@article{standish_gongora-castillo_bowman_childs_tian_quesada-ocampo_2022, title={Development, Validation, and Utility of Species-Specific Diagnostic Markers for Detection of Peronospora belbahrii}, volume={7}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-09-21-0393-R}, DOI={10.1094/PHYTO-09-21-0393-R}, abstractNote={ Peronospora belbahrii is an oomycete and the cause of basil downy mildew, one of the most destructive diseases affecting basil production worldwide. Disease management is challenging due to wind-dispersed sporangia and contaminated seed; therefore, identifying P. belbahrii in seed lots before sale or planting or in the field before symptoms develop could allow for timely deployment of disease management strategies. In this study, a draft genome assembly and next-generation sequencing reads for P. belbahrii, as well as publicly available DNA-seq and RNA-seq reads of several other downy mildew pathogens, were incorporated into a bioinformatics pipeline to predict P. belbahrii-specific diagnostic markers. The specificity of each candidate marker was validated against a diverse DNA collection of P. belbahrii, host tissue, and related oomycetes using PCR. Two species-specific markers were identified and used as templates to develop a highly sensitive probe-based real-time quantitative PCR (qPCR) assay that could detect P. belbahrii in leaf tissue and seed samples. Both markers were capable of reliably detecting as low as 500 fg/µl of P. belbahrii genomic DNA and as few as 10 sporangia. The qPCR assay was then validated with seed samples collected from a basil cultivar experiment. In total, 48 seed samples were collected and tested; P. belbahrii was detected in samples of all cultivars at estimated concentrations of 600 fg/µl up to 250 pg/µl and at as few as 10 sporangia up to >1,000 sporangia. The markers and assays are valuable for diagnostics and identifying P. belbahrii-contaminated seed lots to mitigate the effects of future basil downy mildew epidemics. }, journal={PHYTOPATHOLOGY}, author={Standish, J. R. and Gongora-Castillo, E. and Bowman, M. J. and Childs, K. L. and Tian, M. and Quesada-Ocampo, L. M.}, year={2022}, month={Jul} }
 @misc{salcedo_purayannur_standish_miles_thiessen_quesada-ocampo_2021, title={Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics}, volume={10}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants10030435}, DOI={10.3390/plants10030435}, abstractNote={Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.}, number={3}, journal={PLANTS-BASEL}, publisher={MDPI AG}, author={Salcedo, Andres F. and Purayannur, Savithri and Standish, Jeffrey R. and Miles, Timothy and Thiessen, Lindsey and Quesada-Ocampo, Lina M.}, year={2021}, month={Mar} }
 @article{rahman_standish_d'arcangelo_quesada-ocampo_2021, title={Clade-Specific Biosurveillance of Pseudoperonospora cubensis Using Spore Traps for Precision Disease Management of Cucurbit Downy Mildew}, volume={111}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-06-20-0231-R}, DOI={10.1094/PHYTO-06-20-0231-R}, abstractNote={ Pseudoperonospora cubensis is an obligate oomycete and cause of cucurbit downy mildew (CDM), the most destructive foliar disease affecting cucurbit hosts. Annual epidemics develop throughout the United States as windborne sporangia travel great distances and survive prolonged exposure to solar radiation. Recent genomic evidence suggests that P. cubensis isolates display host adaptation based on their respective clade. Early detection is key for fungicide application timing, and identification of the host-adapted clade provides information on the risk of infection for specific cucurbit crops. In this study, a multiplex quantitative PCR assay was developed based on species- and clade-specific nuclear genomic markers. The assay detected as few as 10 sporangia or DNA at 100 fg/ml for both clades and was validated in the field by deploying rotorod spore samplers in cucurbit sentinel plots located at two research stations in North Carolina. Using this assay, sporangia DNA was detected in spore trap sampling rods before signs of P. cubensis or CDM symptoms were observed in the sentinel plots. Both clade 1 and clade 2 DNA were detected in late-season cucumber and watermelon plots but only clade 2 DNA was detected in the early-season cucumber plots. These results will significantly improve disease management of CDM by monitoring inoculum levels to determine the cucurbit crops at risk of infection throughout each growing season. }, number={2}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Rahman, A. and Standish, J. R. and D'Arcangelo, K. N. and Quesada-Ocampo, L. M.}, year={2021}, month={Feb}, pages={312–320} }
 @article{miller_standish_quesada-ocampo_2020, title={Sensitivity of Fusarium oxysporum f. sp. niveum to Prothioconazole and Pydiflumetofen In Vitro and Efficacy for Fusarium Wilt Management in Watermelon}, volume={21}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-08-19-0056-RS}, abstractNote={ Field experiments were conducted in 2015 and 2016 to determine the effects of drench or drench-plus-foliar applications of prothioconazole and pydiflumetofen on Fusarium wilt (caused by Fusarium oxysporum f. sp. niveum; FON) of watermelon (Citrullus lanatus var. lanatus). In both years, all fungicide treatments reduced final disease incidence, final severity, and area under the disease progress curve, regardless of application rate or method. Yield data were collected in 2016, and both number and weight of marketable fruit were greatest in plots treated with pydiflumetofen as a drench-plus-foliar application at either application rate. Additional experiments were conducted to characterize sensitivity distributions of 48 isolates of FON from North Carolina to prothioconazole and pydiflumetofen. Mean prothioconazole EC50 values ranged from 0.10 to 0.55 µg/ml, and mean pydiflumetofen EC50 values ranged from 0.34 to 1.88 µg/ml. The results presented here validate pydiflumetofen as an effective management option for Fusarium wilt of watermelon, confirm previously observed efficacy of prothioconazole, and provide current evidence of pathogen sensitivity to these fungicides in North Carolina. }, number={1}, journal={PLANT HEALTH PROGRESS}, author={Miller, Nathan F. and Standish, Jeffrey R. and Quesada-Ocampo, Lina M.}, year={2020}, pages={13–18} }