@article {4666, title = {A qPCR Assay for the Detection of Phytophthora cinnamomi Including an mRNA Protocol Designed to Establish Propagule Viability in Environmental Samples}, journal = {Plant Disease}, volume = {103}, year = {2019}, month = {Jan-09-2019}, pages = {2443 - 2450}, abstract = {

Phytophthora cinnamomi causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (cox2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against P. cinnamomi and two closely related clade 7 species, P. parvispora and P. niederhauseri. From these tests, five primer pairs were selected based on specificity and, with a species-specific P. cinnamomi probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 Phytophthora isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of P. cinnamomi DNA and showed no cross-reaction with other Phytophthora species, except for P. parvispora, a very closely related species to P. cinnamomi, which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with P. cinnamomi. Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of P. cinnamomi in recalcitrant environmental samples.

}, issn = {0191-2917}, doi = {10.1094/PDIS-09-18-1641-RE}, url = {https://apsjournals.apsnet.org/doi/10.1094/PDIS-09-18-1641-RE}, author = {Kunadiya, Manisha B. and Dunstan, William D. and White, Diane and Hardy, Giles E. St. J. and Grigg, Andrew H. and Burgess, Treena I.} } @article {899, title = {Quantification of the susceptibility of the native flora of the South-West Botanical Province, Western Australia, to Phytophthora cinnamomi}, journal = {Australian Journal of Botany}, volume = {52 (4)}, year = {2004}, pages = {435 - 443}, abstract = {

This study compares, for the first time, variation in estimates of susceptibility of native flora to Phytophthora cinnamomi Rands among four databases and proposes an estimate of the proportion of the flora of the South-West Botanical Province of Western Australia that is susceptible to the pathogen. Estimates of the susceptibility of south-western native flora to P. cinnamomi infection were obtained from databases for Banksia woodland of the Swan Coastal Plain, jarrah (Eucalyptus marginata Donn. ex Smith) forest, the Stirling Range National Park and Rare and Threatened Flora of Western Australia. For the woodland, forest and national park databases, hosts were naturally infected in uncontrolled diverse natural environments. In contrast, threatened flora were artificially inoculated in a shadehouse environment. Considerable variation occurred within taxonomic units, making occurrence within family and genus poor predictors of species susceptibility. Identification of intra-specific resistance suggests that P. cinnamomi could be having a strong selection pressure on some threatened flora at infested sites and the populations could shift to more resistant types. Similar estimates of the proportion of species susceptible to P. cinnamomi among the databases from the wide range of environments suggests that a realistic estimate of species susceptibility to P. cinnamomi infection in the south-western region has been obtained. The mean of 40\% susceptible and 14\% highly susceptible equates to 2284 and 800 species of the 5710 described plant species in the South-West Botanical Province susceptible and highly susceptible to P. cinnamomi, respectively. Such estimates are important for determining the cost of disease to conservation values and for prioritising disease importance and research priorities. P. cinnamomi in south-western Australia is an unparalleled example of an introduced pathogen with a wide host range causing immense irreversible damage to unique, diverse but mainly susceptible plant communities.

}, doi = {http://dx.doi.org/10.1071/BT03131}, url = {http://www.publish.csiro.au.proxy.library.oregonstate.edu/?paper=BT03131}, author = {Shearer, B. L. and C. E. Crane and A. Cochrane} }