1. Sustainably growing more with less:
fungal control solutions and technology gaps
BioDundee Classification: PUBLIC

2. Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
Issues!
- Biokinetics
Gaps!
- Resistance assessment
● Knowledge gap
2 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
3 Classification: PUBLIC

4. Pressures on existing global farmland
● Pressures on farmland from urbanisation
● Reduction in soil fertility due to poor
agronomic practices
● 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!
4 Classification: PUBLIC

5. Pressures from pests
● 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
5 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
6 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
Science 9 January 2009:
vol. 323 no. 5911 240-244
● 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”!
7 Classification: PUBLIC

8. How to produce more food? New and better technologies
● Three strategies
- Increase intrinsic yield
Stresses
potential
Crop yield
• Convert annual to Pests
perennial crops
Actual
• C3 to C4 photosynthesis yield
• Understanding and de- Current Future?
bottlenecking yield
- 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
8 Classification: PUBLIC

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”
9 Classification: PUBLIC

10. Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
10 Classification: PUBLIC

11. Helping the world grow more from less
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.
8M
large-scale
450M
smallholder
farms farms
>100 Ha ~1.0 Ha
World
11 Classification: INTERNAL USE ONLY

12. Market overview 2010
Global market: ~ $75 bn
Conventional Seeds
(~ $17 bn)
25%
51%
16% GM Seeds
(~ $12 bn)
Crop Protection* 8%
(~ $40 bn)
Non-Crop Chemicals
(~ $6 bn)
*Includes Seed Treatment
Source: Syngenta Analysis, Philips McDougall
Classification: PUBLIC
12

13. Competitors in 2010
14000
12000
10000
$ mill. sales
8000
6000
4000
2000
0
CP Seeds/Traits L&G
Sources: Companies Annual/Quarterly reports, Phillips McDougall, Agreworld, Syngenta Analysis
Classification: PUBLIC
13

14. Syngenta sales 2010: $ 11.6 bn
Crop Protection Seeds
$ 8.8 bn
(77%)
$ 2.8 bn
(23%)
Crop Protection Seeds
Selective Herbicides (26%) Corn & Soybean (58%)
Non-selective Herbicides (11%)
Diverse Field Crops (23%)
Fungicides (30%)
Insecticides (17%) Vegetables (10%)
Seed Care (9%)
Flowers (9%)
Professional Products (5%)
Other (2%)
Classification: PUBLIC
14

15. Syngenta R&D
Over 5000
Syngenta employees
work in Research and Development
We spent around $1 billion in
2010 on R&D
15 Classification: PUBLIC

16. Global R&D capabilities GOA
Chemistry
JEALOTT’S HILL
Chemical Discovery
Weed Control
Formulation
Bioscience Major R&D sites
Environmental Science located on three
continents
BEIJING
Biotechnology
GREENSBORO
R&D
Formulation
Environmental
Science
SBI
Biotechnology
Other sites
R&D
● Marker-assisted and seed
breeding capabilities
STEIN
Fungicides, Insecticides &
● Global field station network
Professional Products
Classification: PUBLIC
16

17. 17 Classification: PUBLIC

18. Syngenta was focused three businesses
Crop Protection Seeds Lawn & Garden*
Selective herbicides Corn & Soybean Flowers
Non-selective herbicides Diverse Field Crops Growing Media**
Fungicides Vegetables Chemical Controls**
Insecticides Turf & Ornamentals**
Seed care
* Newly established in 2008 - Financial reporting for product lines in 2008 under Crop Protection and Seeds respectively
** Reported as Professional Products under Crop Protection
Classification: PUBLIC
18

19. New Syngenta strategy is crop focused
Specialty
Rice
Divers Field Crops
Cereals
Sugar cane
Soybean
Vegetables
Corn
19 Classification: PUBLIC

20. Innovating across technologies to transform the way
crops are grown
Integrated solutions addressing growers’ needs comprehensively
Growers’ needs
Weed Insect Disease Nematode Yield Nitrogen Drought Quality Labor Post
Technology control control control control potential efficiency traits shortage harvest
Breeding
Native traits Biological solutions
GM traits
Seed care Chemical solutions
Crop
protection
Nutrients, w
ater
Machinery
Services
20 Classification: PUBLIC

21. Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
21 Classification: PUBLIC

22. 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
22 Classification: PUBLIC

23. Screening up to 300,000 compounds a year
23 Classification: PUBLIC

24. Discovery pipeline
Activity?
Activity Profile
Performance Profile
Tox Profile
Financial profile
Registration requirements
Hits leads candidates
Research Development
launch
24 Classification: PUBLIC

25. Discovery pipeline
Activity?
Activity Profile
Performance Profile
Tox Issues
Regulatory issues
Financial profile
Registration requirements
Hits leads candidates
Research Development
launch
25 Classification: PUBLIC

26. Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
26 Classification: PUBLIC

27. MoA impact on AI pipeline
● MoA determination:
- Intrinsic potency measurement
- Structure based design strategies
- Valuable for Tox and resistance risk assessment
27 Classification: PUBLIC

28. Mode of action diagnosis
Early projects
Known Unknown
Tools will generally Collect and review information on
MoA MoA “physiological effects”
be available.
Use external collaboration MoA1 “symptomology”
for speed, in-house capability Haploinsufficiency / OER
for SAR support Spectrum
Phys Chem
28 Classification: PUBLIC

29. Target site elucidation
 More than 25 assays
 Identify activity at known
target sites (+/-)
 Identify hits with
interesting activity or
symptomology
M
M
M
29 Classification: PUBLIC

30. Mode of action diagnosis
Early projects
Known Unknown
Tools will generally Collect and review information on
MoA MoA “physiological effects”
be available.
Use external collaboration MoA1 “symptomology”
for speed, in-house capability Haploinsufficiency / OER
for SAR support Spectrum
Phys Chem
Structure Activity Relationships (SAR)
plant pathogen vs mammalian intrinsic potency
30 Classification: PUBLIC

31. Haploinsufficiency and over-expression induced resistance
Haploinsufficiency and over-expression induced resistance
both exploit gene dosage methods
31 Classification: PUBLIC

32. Basis of the assays
Haploinsufficient

More sensitive to 25ppm

Normal cell Target protein
IC50 25ppm

Less sensitive to 25ppm
Overexpressing
32Classification: PUBLIC

33. Haploinsufficiency and OEIR are complementary
Chemical Target identified
Haploinsufficiency OEIR
Tunicamycin  
F-2003-035  
Cerulenin  
Rapamycin  
Oxytriazine  ND
Flutriafol  
Fenpropimorph  
Soraphen  
Eupolauridine  
33 Classification: PUBLIC

34. How do we utilise Haploinsufficiency and OER data
Typically a small gene group is identified. Which is target?
• Data and literature review
• Express proteins and determine if small molecule interact
• Mutate genes and determine if resistant clone can be produced
Could a data integration approach improve this process?
Would like to have the ability to do OER in appropriate plant pathogens
34 Classification: PUBLIC

35. Mode of action diagnosis
Early projects
Known Unknown
Tools will generally Collect and review information on
MoA MoA “physiological effects”
be available.
Use external collaboration MoA1 “symptomology”
for speed, in-house capability Haploinsufficiency / OER
for SAR support Spectrum
Phys Chem
Reverse Genetics
Testable, quality yes
Sustained interest
yes MoA hypothesis? in Chemistry?
Test using reverse genetics
S. cerevisiae
M. graminicola
P. Infestans
Etc.
35 Classification: PUBLIC

36. Mode of action diagnosis
Early projects
Known Unknown
Tools will generally Collect and review information on
MoA MoA “physiological effects”
be available.
Use external collaboration MoA1 “symptomology”
for speed, in-house capability Haploinsufficiency / OER
for SAR support Spectrum
Phys Chem
Reverse Genetics
Testable, quality yes
Sustained interest
yes MoA hypothesis? in Chemistry?
no
Test using reverse genetics Generate resistant strain
S. cerevisiae S. cerevisiae M. graminicola
M. graminicola P. infestans,
P. Infestans M. grisea
Etc
successful Forward Genetics
Collaboration with researchers at the
Identify mutant gene
James Hutton Institute & Dundee University
instrumental to Phytophthora infestans work
36 Classification: PUBLIC

37. Mode of action diagnosis
Early projects
Known Unknown
Tools will generally Collect and review information on
MoA MoA “physiological effects”
be available.
Use external collaboration MoA1 “symptomology”
for speed, in-house capability Haploinsufficiency / OER
for SAR support Spectrum
Phys Chem
Reverse Genetics
Testable, quality yes
Sustained interest
yes MoA hypothesis? in Chemistry?
no
Test using reverse genetics Generate resistant strain Develop affinity assay
S. cerevisiae S. cerevisiae M. graminicola
M. graminicola P. infestans, Affinity Based successful
P. Infestans M. grisea
Etc
unsuccessful Forward Genetics
Generate SAR and Embark on protein
correlate to biology purification
directed by affinity assay
or affinity chromatography
supported by proteomics
37 Classification: PUBLIC

38. 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
38 Classification: PUBLIC

39. 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
Non treated Treated
Photo: GHJ Kema, Wageningen Univerisity and Research Centre,
Plant Research International B.V., Wageningen, The Netherlands.
39 Classification: PUBLIC

40. 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
40 Classification: PUBLIC

41. Published – methods and tools to stimulate external research
41 Internal use only

42. Outline
● Global food security challenges
● Syngenta
● Syngenta seeds and R genes
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
42 Classification: PUBLIC

43. Biokinetics and Microscopy
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
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
43 Classification: PUBLIC

44. Biokinetics and Microscopy
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
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
44 Classification: PUBLIC

45. 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
45 Classification: PUBLIC

46. Outline
● Global food security challenges
● Syngenta
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
46 Classification: PUBLIC

47. 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
47 Classification: PUBLIC

48. 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
48 Classification: PUBLIC

49. Outline
● Global food security challenges
● Syngenta
● Syngenta seeds and R genes
● Fungicide Active Ingredient Pipeline
- MoA diagnosis
- Biokinetics
- Resistance assessment
● Knowledge gap
49 Classification: PUBLIC

50. Major gaps in fundamental understanding of Fungal Biology
S. cerevisiae Neurospora crassa
~ 1200 ~ 1200
Systematic KO projects show similar numbers of lethal genes
50 Classification: PUBLIC

51. Major gaps in fundamental understanding of Fungal Biology
S. cerevisiae Neurospora crassa
500
Overlap is surprisingly poor!!!
• Crude calculations, BlastP, 25% identity cut-off so very permissive
• Rounded numbers!
51 Classification: PUBLIC

52. Major gaps in fundamental understanding of Fungal Biology
S. cerevisiae Neurospora crassa
350
Compare Lethals to M. graminicola
1000/1200 Neurospora lethal are in M. graminicola
850/1200 Yeast lethal are in M. graminicola
Overlap = 350
• Crude calculations, BlastP, 25% identity cut-off so very permissive
• Rounded numbers!
52 Classification: PUBLIC

53. Major gaps in fundamental understanding of Fungal Biology
S. cerevisiae Neurospora crassa
150
350
500 750
M. graminicola
1000/1200 Neurospora lethal are in M. graminicola
850/1200 Yeast lethal are in M. graminicola
• Crude calculations, BlastP, 25% identity cut-off so very permissive
• Rounded numbers!
53 Classification: PUBLIC

54. 54 Classification: PUBLIC

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
55 Classification: PUBLIC

56. A web portal to submit innovative ideas - opportunities and collaboration
www.syngentathoughtseeders.com
56 Classification: PUBLIC

57. 57 Classification: PUBLIC

58. 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
58 Classification: Confidential

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 immunity
pathogen recognition by the plant triggers plant resistance - often seen
as a hypersensitive response.
59 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
60 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.
61 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”.
Methods to deliver Durable Resistance
Methods to assess Durability of Resistance
Mutagenesis approaches – numbers game is a problem
62 Classification: PUBLIC

63. 63 Classification: PUBLIC

64. 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.
65 Classification: PUBLIC

66. 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
66 Classification: Confidential