Evaluating root rot and other pulse diseases · Evaluating root rot and other pulse diseases Plant...
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Evaluating root rot and other pulse diseases Plant Health Summit 2020, Saskatoon SK Syama Chatterton Agriculture and Agri-Food Canada, Lethbridge Research Centre 1
Transcript of Evaluating root rot and other pulse diseases · Evaluating root rot and other pulse diseases Plant...
Evaluating root rot and other pulse diseases
Plant Health Summit 2020, Saskatoon SK
Syama ChattertonAgriculture and Agri-Food Canada, Lethbridge Research Centre
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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
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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
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An unexpected surprise...
• Aphanomyces euteiches!!!
• First report of thisdestructive pathogen in Saskatchewan(2012) and Alberta (2013)
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1. SURVEYS
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• 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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Prec
ipita
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Prevalence Incidence Precipitation
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A. euteiches prevalence and incidence in SK pea
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Root rot is a complex
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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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samples fields
Alberta
Fus+Aph Fus Aph
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Saskatchewan
Fus+Aph Fus Aph
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Manitoba
Fus+Aph Fus Aph
Aphanomyces positive lentil fields AB
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Aphanomyces positive lentil fields SK
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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?
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Oospore (thick-walled, resting spore)
Zoospore (short-lived, swimming cell)
How many oospores to cause disease?
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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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Mea
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d oo
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og10
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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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Yiel
d (k
g/ha
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Dis
ease
sev
erity
DS Yield
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Taber – last pea crop 2014
2117
1337
2158
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2015 2016 2017 2018 2019
Yiel
d (k
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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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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
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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
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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
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Fave Fsol Fred Aph
DS 1 3.2 1.6 2.6
Virulence of Fusarium solani to pulse crops
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Soy (W
arre
n)
Faba
(Sno
wbird
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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
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Soy (W
arre
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Faba
(Sno
wbird
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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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Soy (W
arre
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Faba
(Sno
wbird
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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
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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
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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???
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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
