Page 213 - Plant Canada 2024 Proceeding

PLANT CANADA 2024

[P19] QPCR METHODS TO DETECT AND QUANTIFY THE NOVEL FUSARIUM GRAMINEARUM ANX
CHEMOTYPE VARIANT. Abbey Saunders, Emily Johnstone, and Adam J. Foster. Charlottetown
Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue,
Charlottetown, PE, Canada, C1A 4N6
Correspondence to: adam.foster2@agr.gc.ca

Fusarium head blight (FHB) is an economically important disease of cereal crops globally. FHB is caused
by numerous species of pathogenic fungi in the genus Fusarium, however the greatest concern is
Fusarium graminearum for its contamination of grain with secondary metabolites such as deoxynivalenol
(DON). DON is classified as a trichothecene, a group of mycotoxins known to cause immunotoxic and
neurotoxic effects when ingested. The trichothecene group also includes the novel toxin 7α-hydroxy, 15-
deacetylcalonectrin (ANX), for which there are currently no rapid detection methods available. In this
study, three quantitative polymerase chain reaction (qPCR) assays were developed for detection of the
Tri1 gene polymorphism responsible for ANX strains. Consensus alignment of a collection of Tri1 gene
sequences from ANX isolates and isolates of other chemotypes was conducted. At ANX-specific
polymorphism sites, primers and probes were designed to specifically amplify ANX producing isolate
target DNA. As the probe was designed on a single polymorphic region, a locked nucleic acid (LNA) was
incorporated into the sequence to enhance target specificity. In total, 2 SYBR Green assays and an LNA
HEX labelled probe assay specifically amplified ANX chemotype strains without amplification of other F.
graminearum chemotypes or the 12 other Fusarium spp. tested. A four-fold standard curve was made
from a series of dilutions of ANX isolate DNA to calculate qPCR efficiency and correlation coefficients.
The assays were subsequently evaluated in vivo using the ANX standard curve to assess their efficacy in
detecting and quantifying ANX DNA. This evaluation included target DNA extracted from wheat heads
and seeds infected with ANX hyphae, and soil inoculated with macroconidia from a ANX producing strain.
The results of the in vivo tests found the different SYBR Green assays had detectable limits of 198 DNA
copies per reaction and 98 DNA copies per reaction, respectively. The LNA probe-based assay had a
detectable limit of 198 DNA copies per reaction required for amplification. These assays are a new tool
for rapid detection and quantification of ANX-producing isolates in plant tissue and soil, advancing
research on the epidemiology and geographic distribution of this novel chemotype.

[P20] INFLUENCE OF COVER CROPS ON SOIL AND RESIDUE FUNGAL MICROBIOMES AND
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THEIR IMPACT ON FUSARIUM ROOT AND CROWN ROT. Harini S. Aiyer , Aaron Mills , Andrew
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Mckenzie-Gopsill , and Adam J. Foster . Agassiz Research and Development Centre, Agriculture and
Agri-Food Canada, Agassiz, BC, Canada; Faculty of Land and Food Systems, University of British
2
3
Columbia, Vancouver, BC, Canada; and Charlottetown Research and Development Centre, Agriculture
and Agri-Food Canada, Charlottetown, PE, Canada
Correspondence to: adam.foster2@agr.gc.ca

Cover crops have many befits to agricultural crops including the ability to influence diseases such as
Fusarium root and crown rot (FRCR) in crops grown in subsequent growing seasons. Eight cover crops
including: alfalfa, crimson clover, buckwheat, phacelia, oilseed radish, brown mustard, sorghum-
sudangrass, and annual ryegrass were evaluated in Prince Edward Island Canada for their effects on the
soil microbiomes and residue microbiome and plant disease in barley and soybean crop in the following
seasons. Additionally, three cover crop mixes were examined. Two field trials over two years utilized a
randomized complete block design for cover crops and a split-plot design for subsequent barley and
soybean planting. Internal transcribed spacer (ITS) amplicon sequencing characterized fungal community
changes in the soil during the cover crop growing season and the subsequent year. Fungal alpha
diversity increased over time and was significantly influenced by cover crop choice. Fungal pathotroph
abundance was positively associated with oilseed radish, alfalfa, and phacelia, but negatively with
sorghum-sudangrass. Beneficial symbiotrophic fungal groups were linked to sorghum-sudangrass and
buckwheat. High Fusarium spp. abundance in soil and field residue samples correlated with the
observations of FRCR incidence in barley and soybean roots. A greenhouse trial using soils from
sorghum-sudangrass, buckwheat, brown mustard, alfalfa, phacelia, and no-crop plots, inoculated with
Fusarium, confirmed the protective effect of disease suppressive soils from certain cover crops against
FRCR. These findings suggest that specific cover crops can alter soil microbial communities, impacting
plant health and disease levels in subsequent crops.

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