnaporthe grisea● Rhizoctonia● Phytophthora infestans ● Plasmopara● Pythium● Phakopsora pachyrhizi
● No genome yet
59
Syngenta Seeds Position on R genes
Native traits approach
● Genetic resistances against fungus in plants are used for decades.
● In many crops, resistance traits have been identified and characterized. Some genes have been identified
● A range of commercial varieties exhibiting high or intermediate resistances against obligate or necrotrophic fungus.
● Frequently these resistances are linked to active immunitypathogen recognition by the plant triggers plant resistance - often seen as a hypersensitive response.
Classification: PUBLIC
60
Resistance genes used in Tomato (Solanum lycopersicum)
Some resistance loci commonly used in commercial varieties:
● Ve Verticilium dahliae and Verticilium albo-atrum● Frl Fusarium oxysporum radici-lycopersici● I1,I2,I3 Fusarium oxysporum lycopersici● mlo Oïdium neolycopersici● Lv Leveillula taurica● St Stemphylium solani● Ph1,Ph2,Ph3 Phytophthora infestans
Not an exhaustive list
Classification: PUBLIC
61
Issues
● Necrotrophic fungus are more complex to control by genetic means and only intermediate resistance are currently available.
● Despite the high frequency of resistance in the natural plant diversity, some groups of pathogens such as Oomycetes are more complex to control only from genetic factors
● In some pathosystems, resistance traits spread in commercial germplasm are durable whereas in some others it’s not.
● Continuous effort required to provide resistant variety to growers.
Classification: PUBLIC
62
Perception of many!
● Pathogen diversity and evolution allow rapid breaking resistance – Making GM approaches risky and unattractive
● “Engineering would take much longer than the defeat of the R-gene in the field”.
Classification: PUBLIC
Methods to deliver Durable Resistance
Methods to assess Durability of Resistance
Mutagenesis approaches – numbers game is a problem
63 Classification: PUBLIC
64 Classification: PUBLIC
65
Resistance breeding activities
The classical approach
● Search for phenotypic variability in diverse natural germplasm. ● Genetics of the most favorable phenotype is characterized via the
construction of a genetic map and BSA or QTL studies according to the genetic complexity of the resistance.
New approach ● Utilize fungus effectors to identify host receptor in natural or induced
germplasm diversity.
Classification: PUBLIC
66 Classification: Confidential
Issues/gaps summary
● Data integration approach for yeast work?
● OER in appropriate plant pathogens
● Inducible promoter for M. graminicola work
● Ability to follow movement of compounds within cell!
● Range of efflux reporter strains in a plant pathogen
● Understanding metabolic capacity of plant pathogens
● Range of metabolism reporter strains in a plant pathogen
● Tools for better quality resistance assessment
● Tools for target prioritisation/compound follow up