Research Project: Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data - (Peer Reviewed Journal)
Foster, Z.S.L., Tupper, A.S., Press, C.M., Grunwald, N.J. 2024. Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data. PLoS Computational Biology. 20(5):e1012139. https://doi.org/10.1371/journal.pcbi.1012139.

Evaluation of germicidal UV-C light for suppression of grape powdery mildew and Botrytis bunch rot in Western Oregon - (Peer Reviewed Journal)

It’s a trap! An approachable guide to constructing and using rotating-arm air samplers - (Peer Reviewed Journal)
Check, J., Harkness, R., Heger, L., Chilvers, M.I., Mahaffee, W.F., Sakalidis, M.L., Miles, T.D. 2024. It’s a trap! An approachable guide to constructing and using rotating-arm air samplers. Plant Disease. https://doi.org/10.1094/PDIS-01-24-0131-SR.

First report of Neofabraea actinidiae causing a cranberry fruit rot in Oregon - (Peer Reviewed Journal)

First report of Phytophthora ramorum causing leaf spots on Cornus capitata (evergreen dogwood) in United States - (Peer Reviewed Journal)
Belisle, W.H., Rooney-Latham, S., Soriano, M.C., Grünwald, N.J., Blomquist, C.L. 2024. First report of Phytophthora ramorum causing leaf spots on Cornus capitata (evergreen dogwood) in United States. Plant Disease. https://doi.org/10.1094/PDIS-12-23-2638-PDN.

A fast-response model of turbulence and passive scalar transport in row-organized canopies - (Peer Reviewed Journal)
Ulmer, L., Margairaz, F., Mahaffee, W.F., Stoll, R. 2024. A fast-response model of turbulence and passive scalar transport in row-organized canopies. Agriculture and Forest Meterology. https://doi.org/10.1016/j.agrformet.2024.109919.

Open access and reproducibility in plant pathology research: Guidelines and best practices - (Peer Reviewed Journal)
Grünwald, N.J., Bock, C.H., Chang, J.H., Alves De Souza, A., Del Ponte, E.M., Du Toit, L.J., Dorrance, A.E., Dung, J., Gent, D.H., Goss, E.M., Lowe-Power, T., Madden, L.V., Martin, F.N., Mcdowell, J., Naegele, R.P., Potnis, N., Quesada-Ocampo, L.M., Sundin, G.W., Thiessen, L., Vinatzer, B.A., Zeng, Q. 2024. Open access and reproducibility in plant pathology research: Guidelines and best practices. Phytopathology. https://doi.org/10.1094/PHYTO-12-23-0483-IA.

Multiplex PCR assay for detection and identification of Gnomoniopsis idaeicola, the causal agent of blackberry collapse - (Peer Reviewed Journal)
Stockwell, V.O., Shaffer, B.T. 2024. Multiplex PCR assay for detection and identification of Gnomoniopsis idaeicola, the causal agent of blackberry collapse. Plant Health Progress. https://doi.org/10.1094/PHP-09-23-0080-BR.

Climatic variability, spatial heterogeneity and the presence of multiple hosts drive the population structure of the pathogen Phytophthora ramorum and the epidemiology of Sudden Oak Death - (Peer Reviewed Journal)
Kozanitas, M., Knaus, B.J., Tabima, J.F., Grünwald, N.J., Garbelotto, M. 2024. Climatic variability, spatial heterogeneity and the presence of multiple hosts drive the population structure of the pathogen Phytophthora ramorum and the epidemiology of Sudden Oak Death. Ecography. 2024:e07012. https://doi.org/10.1111/ecog.07012.

Metabarcoding for plant pathologists - (Review Article)
Sudermann, M., Foster, Z.S., Chang, J., Grünwald, N.J. 2023. Metabarcoding for plant pathologists. Canadian Journal of Plant Pathology. 46(2):146-160. https://doi.org/10.1080/07060661.2023.2290041.

It’s a trap! Exploring the application of rotating-arm impaction samplers in plant pathology - (Peer Reviewed Journal)
Check, J., Harkness, R., Heger, L., Chilvers, M.I., Mahaffee, W.F., Sakalidis, M.L., Miles, T. 2024. It’s a trap! Exploring the application of rotating-arm impaction samplers in plant pathology. Plant Disease. https://doi.org/10.1094/PDIS-10-23-2096-FE .

Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics - (Peer Reviewed Journal)
Stockwell, V.O., Kaluzna, M., Prokic, A., Obradovic, A., Pothier, J., Weldon, W. 2023. Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. Frontiers in Plant Science. 14:1254107. https://doi.org/10.3389/fpls.2023.1254107.

Fungicide use patterns in select United States wine grape production regions - (Peer Reviewed Journal)
Oliver, C., Cooper, M., Lewis Ivey, M., Brannen, P., Miles, T., Lowder, S., Mahaffee, W.F., Moyer, M. 2024. Fungicide use patterns in select United States wine grape production regions. Plant Disease. https://doi.org/10.1094/PDIS-04-23-0798-RE.

Contribution of native plasmids of Pantoea vagans C9-1 to epiphytic fitness and fire blight management on apple and pear flowers and fruits - (Peer Reviewed Journal)
Stockwell, V.O., Klein-Gordon, J.M., Johnson, K.B., Loper, J.E. 2023. Contribution of native plasmids of Pantoea vagans C9-1 to epiphytic fitness and fire blight management on apple and pear flowers and fruits. Phytopathology. https://apsjournals.apsnet.org/doi/10.1094/PHYTO-04-23-0144-SA.

High quality genome of the tree pathogen Phytophthora plurivora - a novel resource for epidemiological research - (Peer Reviewed Journal)
Tsyka, T., Mishra, B., Ploch, S., Alcala-Briseno, R.I., Prospero, S., Grunwald, N.J., Thines, M. 2023. High quality genome of the tree pathogen Phytophthora plurivora - a novel resource for epidemiological research. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-05-23-0065-A.

A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology - (Peer Reviewed Journal)
Zaccaron, A.Z., Neill, T.M., Corcoran, J., Mahaffee, W.F., Stergiopoulos, I. 2023. A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology. mBio. Article e00645-23. https://doi.org/10.1128/mbio.00645-23.

Development of a PNA-LNA-LAMP assay to detect a SNP associated with QoI resistance in Erysiphe necator - (Peer Reviewed Journal)
Sharma, N., Neill, T.M., Yang, H., Oliver, C., Mahaffee, W.F., Naegele, R.P., Moyer, M., Miles, T. 2023. Development of a PNA-LNA-LAMP assay to detect a SNP associated with QoI resistance in Erysiphe necator. Plant Disease. https://doi.org/10.1094/PDIS-09-22-2027-RE.

Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora x cambivora - (Peer Reviewed Journal)
Mullett, M., Van Poucke, K., Haegeman, A., Focquet, F., Cauldron, N., Knaus, B., Horta Jung, M., Kageyama, K., Hieno, A., Masuja, H., Uematsu, S., Webber, J., Brasier, C.M., Bakonyi, J., Heungens, K., Grunwald, N.J., Jung, T. 2023. Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora x cambivora. IMA Fungus. 14. Article 4. https://doi.org/10.1186/s43008-023-00109-6.

Multiplex PCR assay for rapid identification of Monilinia rubi, the causal agent of dry-berry disease of caneberries - (Peer Reviewed Journal)
Weldon, W., McGhee, G., DeLong, J.A., Stockwell, V.O. 2023. Multiplex PCR assay for rapid identification of Monilinia rubi, the causal agent of dry-berry disease of caneberries. Plant Health Progress. https://doi.org/10.1094/PHP-09-22-0095-BR.

Whole genome sequencing-based tracing of a 2022 introduction and outbreak of Xanthomonas hortorum pv. pelargonii - (Peer Reviewed Journal)
Bocardo, F.S., Weisberg, A.J., Riutta, E., Kilday, K., Bonkoswki, J.C., Cresswell, T., Daughtrey, M.L., Rane, K., Grunwald, N.J., Chang, J.H., Putnam, M.L. 2022. Whole genome sequencing-based tracing of a 2022 introduction and outbreak of Xanthomonas hortorum pv. pelargonii. Phytopathology. https://doi.org/10.1094/PHYTO-09-22-0321-R.

Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families - (Peer Reviewed Journal)
Cox, M.P., Guo, Y., Winter, D.J., Sen, D., Cauldron, N.C., Shiller, J., Bradley, E.L., Ganley, A.R., Gerth, M.L., Lacey, R.F., McDougal, R.L., Panda, P., Williams, N.M., Grunwald, N.J., Mesarich, C.H., Bradshaw, R.E. 2022. Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families. Frontiers in Microbiology. 13. Article 1038444. https://doi.org/10.3389/fmicb.2022.1038444.