Plant Pathology & Plant-Microbe Biology Projects

2023 projects

1. Drones & disease

Can we track grape disease from the sky? The Gold Lab is trying to find out. Scholars will participate in an interdisciplinary research project that includes aerial imagery acquisition (weekly drone flights), disease scouting, and proximal plant trait measurements. Scholars will:

  • Learn to identify grape pathogens and quantify disease symptoms
  • Measure foliar hyperspectral reflectance in the vineyard with a backpack spectrometer
  • Record evapotranspiration and chlorophyll fluorescence using a handheld fluorometer/porometer
  • Assist with all aspects of weekly drone campaigns

The project team includes researchers in plant pathology, computer science, engineering, and GIS. Students interested in any of these areas are encouraged to apply!

Data wrangling: 25%, Field: 75%

Faculty: Gold

2. “Where is the genetic diversity of Cercospora beticola coming from?” The case study of C. beticola mating types in table beet.

Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, is a major production constraints of table beet industry. C. beticola is resistant to many single-site fungicides due to high genetic diversity within the pathogen population. C. beticola has two different mating types, but there is no evidence of sexual reproduction. Therefore, the reason behind high genetic diversity and rapid development of fungicide resistance is not clear. The pathogen is dispersed via short-ranged water splash and wind-blown conidia. This project will study the secondary spread of CLS in table beet field within a growing season. In addition, it also aims at understanding the role of mating types in the evolution of C. beticola population. The summer scholar involved in this project will get hands on experience in diagnosing CLS and evaluating CLS severity in field and using molecular tools to identify the mating types of C. beticola isolates in laboratory.

Lab: 50%, Field: 50%

Faculty: Pethybridge

3. Better apples faster

The apple growers’ nightmare: Erwinia amylovora, the bacterium that causes a terrible disease called fire blight. One way to limit the impact of this pathogen is through planting fire blight resistant apple cultivars. Our lab has developed several unique apple pre-breeding lines carrying distinct fire blight resistance loci. Your task this summer will be to study the interaction between E. amylovora and these transgenic apples with multiple resistant genes. This will involve bacterial inoculation of greenhouse plants, quantification of disease progression, genotyping of resistance loci with DNA markers, and will contribute greatly to the development of the second generation of disease resistant transgenic apples.

Lab: 25%, Greenhouse: 75%

Faculty: Khan

4. Not all heroes wear grapes!

Grapevine red blotch virus is a significant threat to grapevine production. This virus is transmitted in vineyard settings by an insect vector, the three-cornered alfalfa hopper. You will contribute to research aimed at optimizing transmission assays of the virus by its vector and further understand transmission capabilities of the insect. You will design and optimize assays using techniques such as plant inoculation with infectious virus clones, nucleic acid extraction, polymerase chain reaction, dissection, sequencing, and microscopy, while also learning insect rearing techniques.

Lab: 70%, Greenhouse: 30%

Faculty: Fuchs

5. Putting out the fires

Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most devastating diseases of apple production worldwide, capable of destroying entire orchards in unforeseen epidemics and costing farmers millions of dollars in the United States annually. Modern management of fire blight relies almost exclusively on antibiotic sprays, such as streptomycin, which have come under scrutiny due to the potential development of antimicrobial resistance in both pathogen and off-target bacterial populations. Each year numerous biological control options are developed for managing fire blight, but they often provide poor control and are not optimized for temperate production regions. Scholars will examine alternative management programs, including plant growth regulators, germicidal light, and biological controls, for managing fire blight. In addition, scholars will investigate the distribution and movement of E. amylovora strains and potential implications for management utilizing CRISPR genotyping techniques. Scholars will have opportunities to visit actual fire blight outbreaks and learn about modern apple production.

Lab: 50%, Field: 50%

Faculty: Cox

6. Is there light for Stemphylium vesicarium at the end of the tunnel?

Stemphylium leaf blight (SLB) is an onion disease caused by the fungal pathogen, Stemphylium vesicarium. In recent years, SLB has been causing enormous crop losses in onion fields in NY. In this project, we intend to unravel the effect of physical weather variables, such as light, temperature, water, and wind, in the dispersion mechanism of S. vesicarium. The project will be conducted mostly in the laboratory using a wind tunnel, greenhouses, microscopes, and molecular techniques. Visits to the field will also occur to collect plant disease material and field evaluations. The student will develop skills such as hypothesis-driven research, adaptability, problem-solving, and teamwork. The results of this project will aid in answering epidemiological questions about pathogen dispersal and disease spread. This information will illuminate the path to improved disease forecasting models and avoid unnecessary applications of pesticides culminating in more sustainable onion production at the end of the tunnel.

Lab: 75%, Field: 25%

Faculty: Pethybridge

7. Winning the arms race: unraveling genetic scab resistance of apples

Apple production is strongly affected by the apple scab disease, caused by the Venturia inaequalis fungus. To produce scab-free apples worldwide, over 30 fungicide sprays are needed during scab-conducive seasons, as most commercial apple cultivars are scab-susceptible. Cultivar resistance is the most promising sustainable solution to enhance economic gains and fruit quality. To contribute towards understanding of scab-resistance in apples and towards development of elite scab-resistant cultivars, you will participate in our genetic analysis to map apple scab resistance genes. To achieve this, you will maintain genetic mapping populations of apples, culture V. inaequalis isolates, artificially inoculate the plants and macroscopically evaluate resistance/susceptibility of your population. You will also learn how to develop and apply molecular markers, perform genetic analysis using plant genotyping, gene and QTL mapping, and present your research in a form of a scientific poster.

Lab: 60%, Greenhouse: 40%

Faculty: Khan

8. Behaving 'graply'

The three-cornered alfalfa hopper, Spissistilus festinus, transmits grapevine red blotch virus (GRBV) in the vineyard. Yet, grapevines are not a preferred host of S. festinus. Thus, studies are needed to better understand the behavior of S. festinus on various plant species. You will investigate the ability of snap bean to serve as a rearing host of S. festinus and the effects of GRBV on its reproduction using detached chambers. Your will rely on laboratory skills such as insect rearing, feeding trials, behavioral analyses, insect DNA isolation, polymerase chain reaction, GRBV diagnosis, and other laboratory techniques, to unveil virus-vector-host interactions.

Lab: 50%, Greenhouse/Growth chamber: 50%

Faculty: Fuchs

9. Better biological control!

Apple Scab caused by the fungus Venturia inaequalis and other emerging fungal diseases have limited the sustainable production of apples in temperate climates. The apple scab pathogen has also become resistant to many of the safest and most environmentally responses fungicides. In response, producers are now relying on less-environmentally-friendly multi-site fungicides. There are also new regulations and restrictions being placed on multi-site fungicides leaving growers scrambling for options. Scholars will use horticulture, disease forecasting, and careful selection of biopesticides and single-site fungicides determine how to best help growers produce disease free apples safely and sustainably. In addition, scholars will have opportunities to visit orchards with disease outbreaks and learn about modern apple production.

Lab: 50%, Field: 50%

Faculty: Cox

10. Let nature do the work: Development of a novel genetic mapping method for fire blight resistance in apples utilizing open pollinated populations

Fire blight is a bacterial disease that can be devastating to apple trees and apple production. It causes lesions and necrosis and has the potential to kill entire trees and spread throughout orchards within a single growing season. Improving methods to determine natural resistance to fire blight are crucial in the development and identification of apples that can better withstand and resist infection of the fire blight bacteria. One way to identify resistance is through genetic mapping to pinpoint specific genomic regions. However, traditional mapping methods in apples are time consuming and resource intensive. Open pollinated (OP) populations for mapping in apples have the potential to drastically reduce the time and resources needed to map and fine map genes of interest. In addition, high throughput image analysis can be used to screen populations for fire blight resistance, allowing for non-destructive ranking of OP populations. You will inoculate an established OP seedling population grown in a greenhouse with fire blight bacteria to screen for resistance. You will also get experience in using image analysis for disease resistance evaluation. Finally, you will use a detached leaf assays and extract DNA from plant tissue for genotyping to facilitate mapping of fire blight resistance within the OP population

Lab: 50%, Greenhouse/field: 50%

Faculty: Khan