Plant Pathology & Plant-Microbe Biology Projects

2025 projects

14. Don't eat the mold

Blue mold of apple, caused by the necrotrophic fungus Penicillium expansum, is a major post-harvest disease worldwide. Specifically in apple, losses are estimated around $4.5 million annually. P. expansum undergoes rapid asexual life cycles, produces the mycotoxin patulin, and has a highly plastic genome which contributes to the pathogens’ ability to mutate. Together, these factors contribute to its “high risk” classification as a postharvest pathogen and thus enable rapid onset of resistance to commonly used fungicides. Efforts in the Cox lab aim to understand the development of fungicide resistance and how to effectively manage this devastating disease in real time. Aside from the practical importance of optimizing yield, the broader impact of this research is to reduce blue mold incidence and in turn enhance food safety by reducing the secondary metabolite produced by P. expansum, patulin a potent and toxic mycotoxin. Patulin is heavily regulated in processed apple products, particularly products marketed towards children which are most susceptible to this toxin. Moreover, by optimizing fungicide applications there would be fewer more impactful inputs that would provide downstream benefit to the health of consumers and profitability of producers.

Scholars interested in the system would gain hands on experience in fungal culturing, molecular characterization, fungicide screening bioassays, statistical analyses in R Studio and last but not least get to work in an idyllic apple orchard in Upstate NY. 

Lab: 75%, Field: 25%

Mentor: Kerik Cox

15. Come to the light!

Apple Scab, powdery mildew, apple blotch, and numerous other emerging fungal diseases limit sustainable production of apples in temperate climates. Fungal pathogen populations are becoming resistant to the safest and most environmentally sustainable fungicides. We’re investigating the potential for using germicidal light to mitigate fungal diseases of apple. Organically approved and pesticide residue free, germicidal light in the form of UV-C may be able to eliminate germinating spores and stop disease.  Scholars will need to suit up, enter apple orchards after dark, and carefully use UV-light arrays with their mentors to assess the potential field use of this new technology. In the lab, scholars will conduct experiments on fungal cultures and sporulating lesions to assess the impacts and determine optimal doses. Scholars will also have opportunities to visit orchards with disease outbreaks and learn about modern apple production.

Lab: 50%, Field: 50%

Mentor: Kerik Cox

16. Clearing the path to sustainable disease management: Mapping genetic resistance to apple scab

Apple scab, caused by the fungus Venturia inaequalis, significantly impacts apple production worldwide. Frequent fungicide applications are often required during scab-conducive seasons to produce scab-free apples, as most commercial cultivars are susceptible. Developing scab-resistant apple cultivars offers a sustainable solution to improve fruit quality and reduce economic losses.

This summer, you will contribute to advancing scab resistance research by mapping potential quantitative trait loci (QTLs) in two apple accessions identified as resistant during field evaluations. Your work will include phenotyping bi-parental mapping populations to assess resistance in both progeny and parents, as well as using genetic data to connect genotype to phenotype. Your work this summer will help identify new genetic resistance to apple scab and pave the way to a sustainable future in apple production!

Lab: 10%, Greenhouse: 40%, Computer: 50%

Relevant Literature

Mentors: Awais Khan, Hana Feulner

17. Sweet Success: Exploring Muskmelon Cultivars for Foliar Disease Resilience 

Muskmelon production in New York faces significant challenges from foliar diseases like powdery mildew, downy mildew, and Alternaria leaf spot. These diseases can cause mid-season defoliation, increasing the risk of yield loss through sunscald and poor fruit quality. Evaluating cultivar susceptibility to these diseases helps growers select varieties that maintain productivity, reduce pesticide reliance, and support sustainable farming practices. However, up-to-date field data on cultivar performance under New York’s changing climate is limited, leaving small-scale growers—who produce most of the state’s muskmelons—without reliable information to manage these costly diseases.

This project will assess insect populations, disease incidence, severity, and other characteristics (like taste!) in a trial of eight to ten muskmelon cultivars. The summer scholar will gain hands-on experience setting up and monitoring field trials, collecting data on plant health and disease progression, and identifying key foliar diseases. They will analyze data using R, generate graphs, and interpret results to create extension materials for growers and stakeholders. This project provides valuable training in applied plant pathology, sustainable agriculture, and data analysis, offering practical skills for understanding and addressing agricultural challenges in real-world settings.

Lab: 40%, Field: 60%

Mentors: Sarah Pethybridge, Kaitlin Diggins

18. Overcoming a Vegetable Villain: Insights into Phytophthora capsici management in New York

A formidable member of the infamous “plant destroyer” genus, Phytophthora capsici threatens a wide range of vegetable crops including pepper, eggplant, tomato, and squash. While fungicides remain a cornerstone of disease management, resistance to these treatments is alarmingly common in P. capsici populations. Sensitivity to commonly used chemistries will be evaluated in a diverse collection of P. capsici isolates, and DNA will be extracted for downstream mapping of fungicide resistance loci. In parallel, scholars will look for P. capsici host resistance in a wide array of eggplant cultivars, shedding light on this understudied host-pathogen relationship. Through laboratory, field, and greenhouse experiments, this work aims to provide New York vegetable growers with immediately applicable information to improve management efforts for this relentless disease.

Lab: 60%, Field: 30%, Greenhouse: 10%

Mentors: Emma Nelson, Chris Smart

19. Battling Cucurbit Yellow Vine Disease (CYVD) through Integrated Pest Management

Cucurbit Yellow Vine Disease (CYVD), caused by the bacterium Serratia marcescens, poses a serious threat to cucurbit crops like squash, pumpkins, and melons. A critical component of this disease's cycle is the squash bug (Anasa tristis), which acts as a vector for the pathogen. This project will focus on field and lab experiments determining the preference of the squash bugs and their relationship with CYVD incidence. 

We will also determine the number of squash bugs carrying S. marcescens in infected cucurbit fields in New York. Through field sampling and laboratory analysis, this research aims to shed light on the role of insect vectors in the spread of CYVD and contribute to better disease management strategies. The summer scholar involved in this project will develop skills in field sampling techniques, crop planting, maintenance, and harvesting of field trials; insect identification, and sample preparation, as well as laboratory skills, including DNA extraction, polymerase chain reaction (PCR), and molecular diagnostics. Additionally, the summer scholar will learn about conventional and novel IPM strategies to control the vector of CYVD.

Lab: 40%, Field: 60%

Mentor: Chris Smart