About

Daniel R. Cooley is a Professor of Plant Pathology at the Stockbridge School of Agriculture, University of Massachusetts Amherst. He earned his AB from Harvard College in 1974, his M.S. in Plant & Soil Sciences from the University of Vermont in 1978, and his Ph.D. in Plant Pathology from the University of Massachusetts in 1986. His research focuses on developing sustainable management strategies for diseases affecting economically important temperate fruit crops, particularly apples. His work aims to reduce fungicide use by creating forecast models for disease development and evaluating non-chemical management tactics such as host resistance, cultural modifications, and biological controls. Cooley's research involves collaboration with growers and industry partners to develop integrated pest management practices, especially for organic apple production and diseases like apple scab and sooty blotch and flyspeck. His efforts are directed toward understanding the ecology of the fungi responsible for these diseases to provide environmentally and economically sustainable solutions.

Research topics

• Computer Science
• Environmental science
• Biology
• Water resource management
• Botany
• Engineering
• Geology

Selected publications

• The effects of ozone and Fusarium root and crown rot on the growth and decline of alfalfa, Medicago sativa L.

  Scholarworks (University of Massachusetts Amherst) · 2023-08-15

  articleOpen access1st authorCorresponding

  Plant Pathology

  PublisherDOI

• Center Pivot Irrigation Systems and Where to Find Them: A Deep Learning Approach to Provide Inputs to Hydrologic and Economic Models

  Frontiers in Water · 2021 · 9 citations

  1st authorCorresponding
  • Computer Science
  • Computer Science
  • Water resource management

  Availability and quality of administrative data on irrigation technology varies greatly across jurisdictions. Technology choice, however, will influence the parameters of coupled human-hydrological systems. Equally, changing parameters in the coupled system may drive technology adoption. Here we develop and demonstrate a deep learning approach to locate a particularly important irrigation technology—center pivot irrigation systems—throughout the Ogallala Aquifer. The model does not rely on super computers and thus provides a model for an accessible baseline to train and deploy on other geographies. We further demonstrate that accounting for the technology can improve the insights in both economic and hydrological models.

  PublisherOA PDFDOI

• Toward the Integration of an Attract-and-Kill Approach with Entomopathogenic Nematodes to Control Multiple Life Stages of Plum Curculio (Coleoptera: Curculionidae)

  Insects · 2020 · 13 citations

  • Biology
  • Botany

  has the potential to manage this pest more sustainably in a reduced-spray environment.

  PublisherOA PDFDOI

• Summer pruning of apple: impacts on disease management

  DOAJ (DOAJ: Directory of Open Access Journals) · 2019-09-18 · 13 citations

  articleOpen access1st authorCorresponding

  Pruning, including summer pruning, of apples can have a positive impact on disease management in two basic ways: through removal of dead tissue and inoculum, and through alteration of the canopy microclimate. Summer pruning can also increase diseases if it is done when disease risk is high. However summer pruning is used almost exclusively as a horticultural tool to improve fruit quantity and quality. As orchard planting and training systems have moved from semi-dwarf trees to high-density, fully-dwarf trees, very few summer pruning studies have looked at impacts related to disease, yet summer pruning in high-density systems may have important disease management effects. Growers should avoid summer pruning practices which will increase disease risks, and use those that offer both horticultural and disease management benefits. More research in this area is needed, as cultural components of apple disease management will become increasingly important in sustainable production systems. This review looks at important apple diseases, including apple scab, fire blight, sooty blotch and flyspeck, black rot, white rot, Nectria canker and powdery mildew, and uses dormant pruning studies plus knowledge of the epidemiology of the diseases to suggest ways that summer pruning would be expected to impact disease management.

  PublisherDOI

• Comparative genomics of Spiraeoideae‐infecting <i>Erwinia amylovora</i> strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

  Molecular Plant Pathology · 2017-11-27 · 58 citations

  articleOpen access

  Erwinia amylovora is the causal agent of fire blight, one of the most devastating diseases of apple and pear. Erwinia amylovora is thought to have originated in North America and has now spread to at least 50 countries worldwide. An understanding of the diversity of the pathogen population and the transmission to different geographical regions is important for the future mitigation of this disease. In this research, we performed an expanded comparative genomic study of the Spiraeoideae-infecting (SI) E. amylovora population in North America and Europe. We discovered that, although still highly homogeneous, the genetic diversity of 30 E. amylovora genomes examined was about 30 times higher than previously determined. These isolates belong to four distinct clades, three of which display geographical clustering and one of which contains strains from various geographical locations ('Widely Prevalent' clade). Furthermore, we revealed that strains from the Widely Prevalent clade displayed a higher level of recombination with strains from a clade strictly from the eastern USA, which suggests that the Widely Prevalent clade probably originated from the eastern USA before it spread to other locations. Finally, we detected variations in virulence in the SI E. amylovora strains on immature pear, and identified the genetic basis of one of the low-virulence strains as being caused by a single nucleotide polymorphism in hfq, a gene encoding an important virulence regulator. Our results provide insights into the population structure, distribution and evolution of SI E. amylovora in North America and Europe.

  PublisherOA PDFDOI

• Inclusion of Specialist and Generalist Stimuli in Attract-and-Kill Programs: Their Relative Efficacy in Apple Maggot Fly (Diptera: Tephritidae) Pest Management

  Environmental Entomology · 2016-06-20 · 22 citations

  articleOpen access

  Investigating the chemical ecology of agricultural systems continues to be a salient part of integrated pest management programs. Apple maggot fly, a key pest of apple in eastern North America, is a visual specialist with attraction to host fruit-mimicking cues. These cues have been incorporated into red spherical traps used for both monitoring and behaviorally based management. Incorporating generalist or specialist olfactory cues can potentially increase the overall success of this management system. The primary aim of this study was to evaluate the attractiveness of a generalist olfactory cue, ammonium carbonate, and the specialist olfactory cue, a five-component apple volatile blend, when included as a component of a red attracticidal sphere system. Secondly, we assessed how critical it was to maintain minimal deviation from the optimal, full-round specialist visual stimulus provided by red spheres. Finally, attracticidal spheres were deployed with specialist olfactory cues in commercial apple orchards to evaluate their potential for effective management of apple maggot. Ammonium carbonate did not increase residency, feeding time, or mortality in the laboratory-based trials. Field deployment of specialist olfactory cues increased apple maggot captures on red spheres, while the generalist cue did not. Apple maggot tolerated some deviation from the optimal visual stimulus without reducing captures on red spheres. Attracticidal spheres hung in perimeter trees in orchards resulted in acceptable and statistically identical levels of control compared with standard insecticide programs used by growers. Overall, our study contributes valuable information for developing a reliable attract-and-kill system for apple maggot.

  PublisherOA PDFDOI

• Prevalence of Myclobutanil Resistance and Difenoconazole Insensitivity in Populations of <i>Venturia inaequalis</i>

  Plant Disease · 2015-03-25 · 49 citations

  articleOpen access

  Demethylation inhibitors (DMIs) are a class of single-site fungicides with high levels of protective and curative efficacy against Venturia inaequalis, the causal agent of apple scab. To determine the prevalence of resistance to the DMI fungicide myclobutanil, 3,987 single-lesion conidial V. inaequalis isolates from 141 commercial, research, and baseline orchard populations were examined throughout New England, the mid-Atlantic, and the Midwest from 2004 to 2013. Of these orchard populations, 63% had practical resistance, 13% had reduced sensitivity, and 24% were sensitive to myclobutanil. A sensitivity baseline for the recently introduced DMI fungicide difenoconazole was established to make comparisons with myclobutanil sensitivity in orchard populations. The mean effective concentration of difenoconazole at which mycelial growth was inhibited by 50% (EC 50 ) was determined to be 0.002 μg ml −1 for 44 baseline isolates of V. inaequalis. From 2010 to 2013, 1,012 isolates of V. inaequalis from 37 of the 141 orchard populations above were screened for sensitivity to difenoconazole. In all, 1 orchard population had reduced sensitivity to difenoconazole, while the remaining 36 orchard populations were sensitive to the fungicide. In field experiments, difenoconazole demonstrated high levels of apple scab control on mature apple fruit, despite the fact that the population of V. inaequalis had practical resistance to difenoconazole. Although our results indicate widespread resistance to myclobutanil but not difenoconazole, due to the propensity for cross-sensitivity among DMI fungicides, growers with myclobutanil resistance should be cautious when using difenoconazole for disease management.

  PublisherOA PDFDOI

• Organic Agriculture and Integrated Pest Management: Synergistic Partnership Needed to Improve the Sustainability of Agriculture and Food Systems

  2015-01-01 · 2 citations

  articleOpen access
  PublisherDOI

• Prevalence and Stability of Qualitative QoI Resistance in Populations of <i>Venturia inaequalis</i> in the Northeastern United States

  Plant Disease · 2014-03-13 · 29 citations

  articleOpen access

  Quinone-outside-inhibitor (QoI) fungicides are a safe and effective means of managing apple scab caused by Venturia inaequalis. To determine the prevalence of both quantitative (partial) and qualitative (complete) QoI resistance in V. inaequalis in the northeastern United States, we sampled single-lesion conidial isolates (n = 4,481) from 120 commercial and research orchards from 2004 to 2011 with a range of exposure to QoI fungicides from none to several applications a year. In all, 67% of these orchard populations of V. inaequalis were sensitive to QoI fungicides, 28% exhibited QoI practical resistance, and 5% were not sensitive QoI fungicides but had not become practically resistant. Isolates with qualitative QoI resistance, conferred by the G143A cytochrome b gene mutation, were found in 13 of the 34 QoI-resistant orchard populations. To evaluate the stability of the G143A mutation, 27 isolates were selected from different orchard populations to represent the scope of regional populations. These isolates were subcultured continuously in the presence or absence of the QoI fungicide trifloxystrobin. All isolates that initially possessed qualitative resistance maintained the resistant genotype (G143A) for six transfers over 6 months in both the absence and presence of trifloxystrobin. Given the observed QoI resistance in orchard populations of V. inaequalis and the stability of the G143A mutation in individual isolates, apple scab management paradigms must encompass strategies to limit selection of QoI resistance in the sensitive orchard populations remaining in the region.

  PublisherOA PDFDOI

• Evaluating Electrophysiological and Behavioral Responses to Volatiles for Improvement of Odor-Baited Trap Tree Management of<i>Conotrachelus nenuphar</i>(Coleoptera: Curculionidae)

  Environmental Entomology · 2014-05-25 · 9 citations

  articleOpen access

  Plum curculio, Conotrachelus nenuphar (Herbst), one of the most important pests of apple in eastern and central North America, is usually managed in New England apple orchards by multiple full-block insecticide applications. Efforts to reduce insecticide inputs against plum curculio include using an "attract and kill" approach: odor-baited trap trees deployed in the perimeter row of apple orchards. The standard approach is based on baiting apple trees with two olfactory stimuli, the fruit volatile benzaldehyde and the aggregation pheromone of plum curculio, grandisoic acid. We attempted to improve attraction, aggregation, and retention of adult plum curculios within specific baited trap tree canopies within apple orchards using an additional host plant volatile found to be highly stimulating in electroantennogram studies, trans-2-hexenal. We also attempted to increase aggregation using increased release rates of grandisoic acid. We found that trans-2-hexenal did not provide increased aggregation when deployed as an additional attractant within trap trees or when conversely deployed as a "push" component or repellent in perimeter trees lateral to the baited trap tree. Although increasing the release rate of grandisoic acid 5× actually appeared to increase overall aggregation within trap trees, it was not significantly different than that obtained using the standard dose. Therefore, we believe that the standard olfactory stimuli are sufficient to provide aggregation within trap trees, but that other means should be used to manage them after their arrival.

  PublisherOA PDFDOI

Frequent coauthors

• A. F. Tuttle

  University of Massachusetts Amherst

  10 shared

• Wesley R. Autio

  University of Massachusetts Amherst

  10 shared

• Alan R. Biggs

  West Virginia University

  7 shared

• William J. Manning

  Massachusetts General Hospital

  6 shared

• David A. Rosenberger

  6 shared

• Kerik D. Cox

  Cornell University

  5 shared

• Tracy Leskey

  Appalachian Fruit Research Laboratory

  5 shared

• Sara M. Villani

  North Carolina State University

  5 shared

Education

• B.A.

  Harvard College

  1974

• M.S., Plant & Soil Sciences

  University of Vermont

  1978

• Ph.D., Plant Pathology

  University of Massachusetts

  1986