Table 1.
Primers and probe used in the P. abietivora (P_abi_detect) detection assay.
Fig 1.
The P_abi_detect assay is specific and sensitive.
(A) The P_abi_detect qPCR assay showed specific amplification from P. abietivora and P. europaea genomic DNA while DNA from the other species tested do not result in reliable amplification under the established cut-off. (B) The P_abi_detect assay showed a linear response between Cq values and the ITS2 copy numbers. (C) The Probit regression analysis used to estimate the LOD95% of the assay. The dashed lines intercept at the theoretical 95%. (D) The P_abi_detect shows a linear response between Cq values and the quantity of oospores present in samples spiked with known quantities of cells.
Fig 2.
Phytophthora abietivora is present in major Christmas tree producing regions of the province of Québec.
(A) Map of the province of Québec with the regions of Estrie (Southward) and Chaudière-Appalaches (Northward) highlighted in white. (B) Proportion of positive detections in soil samples of PRR symptomatic firs trees for each sampled site. (C) Proportion of positive detections in soil samples of healthy-looking firs trees for each sampled site. (D) Proportion of positive detections in soil samples of healthy-looking firs trees in natural forest stands in the vicinity of each sampled site. The insets in (B), (C), and (D) represent an enlarged region with a high density of sampled Christmas tree productions. The data used to create these maps was obtained from the Ministry of Natural Resources and Forests under a CC BY 4.0 license, with permission from MNRF, original copyright 2024. [https://www.donneesquebec.ca/recherche/dataset/base-de-donnees-geographiques-et-administratives] [37].
Fig 3.
PRR-like symptoms are a predictor of the presence of P. abietivora in the associated rhizosphere soil.
(A) Bar plot showing the proportion of positive detections for the soil samples of different tree status. The number of samples in each category is indicated above the bars. (B) Binary logistic regression using the result of the assay (positive, negative) as the dependent variable. For both cultivated Abies species, samples taken in the rhizosphere soil of PRR-like symptomatic trees have higher odds of being positive for the presence of P. abietivora than the other tree status.
Fig 4.
DNA from P. abietivora is found in soil and root fragments samples in comparable quantities.
(A) Scatter plot of Cq values for the 164 samples from PRR-like symptomatic trees. (B) Boxplot of the Cq values obtained for positive soil and unidentified root fragments samples. Number of samples is displayed above the individual plots.