Where to Invest Project Efforts for Greater Benefit: A Framework for Management Performance Mapping with Examples for Potato Seed Health.

Policymakers and donors often need to identify the locations where technologies are most likely to have important effects, to increase the benefits from agricultural development or extension efforts. Higher-quality information may help to target the high-benefit locations, but often actions are needed with limited information. The value of information (VOI) in this context is formalized by evaluating the results of decision making guided by a set of specific information compared with the results of acting without considering that information. We present a framework for management performance mapping that includes evaluating the VOI for decision making about geographic priorities in regional intervention strategies, in case studies of Andean and Kenyan potato seed systems. We illustrate the use of recursive partitioning, XGBoost, and Bayesian network models to characterize the relationships among seed health and yield responses and environmental and management predictors used in studies of seed degeneration. These analyses address the expected performance of an intervention based on geographic predictor variables. In the Andean example, positive selection of seed from asymptomatic plants was more effective at high altitudes in Ecuador. In the Kenyan example, there was the potential to target locations with higher technology adoption rates and with higher potato cropland connectivity, i.e., a likely more important role in regional epidemics. Targeting training to high management performance areas would often provide more benefits than would random selection of target areas. We illustrate how assessing the VOI can contribute to targeted development programs and support a culture of continuous improvement for interventions.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Effective Altruism as an Ethical Lens on Research Priorities.

Effective altruism is an ethical framework for identifying the greatest potential benefits from investments. Here, we apply effective altruism concepts to maximize research benefits through identification of priority stakeholders, pathosystems, and research questions and technologies. Priority stakeholders for research benefits may include smallholder farmers who have not yet attained the minimal standards set out by the United Nations Sustainable Development Goals; these farmers would often have the most to gain from better crop disease management, if their management problems are tractable. In wildlands, prioritization has been based on the risk of extirpating keystone species, protecting ecosystem services, and preserving wild resources of importance to vulnerable people. Pathosystems may be prioritized based on yield and quality loss, and also factors such as whether other researchers would be unlikely to replace the research efforts if efforts were withdrawn, such as in the case of orphan crops and orphan pathosystems. Research products that help build sustainable and resilient systems can be particularly beneficial. The "value of information" from research can be evaluated in epidemic networks and landscapes, to identify priority locations for both benefits to individuals and to constrain regional epidemics. As decision-making becomes more consolidated and more networked in digital agricultural systems, the range of ethical considerations expands. Low-likelihood but high-damage scenarios such as generalist doomsday pathogens may be research priorities because of the extreme potential cost. Regional microbiomes constitute a commons, and avoiding the "tragedy of the microbiome commons" may depend on shifting research products from "common pool goods" to "public goods" or other categories. We provide suggestions for how individual researchers and funders may make altruism-driven research more effective.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Summary Measures of Predictive Power Associated with Logistic Regression Models of Disease Risk.

For an ordinary least-squares regression model, the coefficient of determination (R2) describes the proportion (or percentage) of variance of the response variable explained by the model, and is a widely accepted summary measure of predictive power. A number of R2-analogues are available as summary measures of predictive power associated with logistic regression models, including models of disease risk. Tjur's R2 and McFadden's R2 are of particular interest in this context. Both of these metrics have transparent derivations, which reveal that they apply to different aspects of model evaluation. Tjur's R2 is a measure of separation between (known) actual states (e.g., gold standard determinations of "healthy" or "diseased" status) whereas McFadden's R2 is a measure of separation between predicted states (e.g., forecasts of disease status based on models of disease risk). This clarifies their interpretation in the context of evaluation of logistic regression models of disease risk. In addition, versions of both Tjur's R2 and McFadden's R2 may be obtained from analyses of disease risk that are not preceded by logistic regression analysis. Tjur's R2 and McFadden's R2 are shown to be useful, distinct summary measures of predictive power for epidemiological models of disease risk.

Network Analysis: A Systems Framework to Address Grand Challenges in Plant Pathology.

Plant pathology must address a number of challenges, most of which are characterized by complexity. Network analysis offers useful tools for addressing complex systems and an opportunity for synthesis within plant pathology and between it and relevant disciplines such as in the social sciences. We discuss applications of network analysis, which ultimately may be integrated together into more synthetic analyses of how to optimize plant disease management systems. The analysis of microbiome networks and tripartite phytobiome networks of host-vector-pathogen interactions offers promise for identifying biocontrol strategies and anticipating disease emergence. Linking epidemic network analysis with social network analysis will support strategies for sustainable agricultural development and for scaling up solutions for disease management. Statistical tools for evaluating networks, such as Bayesian network analysis and exponential random graph models, have been underused in plant pathology and are promising for informing strategies. We conclude with research priorities for network analysis applications in plant pathology.

Spatiotemporal Patterns in the Airborne Dispersal of Spinach Downy Mildew.

Downy mildew is the most devastating disease threatening sustainable spinach production, particularly in the organic sector. The disease is caused by the biotrophic oomycete pathogen Peronospora effusa, and the disease results in yellow lesions that render the crop unmarketable. In this study, the levels of DNA from airborne spores of P. effusa were assessed near a field of susceptible plants in Salinas, CA during the winter months of 2013-14 and 2014/15 using rotating-arm impaction spore-trap samplers that were assessed with a species-specific quantitative polymerase chain reaction (qPCR) assay. Low levels of P. effusa DNA were detectable from December through February in both winters but increased during January in both years, in correlation with observed disease incidence; sharp peaks in P. effusa DNA detection were associated with the onset of disease incidence. The incidence of downy mildew in the susceptible field displayed logistic-like dynamics but with considerable interseason variation. Analysis of the area under the disease progress curves suggested that the 2013-14 epidemic was significantly more severe than the 2014-15 epidemic. Spatial analyses indicated that disease incidence was dependent within an average range of 5.6 m, approximately equivalent to the width of three planted beds in a typical production field. The spatial distribution of spores captured during an active epidemic most closely fit a power-law distribution but could also be fit with an exponential distribution. These studies revealed two important results in the epidemiology of spinach downy mildew in California. First, they demonstrated the potential of impaction spore-trap samplers linked with a qPCR assay for indicating periods of high disease risk, as well as the detection of long-distance dispersal of P. effusa spores. Second, at the scale of individual crops, a high degree of spatial aggregation in disease incidence was revealed.

Season-Long Dynamics of Spinach Downy Mildew Determined by Spore Trapping and Disease Incidence.

Peronospora effusa is an obligate oomycete that causes downy mildew of spinach. Downy mildew threatens sustainable production of fresh market organic spinach in California, and routine fungicide sprays are often necessary for conventional production. In this study, airborne P. effusa spores were collected using rotating arm impaction spore trap samplers at four sites in the Salinas Valley between late January and early June in 2013 and 2014. Levels of P. effusa DNA were determined by a species-specific quantitative polymerase chain reaction assay. Peronospora effusa was detected prior to and during the growing season in both years. Nonlinear time series analyses on the data suggested that the within-season dynamics of P. effusa airborne inoculum are characterized by a mixture of chaotic, deterministic, and stochastic features, with successive data points somewhat predictable from the previous values in the series. Analyses of concentrations of airborne P. effusa suggest both an exponential increase in concentration over the course of the season and oscillations around the increasing average value that had season-specific periodicity around 30, 45, and 75 days, values that are close to whole multiples of the combined pathogen latent and infectious periods. Each unit increase in temperature was correlated with 1.7 to 6% increased odds of an increase in DNA copy numbers, while each unit decrease in wind speed was correlated with 4 to 12.7% increased odds of an increase in DNA copy numbers. Disease incidence was correlated with airborne P. effusa levels and weather variables, and a receiver operating characteristic curve analysis suggested that P. effusa DNA copy numbers determined from the spore traps nine days prior to disease rating could predict disease incidence.

First Report of Diplodia seriata Causing Pear Branch Canker Dieback in California.

California produces 26% of the United States pear crop on approximately 5,600 ha. A survey of seven northern California pear orchards (Pyrus communis cv. Bartlett) in summer 2010 revealed the presence of wedge-shaped cankers on 2- to 5-cm diameter branches, equating to 1- to 3-year-old wood. Many of the observed cankers occurred near pruning wounds, and there was decreased foliation on infected branches. Infected wood was surface disinfected with 95% ethanol and briefly flamed. After removing bark, small sections of diseased tissue were plated onto 4% potato dextrose agar (PDA) amended with 0.01% tetracycline and placed on the lab bench at 22°C until fungal growth emerged. Fungal colonies that were consistently isolated were transferred to fresh PDA using hyphal tip isolation. Fungal colonies were dark brown to gray with aerial mycelium and formed pycnidia after 15 days of incubation at 22°C. Conidia were brown, oval to oblong, and measured (16.5-) 20 to 24 (-26) × (7.5) 8.75 to 11 (-12.5) µm (n = 50). DNA from 14- to 21-day-old colonies was extracted and sequences of the rDNA internal transcribed spacer region and part of the ß-tubulin gene were amplified using primers ITS4/ITS5 and Bt2a/Bt2b, respectively (2). The DNA sequences of fungal isolates from California showed 99 to 100% homology with the ex-type Diplodia seriata De Not. (1) CBS112555 deposited in GenBank. DNA sequences from three California isolates were submitted to GenBank with accession numbers KC937062, KC937065, KF481957, KF481598, KF481959, and KF481960. Pathogenicity tests were performed in March 2011 on 3-year-old Bartlett pear trees planted at an experimental farm in Davis, CA. A single, circular, 2-cm pruning wound at the top of the trunk was inoculated on each of three single-tree replications using 2-cm mycelial plugs from 14-day-old colonies growing on PDA. After inoculation, mycelial plugs were covered and sealed with Parafilm and aluminum foil for the duration of the trial. Three control trees were inoculated using sterile PDA plugs. Twelve months after inoculation, UCD103 and UCD105 were consistently re-isolated from the margin between necrotic and healthy tissue using the same methods described for the original isolation, and UCD102 was re-isolated in two out of three plants. The average lesion lengths of UCD102, UCD103, UCD105, and control plants were 12.5, 17.3, 23, and 1 mm, respectively. Control lesions were short and sterile, and seemed to be a physiological reaction from the plant. A second pathogenicity test was completed in 5 months beginning in June 2012. UCD105 was consistently re-isolated, and UCD102 and UCD103 were re-isolated in two out of three plants. The average lesion lengths for UCD102, UCD103, UCD105, and control plants were 2, 3, 5, and 1 mm, respectively. Compared to grapevine (Vitis vinifera), the pathogen grows more slowly in pear tissue under natural conditions. To our knowledge, this is the first report describing D. seriata as a causal agent of pear branch canker in California. Canker diseases can reduce the lifespan of perennial plants, ultimately leading to long term economic losses for growers (3). References: (1) A. J. L. Phillips et al. Fungal Diversity 25:141, 2007. (2) J. R. Urbez-Torres et al. Plant Dis. 90:1490, 2006. (3) J. R. Urbez-Torres and W. D. Gubler. Plant Dis. 93:584, 2009.

First Report of Cytospora punicae Causing Wood Canker and Branch Dieback of Pomegranate (Punica granatum) in the United States.

Pomegranates (Punica granatum L.) are an expanding industry in the United States with California growing approximately 32,000 acres with a crop value of over $155 million (1). During June and July of 2012, we observed severe limb and branch dieback in pomegranate orchards cv. Wonderful located in Contra Costa, Kings, and Kern counties of California. Disease symptoms included yellowing of leaves, branch and limb dieback, wood lesions, and canker formation. Dark brown Cytospora-like cultures were consistently isolated from active cankers on potato dextrose agar (PDA) amended with 100 mg l-1 tetracycline hydrochloride. Three isolates (UCCE1223, UCCE1233, and UCCE1234) representative of each orchard were sub-cultured onto PDA and incubated at 22°C under fluorescent intermittent light (12 h light, 12 h dark). Fungal colonies had whitish mycelia that turned olive green to dark brown with maturity and formed globose and dark brown pycnidia after 12 days. Conidia were hyaline, aseptate, allantoid, and (4) 4.5 to 5 (6) × (1) 1.5 (2) µm (n = 180). Pycnidia formed in culture measured (250) 350 to 475 (650) µm in diameter (n = 40). Identification of the isolates was confirmed by sequence comparison of the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rDNA and part of the translation elongation factor 1-α gene (EF1-α) with sequences available in GenBank. Consensus sequences of both genes of all isolates showed 99% homology to the species Cytospora punicae Sacc. (2). All sequences were deposited in GenBank (Accession Nos. KJ621684 to 89). Pathogenicity of the isolates was determined by branch inoculation. In December 2012, 3-year-old branches of P. granatum cv. Wonderful were inoculated by placing 5-mm-diameter mycelium plugs from the growing margin of 14-day-old PDA cultures in fresh wounds made with a 5-mm-diameter cork-borer. Eight branches per isolate were inoculated on eight different trees. Eight control branches were inoculated with non-colonized PDA agar plugs. Inoculations were covered with Vaseline and wrapped with Parafilm to retain moisture. Branches were harvested in August 2013 and examined for canker development and the extent of vascular discoloration spreading downward and upward from the inoculation point. Isolations from the edge of discolored tissue were conducted to fulfill Koch's postulates. C. punicae was re-isolated from 100% of the inoculated branches. Total length of vascular discoloration averaged 30.2 mm in branches inoculated with the three C. punicae isolates and 9 mm in the control branches. No fungi were isolated from the slightly discolored tissue of the controls. To our knowledge, this is the first report of C. punicae as a fungal trunk pathogen of pomegranate trees in the United States. References: (1) California County Agricultural Commissioners' Data, 2010 Crop Year. USDA NASS California field office, retrieved from http://www.nass.usda.gov/Statistics_by_State/California/ Publications/AgComm/201010cactb00.pdf , 2011. (2) P. A. Saccardo. Sylloge Fungorum 3:256, 1884.