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Recent developments concerning the population

biology and management of Phytophthora


infestans in the USA.
USA populations
local sexual
recombination?
management

Whats next?
Phytophthora infestans
2
1840s 1950s: asexual
(A1 Mating type worldwide)

1950s: A2 discovered in Mexico

1990s-2000s: sexual populations in
Northern Europe (others asexual)

USA strongly clonal (asexual)
Glucose-6-phosphate
isomerase (Gpi)
RFLP probe RG57
Microsatellite
markers
Mitochondrial
haplotyping
Nuclear genes
Mating type
Markers
Virulence
avirulence
Slide: G. Danies
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
2009 2010 2011 2012 2013
Multilocus
genotypes
US-8
US-11
US-22
US-23
US-24
Rare and diverse
genotypes (GDT)
US-7
P
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Year
(80) (51) (137) (237) (274)
Genotypes of Phytophthora infestans in the
United States from 2009 to 2013
http://www.usablight.org/map
2012

>240 samples
US8 - 7
US11 - 85
US22 - 1
US23 - 130
US24 - 23

5
Epidemics almost exclusively clonal only one genotype
0 g mL
-1

5 g mL
-1

100 g mL
-1

Mefenoxam concentration
US22
0 g mL
-1

5 g mL
-1

100 g mL
-1

Mefenoxam concentration
US23
0 g mL
-1

5 g mL
-1

100 g mL
-1

Mefenoxam concentration
US24
0 g mL
-1

5 g mL
-1

100 g mL
-1

Mefenoxam concentration
US8
Sensitivity to mefenoxam
Phenotypes of common lineages
Host preference
(8)
(34)
(7)
(9)
(Danies, 2013. Plant Disease)

A.
B.
7
0
10
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30
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50
60
70
80
90
100
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%
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US-8 vs US-24 on potato
US-8 (default)
US-24 Spor. Rate (0.31)
Recent developments concerning the population
biology and management of Phytophthora
infestans in the USA.
USA populations
local sexual
recombination?
management

Whats next?
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
2009 2010 2011 2012 2013
Multilocus
genotypes
US-8
US-11
US-22
US-23
US-24
Rare and diverse
genotypes (GDT)
US-7
P
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Year
(80) (51) (137) (237) (274)
Genotypes of Phytophthora infestans in the
United States from 2009 to 2013
A1
A2
A1 and A2
Mating types
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
New York State
2010 and 2011
Diverse genotypes for:
Allozyme Glucose-6-phosphate isomerase
Microsatellite
RFLP probe RG57
Nuclear genes
Mefenoxam sensitivity

Monomorphic for mitochondrial haplotype

Phytophthora infestans genotypes from
central NYS in 2011 and 2012
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
A1
A2
A1 and A2
Mating types
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
GDT-1
GDT-1
GDT-2
GDT-4
GDT-7
GDT-9
GDT-11
GDT-18
GDT-3
GDT-8
GDT-4 GDT-4
GDT-4
GDT-6
GDT-8
GDT-5
GDT-10
GDT-19
GDT-20
New York State
2010 and 2011
d = 0.5
1
2
3
Eigenvalues
US-12
US-7
US-11
US-20
US-16
US-19
US-17
US-6
GDT-09
GDT-18
GDT-02
GDT-20
GDT-07
US-21
GDT-19
GDT-14
GDT-13
GDT-08.1
GDT-08
US-22
GDT-12
GDT-01
GDT-11 GDT-06
US-24
US-23var
US-1
US-23
US-14
US-8
GDT-10
GDT-16
GDT-03
GDT-04
GDT-05
GDT-17
GDT-15
U
S
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1

U
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-
6

U
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7

U
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1
2

U
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1
4

U
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1
6

U
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1
7

U
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1
9

U
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8

U
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1
1

U
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2
0

U
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1

U
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2

U
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2
3
v
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U
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3

U
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4

G
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G
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2

G
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3

G
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G
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G
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G
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0
7

G
D
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-
0
8

G
D
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-
0
8
.
1

G
D
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-
0
9

G
D
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-
1
0

G
D
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-
1
1

G
D
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-
1
2

G
D
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1
3

G
D
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G
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G
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G
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G
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0

1 2 3
1.00
0.80
0.60
0.40
0.20
0.00
STRUCTURE analysis of 12
microsatellite loci
1. Lineages that have not been prevalent in the United States for the past 10 years

2. Lineages that have been dominant in the past five years or that have been first
described during the past five years in the United States

3. NYS-2010/11 P. infestans isolates that are the focus of this study
Diverse genotypes of Phytophthora infestans
in 2011
Possible explanations are mutation, migration and/or
recombination.


Much more diversity than
can be explained by
mutation in a short time.
Niagara
Erie
Wyoming
Genesee
Orleans
Livingston
Monroe
Wayne
Cayuga
Tompkins
Seneca
Schuyler
Yates
Ontario
GDT-1
GDT-1
GDT-2
GDT-4
GDT-7
GDT-9
GDT-11
GDT-18
GDT-3
GDT-8
GDT-4 GDT-4
GDT-4
GDT-6
GDT-8
GDT-5
GDT-10
GDT-19 GDT-20
Could one of the dominant lineages be
one of the possible parents?
Through parentage exclusion testing, using microsatellite data,
lineages US-8, US-23 and US-24 are excluded as parents for
these new genotypes.
Microsatellite loci
Multilocus
genotype
D13 PiG11 Pi04
US-8
108 156 166
112 170

All new
genotypes
110 134 166
- 156 170



Multilocus
genotype
Mitochondrial
haplotype
GPI Mating type
Mefenoxam
sensitivity
US-22 H20 100/122 A2 Sensitive
All new
genotypes
H20 100/111/122 A1 or A2
Sensitive or
Intermediate
Could one of the dominant lineages be
one of the possible parents?
US-22
GDT-1
GDT-2
GDT-3
GDT-6
GDT-7
GDT-8
GDT-10
GDT-11
PITG_11126
GDT-1 G T G
GDT-2 G/A C/T G/A
GDT-3 G T G
GDT-4 A C A
GDT-5 A C A
GDT-6 G T G
GDT-7 G T G
GDT-8 G/A C/T G/A
GDT-9 A C A
GDT-10 G/A C/T G/A
GDT-11 G/A C/T G/A

US-22 G T G
Could one of the dominant lineages be
one of the possible parents?
20 diverse genotypes
(A1 and A2)
Recombination involving US22?
Migration?
Recent developments concerning the population
biology and management of Phytophthora
infestans in the USA.
USA populations
local sexual
recombination?
management

Whats next?
Decision Support System screenshot
22
Decision Support System components
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Location-specific weather data
Disease forecasting tools
Late blight disease simulator
Alert system
Weather data
Observed and forecast data obtained for Late Blight DSS

Weather obtained for late blight source and grower locations


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Screenshot: Input page for disease forecasters
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Potato cultivar resistance database
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Tomato cultivar resistance database
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Variety Susceptibility to LB
Defiant PHR F1 Resistant (Ph2 & Ph3)
Matt's Wild Cherry Resistant
Mountain magic F1 Resistant (Ph2 & Ph3)
Plum regal F1 Resistant (Ph3)
Aunt Ginny's Purple Moderately resistant
Aunt Ruby's German Green Moderately resistant
Black Krim Moderately resistant
Black Plum Moderately resistant
Brandywine Moderately resistant
Prudens Purple Moderately resistant
Red Currant Moderately resistant
Yellow Currant Moderately resistant
Yellow Pear Moderately resistant
BHN 589 Moderately susceptible
BHN 961 Moderately susceptible
Big Beef Moderately susceptible
Celebrity Moderately susceptible
Mountain Fresh Plus F1 Moderately susceptible
Mountain Supreme Moderately susceptible
West VA 63 Moderately susceptible
Glamour Susceptible
Gold Nugget Susceptible
Jetstar F1 Susceptible
Market Pride Susceptible
New girl F1 Susceptible
New Yorker Susceptible
Pik Rite Susceptible
Pilgrim Susceptible
Primo red F1 Susceptible
Scarlet red Susceptible
Sunbrite VFF Susceptible
Sunrise Susceptible
Supersonic F1 Susceptible
Ultra Sweet Susceptible
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Mod. susceptible cultivar
Mod. resistant cultivar
Mod. susceptible cultivar
Mod. resistant cultivar
6 applications
5 applications
Late blight simulator: management scenarios
Screenshot: Input page for disease forecasters
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Pathogen lineage information
30
Pathogen lineage Sensitivity to mefenoxam
Unknown (default) Potato Tomato ?
US-1 Potato Tomato Sensitive
US-2 Potato Tomato ?
US-3 Potato Tomato ?
US-4 Potato Tomato ?
US-5 Potato Tomato Sensitive
US-6 Potato Tomato Resistant
US-7 Potato Tomato Resistant
US-8 Potato Intermediate/Resistant
US-9 Potato Tomato Resistant
US-10 Potato Tomato Sensitive
US-11 Potato Tomato Resistant
US-12 Potato Tomato Resistant
US-13 Potato Tomato Resistant
US-14 Potato Tomato Resistant
US-15 Potato Tomato Resistant
US-16 Potato Tomato Resistant
US-17 Tomato Resistant
US-18 Potato Tomato Sensitive (Intermediate)
US-19 Potato Tomato Sensitive (Intermediate)
US-20 Potato Tomato Intermediate/Resistant
US-21 Potato Tomato Sensitive//Intermediate/Resistant
US-22 Potato Tomato Sensitive (Intermediate)
US-23 Potato Tomato Sensitive (Intermediate)
US-24 Potato Sensitive (Intermediate)
Susceptible crop
Photos courtesy G. Danies
DSS evaluation Simulation experiments
(Late Blight 2004)
~770 field expts
6930 simulations
Historic weather data 2000 2013
Maine, Massachusetts, New York, North Carolina,
North Dakota, and Wisconsin 59 locations
Andrade et al 2005
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# fungicide applications/season

11 11
11
7
9
14
0 0 0
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disease severity first infection 6 days after 18 SV
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Late blight resistance
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Simulated disease severity by state
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Each error bar is constructed using 1
standard deviation from the mean. Late blight resistance
Summary: DSS vs weekly schedule
Unfavourable weather (for late blight), DSS fewer
fungicide applications with no loss of disease suppression

Favourable weather (for late blight), DSS more fungicide
applications with improved disease suppression.

The DSS was capable of improving the efficiency of fungicide
use with no loss of disease suppression

35
Recent developments concerning the population
biology and management of Phytophthora
infestans in the USA.
USA populations
local sexual
recombination?
management

Whats next?
2014: Infection alert
Worst conditions:
sunny morning: enhanced release
cloudy mid-day: enhanced survival
wet leaves at night: germination
0
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0 2 4 6 8 10
time (hours)
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sunny
sunny-cloudy
Recent developments concerning the population
biology and management of Phytophthora
infestans in the USA.
USA populations
local sexual
recombination?
management

Whats next?
Recent developments concerning the population
biology and management of Phytophthora
infestans in the USA.
Thanks to you and to
Ian Small
Giovanna Danies Kevin Myers
USDA NIFA program on global food security