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.)

Heat-tree: Cross-platform software for interactive and embeddable phylogenetic tree visualization and editing - (Pre-print Publication)
Foster, Z.S.L., Chang, J.H., Grünwald, N.J. 2026. Heat-tree: Cross-platform software for interactive and embeddable phylogenetic tree visualization and editing. ArXiv. https://doi.org/10.48550/arXiv.2605.01109.

Fungicide sensitivity profiles of Botrytis isolates from blueberry and red raspberry fields in Washington and Oregon - (Peer Reviewed Journal)
Baral, R., DeLong, J.A., Steele, M.E., Stockwell, V.O., Mattupalli, C. 2026. Fungicide sensitivity profiles of Botrytis isolates from blueberry and red raspberry fields in Washington and Oregon. Plant Disease. https://doi.org/10.1094/PDIS-01-26-0162-RE.

Differential responses of Botrytis isolates to Pristine, Luna Tranquility, Switch, and their active ingredients - (Peer Reviewed Journal)
Baral, R., Steele, M.E., DeLong, J.A., Stockwell, V.O., Mattupalli, C. 2026. Differential responses of Botrytis isolates to Pristine, Luna Tranquility, Switch, and their active ingredients. Plant Disease. https://doi.org/10.1094/PDIS-12-25-2509-SC.

Characterizing aerial dispersal of Xanthomonas hortorum pv. carotae in central Oregon carrot seed production systems during harvest - (Peer Reviewed Journal)
Baldino, K.D., Huckins, M.K., Mahaffee, W.F., Chang, E., Stoll, R., Pardyjak, E.R., Scott, J.C., Dung, J.K. 2026. Characterizing aerial dispersal of Xanthomonas hortorum pv. carotae in central Oregon carrot seed production systems during harvest. Plant Disease. https://doi.org/10.1094/PDIS-09-25-1995-RE.

Cryptostroma corticale, a plant pathogen associated with a human immune respiratory syndrome displaying mixed viral infections of mycoviruses - (Peer Reviewed Journal)
Alcalá Briseño, R. I., Feau, N., Gomez-Gallego, M., Muller, E., Marcais, B., Aguayo, J., Grünwald, N.J., LeBoldus, J.M. 2026. Cryptostroma corticale, a plant pathogen associated with a human immune respiratory syndrome displaying mixed viral infections of mycoviruses. Virology. 618. Article 110815. https://doi.org/10.1016/j.virol.2026.110815.

The poplar pathogen Sphaerulina musiva has a dynamic genome architecture marked by chromosomal inversions and changes in transposable element abundance - (Peer Reviewed Journal)
Zaccaron, A.Z., Lassagne, A., Søndreli, K.L., Sudermann, M.A., Alcalá Briseño, R.I., Grünwald, N.J., Weisberg, A.J., LeBoldus, J.M. 2026. The poplar pathogen Sphaerulina musiva has a dynamic genome architecture marked by chromosomal inversions and changes in transposable element abundance. Microbial Genomics. 12(1):001603. https://doi.org/10.1099/mgen.0.001603.

Identification and survey of new and emerging viruses infecting blueberry in the Pacific Northwest - (Peer Reviewed Journal)
Topham, K., Alvarez-Quinto, R., Stockwell, V.O., Grinstead, S.C., Mollov, D.S. 2025. Identification and survey of new and emerging viruses infecting blueberry in the Pacific Northwest. Acta horticulturae. 1440:157-162. https://doi.org/10.17660/ActaHortic.2025.1440.22.

Genomic and biological characterization of blackberry calico virus - (Peer Reviewed Journal)
Fager, D., Stockwell, V.O., Grinstead, S.C., Mollov, D. 2025. Genomic and biological characterization of blackberry calico virus. Plant Disease. https://doi.org/10.1094/PDIS-06-25-1232-RE.

John Matthew McDowell: A Visionary Leader in Molecular Oomycete - Plant Interactions and a Wonderful Mentor and Friend to Many - (Other)
Anderson, R.G., Chang, J.H., Dangl, J.L., Kinkeloo, K., Donofrio, N., Eulgem, T., Grunwald, N.J., Long, T., Mukhtar, M.S., Sonawali, U., Guillaume, P., Sherif, S.M., Mahmut, T., Winkel, B., Vinatzer, B.A. 2025. John Matthew McDowell: A Visionary Leader in Molecular Oomycete - Plant Interactions and a Wonderful Mentor and Friend to Many. Molecular Plant-Microbe Interactions. https://doi.org/10.1094/MPMI-06-25-0072-LE.

Genomic demography predicts community dynamics in a temperate montane forest - (Peer Reviewed Journal)
O’Dwyer, J.P., Lutz, J.A., Schappe, T., Alegre, D., Black, A.N., Grünwald, N.J., Jones, F. 2025. Genomic demography predicts community dynamics in a temperate montane forest. Science. 389(6766). Article eadu6396. https://doi.org/10.1126/science.adu6396.

Phytophthora cinnamomi populations affecting avocado in California show low differentiation, phenotypic variability, and introductions from Mexico - (Peer Reviewed Journal)
Shands, A.C., Mondragón-Flores, A., Valencia, V., Hua, V., Cauldron, N.C., Grünwald, N.J., Fernández-Pavía, S.P., Manosalva, P.M. 2025. Phytophthora cinnamomi populations affecting avocado in California show low differentiation, phenotypic variability, and introductions from Mexico. Molecular Plant-Microbe Interactions. 38(5):708-721. https://doi.org/10.1094/MPMI-08-24-0101-R.

Demulticoder: An R package for the simultaneous analysis of multiplexed metabarcodes - (Peer Reviewed Journal)
Sudermann, M.A., Foster, Z.S., Dawson, S., Phan, H., Fieland, V., Martin, F.N., Chang, J., Grunwald, N.J. 2025. Demulticoder: An R package for the simultaneous analysis of multiplexed metabarcodes. Phytopathology. https://doi.org/10.1094/PHYTO-02-25-0043-FI.

Population genomic analysis of two independent clonal invasions of the sudden oak death pathogen into one forest - (Peer Reviewed Journal)
Cauldron, N.C., Daniels, H.A., LeBoldus, J.M., Grünwald, N.J. 2025. Population genomic analysis of two independent clonal invasions of the sudden oak death pathogen into one forest. Phytopathology. 115(10):1382-1391. https://doi.org/10.1094/PHYTO-10-24-0329-FI.

Soil temperature and moisture conditions affect the recovery and sporulation capacity of Phytophthora ramorum from infested Rhododendron leaf disks - (Peer Reviewed Journal)
Peterson, E.K., Grünwald, N.J., Parke, J.L. 2025. Soil temperature and moisture conditions affect the recovery and sporulation capacity of Phytophthora ramorum from infested Rhododendron leaf disks. Journal of Phytopathology. 115(8):968-977. https://doi.org/10.1094/PHYTO-02-25-0056-R.

Molecular characterization of Botrytis isolates from blueberries and red raspberries in the Pacific Northwest with resistance to SDHI fungicides - (Peer Reviewed Journal)
Baral, R., Delong, J.A., Mcghee, G., Stockwell, V.O., Mattupalli, C. 2025. Molecular characterization of Botrytis isolates from blueberries and red raspberries in the Pacific Northwest with resistance to SDHI fungicides. Plant Disease. https://doi.org/10.1094/PDIS-12-24-2576-SC.

The perils of naïve use of open source data: A comment on “Spatiotemporal distribution of sudden oak death in the US and Europe” - (Peer Reviewed Journal)
Frankel, S.J., Garbelotto, M., Jones, C., Grunwald, N.J., Venette, R. 2025. The perils of naïve use of open source data: A comment on “Spatiotemporal distribution of sudden oak death in the US and Europe”. Agricultural and Forest Meteorology. 368. Article 110553. https://doi.org/10.1016/j.agrformet.2025.110553.

First report of Phytophthora ramorum causing leaf spot on Arbutus × reyorum ‘Marina’ in the United States - (Peer Reviewed Journal)
Deuitch, E.T., Rooney-Latham, S., Blomquist, C.L., Belisle, W.H., Soriano, M.C., Grunwald, N.J. 2025. First report of Phytophthora ramorum causing leaf spot on Arbutus × reyorum ‘Marina’ in the United States. Plant Disease. 109(5):1183. https://doi.org/10.1094/PDIS-11-24-2379-PDN.

Global trends in research on biological control agents of Drosophila suzukii: A systematic review - (Peer Reviewed Journal)
Abeijon, L.M., Birkhan, J.D., Lee, J.C., Ovruski, S.M., Garcia, F.R. 2025. Global trends in research on biological control agents of Drosophila suzukii: A systematic review. Insects. 16(2). Article 133. https://doi.org/10.3390/insects16020133.

Intraspecific variation and recent loss of ancient, conserved effector genes in the sudden oak death pathogen Phytophthora ramorum - (Peer Reviewed Journal)
Cauldron, N.C., Press, C.M., Weisberg, A.J., Horta Jung, M., Corcobado, T., Webber, J.F., Kageyama, K., Hieno, A., Masuya, H., Uematsu, S., Scanu, B., Brasier, C.M., Jung, T., Chang, J.H., Grunwald, N.J. 2025. Intraspecific variation and recent loss of ancient, conserved effector genes in the sudden oak death pathogen Phytophthora ramorum. Molecular Plant-Microbe Interactions. 38(3):440-453. https://doi.org/10.1094/MPMI-10-24-0131-R.

Canker and dieback of Alnus rubra is caused by Lonsdalea quercina - (Peer Reviewed Journal)
Iruegas-Bocardo, F., Sutton, W., Buchanan, R.A., Grunwald, N.J., Chang, J.H., Putnam, M.L. 2024. Canker and dieback of Alnus rubra is caused by Lonsdalea quercina. Phytopathology. 115(2):112-116. https://doi.org/10.1094/phyto-06-24-0192-sc.

Genomic characterization and survey of a second luteovirus infecting blueberry - (Peer Reviewed Journal)
Topham, K., Stockwell, V.O., Grinstead, S.C., Mollov, D.S. 2024. Genomic characterization and survey of a second luteovirus infecting blueberry. Virus Research. 350. Article 199480. https://doi.org/10.1016/j.virusres.2024.199480.

A survey of cranberry fruit rots in commercial production beds in Oregon and Washington - (Peer Reviewed Journal)
Valentine, D.C., Bouska, C., Stockwell, V.O. 2024. A survey of cranberry fruit rots in commercial production beds in Oregon and Washington. Frontiers in Plant Science. 15. Article 1457320. https://doi.org/10.3389/fpls.2024.1457320.

Managing fruit rot diseases of Vaccinium corymbosum - (Review Article)
Neugebauer, K.A., Mattupalli, C., Hu, M., Oliver, J.E., VanderWeide, J., Lu, Y., Sullivan, K., Stockwell, V.O., Oudemans, P., Miles, T.D. 2024. Managing fruit rot diseases of Vaccinium corymbosum. Frontiers in Plant Science. 15. Article 1428769. https://doi.org/10.3389/fpls.2024.1428769.

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., Tupper, A., 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). Article 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)
Wong, A., Gadoury, D., Mahaffee, W.F. 2024. Evaluation of germicidal UV-C light for suppression of grape powdery mildew and Botrytis bunch rot in Western Oregon. Plant Disease. 108(9):2894-2905. https://doi.org/10.1094/PDIS-02-24-0279-RE.

It’s a trap! Part II: 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! Part II: An approachable guide to constructing and using rotating-arm air samplers. Plant Disease. 108(7):1923-1936. 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)
Valentine, D.C., Shaffer, B.T., McGhee, G., Bouska, C., Stockwell, V.O. 2024. First report of Neofabraea actinidiae causing a cranberry fruit rot in Oregon. Plant Disease. 108(5):1405. https://doi.org/10.1094/PDIS-11-23-2526-PDN.

Old foe, new crop: Neofabraea actinidiae causes a cranberry fruit rot in Oregon and Washington - (Abstract Only)
Valentine, D.C., McGhee, G., Shaffer, B.T., Bouska, C., Stockwell, V.O. 2024. Old foe, new crop: Neofabraea actinidiae causes a cranberry fruit rot in Oregon and Washington [abstract]. American Phytopathological Society Annual Meeting.

Aluminum foils growth of Botrytis and Gnomoniopsis idaeicola - (Abstract Only)
Keller, R., Stockwell, V.O. 2024. Aluminum foils growth of Botrytis and Gnomoniopsis idaeicola [abstract]. American Phytopathological Society Annual Meeting.

Phenotypic and molecular characterization of Botrytis cinerea from blueberry fields in the Pacific Northwest for tolerance of SDHI fungicides - (Abstract Only)
Baral, R., DeLong, J.A., Stockwell, V.O., Mattupalli, C. 2024. Phenotypic and molecular characterization of Botrytis cinerea from blueberry fields in the Pacific Northwest for tolerance of SDHI fungicides [abstract]. American Phytopathological Society Annual Meeting.

Characterization of Botrytis spp. on red raspberries in Northwestern Washington - (Abstract Only)
DeLong, J.A., Mattupalli, C., Stockwell, V.O. 2024. Characterization of Botrytis spp. on red raspberries in Northwestern Washington [abstract]. American Phytopathological Society Annual Meeting.

First report of Phytophthora ramorum causing leaf spots on Cornus capitata (evergreen dogwood) in the United States - (Peer Reviewed Journal)
Belisle, W.H., Rooney-Latham, S., Soriano, M.C., Grunwald, N.J., Blomquist, C.L. 2024. First report of Phytophthora ramorum causing leaf spots on Cornus capitata (evergreen dogwood) in the United States. Plant Disease. 108(4):1119. 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. 349. Article 109919. https://doi.org/10.1016/j.agrformet.2024.109919.

Open access and reproducibility in plant pathology research: Guidelines and best practices - (Peer Reviewed Journal)
Grunwald, 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. 114(5):910-916. 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. 25(2):214-217. 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., Grunwald, 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. Article e07012. https://doi.org/10.1111/ecog.07012.

Metabarcoding for plant pathologists - (Review Article)
Sudermann, M., Foster, Z.S., Chang, J., Grunwald, N.J. 2023. Metabarcoding for plant pathologists. Canadian Journal of Plant Pathology. 46(2):142-160. https://doi.org/10.1080/07060661.2023.2290041.

Krisp: A python package for designing CRISPR and amplification-based diagnostic assays from whole genome data - (Other)
Foster, Z.S., Tupper, A., Press, C.M., Grunwald, N.J. 2023. Krisp: A python package for designing CRISPR and amplification-based diagnostic assays from whole genome data. bioRxiv. 1/1-44. https://doi.org/10.1101/2023.11.16.567433.

It’s a trap! Part I: Exploring the applications of rotating-arm impaction samplers in plant pathology - (Peer Reviewed Journal)
Check, J., Harkness, R., Heger, L., Sakalidis, M.L., Chilvers, M.I., Mahaffee, W.F., Miles, T. 2024. It’s a trap! Part I: Exploring the applications of rotating-arm impaction samplers in plant pathology. Plant Disease. 108(7):1910-1922. https://doi.org/10.1094/PDIS-10-23-2096-FE .

Phyllosphere, front and center: focus on a formerly ‘ecologically neglected’ microbial milieu - (Other)
Leveau, J., Beattie, G., Lindow, S., Mahaffee, W.F. 2023. Phyllosphere, front and center: focus on a formerly ‘ecologically neglected’ microbial milieu. Phytobiomes Journal. 7:140-144. https://doi.org/10.1094/PBIOMES-08-23-0088-E.

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)
Kaluzna, M., Prokic, A., Obradovic, A., Weldon, W., Stockwell, V.O., Pothier, J., 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. 108(1):104-112. 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)
JM Klein-Gordon, KB Johnson, JE Loper, VO Stockwell. 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 113 (12), 2187-2196. https://doi.org/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 an 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 an SNP associated with QoI resistance in Erysiphe necator. Plant Disease. 107(1):3238-3247. 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.