Post on 10-Mar-2021
Evaluating root rot and other pulse diseases
Plant Health Summit 2020, Saskatoon SK
Syama ChattertonAgriculture and Agri-Food Canada, Lethbridge Research Centre
1
Overview
1. Survey results 2014 - 2019
2. Lab research projects• Threshold inoculum dose to cause disease
• DNA detection in soils
3. Management options (Field trials)• Seed treatments
• Aphanomyces inoculum changes over time
• Rotation with other pulse crops
• Cover crops
• Liming2
3
The root rot problem
• 2011 – 2012 increasing calls and reports fromproducers about peas yellowing duringflowering
• Assumption that it was Fusarium root rot– Most isolated group in culture
– Reported in previous surveys– But some things didn’t add up
4
An unexpected surprise...
• Aphanomyces euteiches!!!
• First report of thisdestructive pathogen in Saskatchewan(2012) and Alberta (2013)
5
1. SURVEYS
7
• Prevalence of Aphanomyces root rot• Other pathogens causing root rot
Aphanomyces positive pea and lentil fields
A. euteiches prevalence and incidence in AB pea
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10
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60
70
2014 2015 2016 2017 2018 2019
Prec
ipita
tion
(mm
)
Perc
ent
Prevalence Incidence Precipitation
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A. euteiches prevalence and incidence in SK pea
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0
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350
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2015 2016 2017 2018 2019
Prec
ipita
tion
(mm
)
Perc
ent
Prevalence Incidence Precipitation
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Root rot is a complex
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0
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80
90
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P. ult P. irre R.solani
F.ave/acu
F. sol F. red F. oxy F. gram F. cul
AB SK MB
Fusarium species are a problem on their own
Fusarium = F. avenaceum + F. solani + F. redolens
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0
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40
60
80
100
samples fields
Alberta
Fus+Aph Fus Aph
0
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40
60
80
100
samples fields
Saskatchewan
Fus+Aph Fus Aph
0
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40
60
80
100
samples fields
Manitoba
Fus+Aph Fus Aph
Aphanomyces positive lentil fields AB
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20
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60
70
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2015 2016 2017
Prec
ipita
tion
(mm
)
Perc
ent
Prevalence Incidence Precipitation
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Aphanomyces positive lentil fields SK
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0
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350
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2016 2017
Prec
ipita
tion
(per
cent
)
Perc
ent
Prevalence Incidence Precipitation
Pea vs lentil
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2. LAB RESEARCH
Current recommendations to growers
• Avoid planting peas and lentils in Aphanomyces-infested fields, get soil tested to confirm presence of Aphanomyces
• Can we quantify risk levels >>> decision support system?1. How much inoculum is required to cause
disease?2. Can we use molecular quantification tools
rather than laborious soil baiting assays?3. Where do we need to sample?
19
Oospore (thick-walled, resting spore)
Zoospore (short-lived, swimming cell)
How many oospores to cause disease?
21
Sandy loam soil (black soil zone)
Threshold oospore levels to cause disease
• Threshold ranges from 40 – 275 oospores/ g dry soil
• Highly dependent on soil type• Threshold is lowered in presence of Fusarium – more lab
trials to validate this
Soil Type Estimate (μ � se) Clay Loam 275.2 � 36.5a
Loam 98.8 � 42.9ab
Sandy Loam 81.3 � 76.7ab
Silty Loam 44.3 � 38.3b
Can we use DNA tests to quantify pathogen level and determine risk?
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1.5
2
2.5
3
3.5
4
0 1 2 3 4
Mea
sure
d oo
spor
es (l
og10
)
Actual oospores (log10)
Sandy loam Silty loam Clay loam
Both qPCR and ddPCR underestimated the incidence and severity of disease observed in the field because:
1) DNA extraction methods don’t adequately lyse thick-walled oospores
2) Severity is a function of multiple pathogens interacting
Recommendations for soil sampling
• DNA test of live roots is the best method• Remove stubble layer and take soil from top
15 cm from low spots in the field or with history of yellowing
• Pea or lentil post-harvest soil sampling gives better results than a pre-seeding spring sampling
• Beware false negatives– False negative rate is high, especially from dry
soils
Summary of research
• Oospore threshold to cause disease is low, zoospores multiply from oospores
• DNA test can identify high risk (high oospore load) fields, still difficult at low oospore levels
• Working on methods to improve oospore detection
• A. euteiches is highest in top soil layer, but present in all layers
3. FIELD TRIALS
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Current recommendations to growers
• Consider using a seed treatment that targets the root rot complex – Which ones? How effective are they?
• Prolonged rotations away from susceptible hosts (peas and lentils) in infested fields– How long is long enough? – Which other pulse crops can be grown
instead?
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FIELD TRIALS
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• Inoculated field trials DO NOT work!
• Field trials located in producer’s fields identified from surveysBUT no healthy check
• Provide opportunity to track changes over time out of peas
FIELD TRIALS
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• Seed Treatments• Rotation
– Length away from pea
– Alternate pulse crops
• Cover crops– Biofumigants– Potential legume
hosts• Lime products?
Treatments
• A number of seed treatments• Trifluralin (Edge) as pre-seed burn (effect on
Aphanomyces root rot?)• Phostrol as foliar spray to seedlings
No effect of most treatments over 4 years at 4 locations!
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Red Deer – last pea crop 2011
RAIN (mm)
215 239 176 190
(LTA) 282 -25 -1 -64 -50
44903945
60746408
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6000
7000
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7
2015 2016 2017 2018
Yiel
d (k
g/ha
)
Dis
ease
sev
erity
DS Yield
34
35
Taber – last pea crop 2014
2117
1337
2158
1200
0
500
1000
1500
2000
2500
0
1
2
3
4
5
6
7
2015 2016 2017 2018 2019
Yiel
d (k
g/ha
)
Dis
ease
sev
erity
RAIN (mm)
97.8 235 119 101 120
LTA (192) -94 +43 -73 -91 -7236
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Pathogen composition changes over time
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50
100
150
200
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300
Aph F ave F sol F red
Path
ogen
#/ g
root
June July
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• 1 – 8 year breaks between a pea crop– Cereal and canola as standard rotational crops
– With or without an alternate pulse crop
• Chickpea = Swift Current, Lethbridge• Faba bean = Saskatoon, Lacombe• Soybean = Redvers, Brooks, Morden• Assess roots and soil for pathogen levels in
pulse crop treatments
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Rotation frequency + non-host pulse crops
Soybean
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Soybean Pea Soybean PeaLomond Redvers
Aph 0.3 325.8 0.1 118.6Fred 2.2 12.0 7 1.2Fsol 1.78 44.9 0.1 11.0Fave 0.1 0.1 3.9 1.0
0.0
100.0
200.0
300.0
400.0
cells
/ g
root
Fave Fsol Fred Aph
DS 2 6.5 2.8 6.3
Faba bean
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Faba bean Pea Faba bean PeaLacombe Sask
Aph 0.0 5.1 0.1 20.2Fred 10.4 5.4 95.9 280.4Fsol 0.3 1.1 5.7 135.5Fave 36.7 56.9 7.2 15.5
0.0
100.0
200.0
300.0
400.0
500.0
cells
/ g ro
ot
Fave Fsol Fred Aph
DS 1 2 1.6 1.6
Chickpea
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Chickpea Pea Chickpea PeaTaber Swift
Aph 0.1 86.6 1.9 25.7Fred 37.9 438.6 37 88.0Fsol 12.5 121.6 129.7 73.5Fave 0.4 356.9 6.9 6.4
0.0
200.0
400.0
600.0
800.0
1000.0
1200.0
cells
/ g
root
Fave Fsol Fred Aph
DS 1 3.2 1.6 2.6
Virulence of Fusarium solani to pulse crops
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0
10
20
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50
60
70
80
90
100
Soy (W
arre
n)
Faba
(Sno
wbird
)
Chick
pea (C
onsu
l)
Chick
pea (L
imer
ick)
Chick
pea (L
eade
r)
Chick
pea (O
rion)
Lentil (
Max
im)
Lentil (
Daz
il)
Lentil (
Impo
wer)
Pea (M
eado
w)
% Emergence
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
5
Soy (W
arre
n)
Faba
(Sno
wbird
)
Chick
pea (C
onsu
l)
Chick
pea (L
imer
ick)
Chick
pea (L
eade
r)
Chick
pea (O
rion)
Lentil (
Max
im)
Lentil (
Dazil)
Lentil (
Impo
wer)
Pea (M
eado
w)
Disease Severity
Virulence of Fusarium avenaceum to pulse crops
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0
10
20
30
40
50
60
70
80
90
100
Soy (W
arre
n)
Faba
(Sno
wbird
)
Chick
pea (C
onsu
l)
Chick
pea (L
imer
ick)
Chick
pea (L
eade
r)
Chick
pea (O
rion)
Lentil (
Max
im)
Lentil (
Dazil)
Lentil (
Impo
wer)
Pea (M
eado
w)
% Emergence
0
1
2
3
4
5
6
Soy (W
arre
n)
Faba
(Sno
wbird
)
Chick
pea (C
onsu
l)
Chick
pea (L
imer
ick)
Chick
pea (L
eade
r)
Chick
pea (O
rion)
Lentil (
Max
im)
Lentil (
Dazil)
Lentil (
Impo
wer)
Pea (M
eado
w)
Disease Severity
Brassica cover crops
• Green manure break-down products “biofumigate” soil and suppress oospores
• Feasibility in no-till systems if green manure needs to be incorporated?
• Increased disease risk to canola?• Climate constraints in Canadian prairies for
cover cropping• Long-term effects as amending inoculum
levels in soil
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Cover crop treatments for potential biofumigation
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Treatment Green Manure
Seed
1 Pea (control) X2 Cereal (control) X3 Canola (control) X4 Oats X X5 Rye X X6 Mustard (Sinapsis alba) X X7 Caliente mustard X X8 Faba bean (Vicia fabae) X X9 Clover X10 - 15 Various Brassica blends X
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Cover crop – data collection
• Pea to be planted into cover crop footprint in 2020
• Attempting to quantify oospore numbers in soil before and after cover crops, with and without tillage
• Changes in soil microbial community• Whole trial repeated in 2020, with pea grown
in 2021
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What about legumes used in cover crop mixes?
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Type Species DSI Ae Ae copies Fave Fred
Vetch Chickling 4.3 + 1014.2 9.1 0.4Ebina 4.2 + 317.7 12.2 0.6Hungvillosa 2.6 + 128.7 8.0 0.0
Clover
Crimson 1 + 8.1 1.0 0.0Yellow blossom 1 + 1.0 1.3 0.0Persian 1 ? 0.3 5.6 0.0White Dutch 1 - 0.0 2.6 0.0Red 1.2 - 0.0 2.1 0.0Subterranean 1 - 0.0 0.8 0.0Berseem 1.9 - 0.0 0.6 0.0
Lupin Lupin 2.6 - 0.0 1.9 0.0Pea Pea 5 + 636.5 7.7 22.7
Clovers
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Yellow Blossom (+)
Berseem (-)Persian (?)Crimson (+)
Vetches
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Hungvillosa Chickling Ebina
Liming
• Calcium prevents the oospore > zoospore process
• Widely used in the U.S. in sugar beet operations to manage Aphanomyces root rot– High dose needed
– Tillage may be required?– Does seem to provide long-term effects
• Also evidence that it is effective against clubroot – manage 2 diseases with one operation
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Greenhouse trial with lime products using soil from Taber site
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0.0
1.0
2.0
3.0
4.0
5.0
6.0
Hydrated Quick ZeroG
Dis
ease
sev
erity
0 0.82 1.42 1.99 2.5
Significant increase in root weight
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0.0
0.1
0.2
0.3
0.4
0.5
0.6
Hydrated Quick ZeroG
Roo
t wei
ght (
g)
0.00 0.82 1.42 1.99 2.50
600 1.420.82 2.51.99
Summary field trials
• Seed treatment efficacy variable• Reduction in disease and increased yield
after 6-7 years at some sites• Aphanomyces colonizes first, other
pathogens secondary• Soybean, faba bean good pulse crop options,
chickpea?• Watch out if using legumes as cover crops!• Liming???
61
Conclusions
• Aphanomyces root rot widespread across Prairies – impact varies with moisture levels
• Inoculum threshold dose low, makes it difficult to soil test
• Management options remain limited– Field avoidance works, but length of time variable
– Seed treatments against Aphanomyces don’t provide season-long control
– Ongoing research into options that will reduce oospore levels
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Collaborators• Robyne Bowness, Mike
Harding• Bruce Gossen, Michelle
Hubbard, Arlen Kapiniak• Sabine Banniza, Steve
Shirtliffe• Lana Shaw• Debbie McLaren, Bob Conner