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These are the Plant Pathology and Plant-Microbe Biology projects that our Summer Research Scholars will be tackling in 2020.  Faculty members or project leaders associated with each project are also listed. You can read more about their programs by clicking on their names. More project listings coming soon.

1. Assessing powdery mildew on industrial hemp

hemp white moldIndustrial hemp is Cannabis sativa with low levels of THC production and has recently made a return to New York State after almost a century. Industrial hemp has a wide range of uses and there are growing potential markets in fiber, oilseed, and pharmaceutical production. Powdery mildew, caused by the fungus Golovinomyces spadiceus, has been a significant problem for greenhouse and field hemp production.  Understanding how various cultivars of hemp stand up to this fungus will be an important piece of information for both new growers and the hemp breeding program here at Cornell. You will gain useful plant pathology skills as you inoculate cultivars and evaluate their susceptibility in the greenhouse. This project will also involve DNA extraction to genotype isolates of G. spadiceus. This research will help to inform future field trials and experiments to better understand how we can deal with this disease as Industrial hemp becomes a more widespread crop in New York.

  • Lab: 40%, Greenhouse: 60%
  • Faculty: C. Smart

2. Finicky Fungi in High Tunnels 

passalora fulvaHigh tunnels are the perfect environment for high value crops like tomatoes. Unfortunately, the environment is also conducive to the spread of tomato leaf mold. The causal fungus Passalora fulva creates characteristic olive-green spots on leaves, then plants will defoliate leading to yield losses. As a researcher on our team, you will help us to better understand the diversity of the pathogen population through experimentation in the field and lab. You will perform high tunnel experiments to assess the susceptibility of several tomato varieties after being inoculated with fungal isolates collected around the Northeast.  Molecular tools will be used to better understand genetic diversity between fungal isolates at the same time. A mysterious association also appears to be present between the causal fungus and other fungal species and you will help design and implement experiments to better understand this observation. The results from our experiments will help growers manage a disease that has not been well studied in the Northeast.  

  • Lab: 50%, Field: 50% 
  • Faculty: C. Smart

3.  “Light, pathogens, action!”

Reflectance spectroscopy is a newly-established but highly effective tool for non-destructively assessing plant disease physiology, and can be used to detect early, and even pre-symptomatic,  pathogen infection. This project will explore early detection of grape powdery mildew and grape downy mildew in the field and greenhouse with non-destructive spectroscopy. Through this project, you will gain skills in applied precision agriculture research and data analysis in R. This project will directly contribute to a broader effort building the foundation of an early disease detection system for NY state grape growers. An added bonus will be visits to see the diseases in the field, understanding their impact and management options available to grape growers. 

  • Computer work/data analysis: 50% , Field and greenhouse: 40%, Lab 10%
  • Faculty: Gold

4. Fighting an Old Battle with Modern Weapons: Can We Defeat Fire Blight With Next-Gen Genomics?

genomics toolsFire blight, caused by the gram-negative bacterium Erwinia amylovora, is one of the most destructive bacterial diseases of apple trees. In recent years, research has been revolutionized due to increased throughput technologies and a reduction in genome sequencing costs. You will be involved in a project that takes advantage of high-throughput genomics and phenomics to better understand host-pathogen interactions. With this information we can characterize natural resistance sources in apples, identify genomic regions (QTLs), molecular markers, and underlying genes using the genetic diversity available at the US apple germplasm repository in Geneva, NY. You will inoculate apple trees in the greenhouse to determine susceptibility to fire blight and then participate in mapping out the genetic resistance source. In addition, you will use chlorophyll fluorescence, infrared thermal, and multispectral imaging to detect early symptoms in response to fire blight infection and to quantify disease susceptibility/resistance. Results of this research will ultimately be used for genetic enhancement of fire blight resistance in apples by deploying resistance alleles in commercially favored backgrounds.

  • Lab: 50%, Greenhouse/field: 50%
  • Faculty: Khan

5. Can Machines be Taught to Accurately Diagnose Diseases in Apple Orchards?

diseased apple leavesApple orchards suffer from large numbers of diseases that can incur serious damage to trees, fruits, and the industry. Rapid and accurate disease diagnosis is critical in commercial apple orchards for timely control and to implement successful and environmentally-sound management. Appearance of disease symptoms can vary based on image capture conditions or traits of host and disease making it challenging for computer vision models to accurately distinguish between the many symptoms of many diseases. Large datasets of high-quality images are critical to train computer vision models. You will help collect, annotate, and classify high-resolution images of biotic and abiotic stresses using digital cameras and smart phone during the growing season. This image dataset will be used to develop automated image-based disease classification and quantification of symptoms of biotic and abiotic stresses of apple for the accelerated and automated stress diagnostics and management in apple orchards. Students at Cornell Tech in NYC will use these images to develop and train machine learning models for automatic disease detection, and you will collaborate with them to test the models.

  • Computer: 50%, Field: 50%
  • Faculty: Khan

6. The Key to Appealing Apples: Apple Scab Fungal Population Diversity, Virulence, and Host Genetic Resistance

apple scabApple scab, caused by Venturia inaequalis, is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Cultivar resistance is the best long-term solution to reduce overall production costs and preserve fruit quality. Isolates of V. inaequalis vary in their ability to overcome resistance genes found among the commercial apple cultivars used in breeding programs for decades. You will participate in a project to characterize virulence of fungal isolates and the genetics of apple scab resistance. This will involve collection and culture of V. inaequalis isolates and their phylogenetic analysis based on genome resequencing data. Additionally, the project will require artificial inoculation and resistance/susceptibility evaluation of a genetic mapping population and a differential host set in the greenhouse,  as well as field data collection in an apple orchard with a diverse apple germplasm collection from all over the world.

  • Lab: 50%, Greenhouse/field: 50%,
  • Faculty: Khan

7. Un-beet-able fungi? Rhizoctonia solani and table beet production

New York is the nation's second-largest producer of table beets (Beta vulgaris ssp. vulgaris). Recent industry expansion has increased the need for sustainable disease management strategies, especially for root rot caused by the Rhizoctonia solaniR. solani is a yield-limiting pathogen of table beets, sugar beets, and many other vegetable and grain crops. In beets, current control options are limited to in-furrow applications of azoxystrobin fungicides. The summer scholar will work in the lab and in the field to investigate alternative disease management strategies, including biocontrols/biofungicides. Additional skills will be developed collecting and characterizing isolates by anastomosis group determination and population studies. 

8. Don't let their size fool you...

Despite their small genomes and lack of cellular machinery, viruses still pack a big punch: plants infected with viruses show a number of symptoms ranging from leaf discoloration to fruit deformities or death. You will learn how to use genetically engineered grapevine fanleaf virus to study how plant viruses cause symptoms in their host. You will also use proteomics techniques to probe the protein-protein interaction underpinnings of symptom development. You will gain skills in molecular biology, plant virus biology, and diagnosing virus infection, as well as protein extraction, detection, and proteomic analysis.

  • Lab: 90%, Greenhouse: 10%
  • Faculty: Fuchs

9. A virus’ arm race with host defenses

orange leavesRNA silencing plays a critical role in plant resistance against viruses. To evade the antiviral host defense through RNA silencing, plant viruses have evolved RNA silencing suppressors that are potent arms in the arm race between plant and invading viruses. Research will involve the characterization of the RNA silencing suppressor of grapevine fanleaf virus using cell, biochemical, genetic and molecular technologies to improve our basic knowledge about plant-virus interactions and unravel the mechanisms of suppression of RNA silencing by this virus.

  • Lab: 80%, Greenhouse: 20%
  • Faculty: Fuchs

10. Grapes and a virus and an insect and symbionts: Oh my!

alfalfa hopperRed blotch is a recently recognized viral disease of grapevines that is caused by a DNA virus named grapevine red blotch virus. This virus is transmitted by the three-cornered alfalfa hopper.  There is much to uncover regarding the multitrophic interactions between the host, the virus, the treehopper vector, and symbiotic bacteria within the treehopper. You will use techniques such as nucleic acid extraction, polymerase chain reaction, dissection, and confocal microscopy to address questions about virus transmission and insect biology. You will take an active role in designing, optimizing, and implementing experiments, as well as analyzing and presenting data.

  • Lab: 80%, Greenhouse: 20%
  • Faculty: Fuchs

11. Code red: When a virus attacks!

red blotch virus infected leafGrapevine red blotch virus is the recently identified causal agent of red blotch disease of grapevine. This virus is vectored by the three-cornered alfalfa hopper in vineyards. You will contribute to research aimed at developing efficient transmission assays of the virus by its vector, to both grape and alternative hosts, to help characterize the transmission mode. 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

12. No gut, no glory!

alfalfa hopperThe three-cornered alfalfa hopper vectors a DNA virus named grapevine red blotch virus. Little is understood about the landscape-level movement of this viral transmitter; yet virus spread is occurring although grape is not a reproductive host and the hoppers are only found in vineyards during brief summer months. This project will look at the optimization of molecular gut content analysis to address feeding preferences of the treehoppers in a vineyard ecosystem. Research will involve insect rearing, feeding trials, dissections, molecular dietary composition, PCR, sequencing, and other laboratory techniques, to unveil virus-vector-host interactions.

  • Lab: 70%, Greenhouse: 30%
  • Faculty: Fuchs

13. The orchard is on fire!

fire blight on leavesFire 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, chiefly 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 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

14. Endangered apples!

apple scabApple Scab caused by the fungus Venturia inaequalis has limited the sustainable production of apples in temperate climates. The pathogen has become resistant to many of the safest and most environmentally responses fungicides. Multi-drug resistant V. inaequalis has caused disastrous production failures in apple production operations throughout the eastern US apple industry. Scholars will determine how farm management practices impact the evolution of resistant populations of V. inaequalis in an effort to help growers produce disease free apples safely and sustainably. They will look at population changes in fungicide target site genes and microscopic growth. In addition, scholars will have opportunities to visit orchards with disease outbreaks and learn about modern apple production.

  • Lab: 50%, Field: 50% 
  • Faculty: Cox

15. Mildew Mission

apple powdery mildewApple powdery mildew (Podosphaera leucotricha) is a fungal disease found in most apple-growing regions of the world. P. leucotricha spreads on new growth as apple trees break dormancy in the spring, reducing tree vigor and hindering blossom development. The pathogen is obligate (meaning it requires its host to survive), which makes study difficult. Historically, P. leucotricha management in the orchard has relied on a narrow group of fungicides to maintain control. Little is known whether P. leucotricha populations have developed resistance to these compounds. Scholars will aid in the development of an in vitro culturing method for P. leucotricha to allow study, as well as establish a detached-leaf fungicide assay with which to test fungal isolates’ relative fungicide resistance. Scholars will also learn DNA extraction, PCR, and sequence analysis protocols to evaluate isolates for known resistance mutations to commonly-used fungicides. In addition, scholars will have opportunities to visit research and commercial orchards to learn about modern apple production.

  • Lab: 80%, Field: 20%
  • Faculty: Cox

16. How do bacteria zombify plants?

Plant pathogens enjoy eating vegetables as much as we do! To promote disease, plant pathogens use an array of molecular mechanisms against their hosts. Effectors are proteins that pathogens deploy to manipulate the host metabolism and thus support their own growth. By suppressing plant immunity, pathogens proliferate and induce characteristic symptoms in the plant. In this project, you will evaluate the role of specific effectors from the tomato infecting bacterium Xanthomonas cynarae pv. gardneri. You will clone effector genes, inoculate different accessions of the host, and evaluate the plant response. By the end of the summer, you will have gained a deep understanding of the molecular interaction between plants and microorganisms, how do plants defend themselves, the dynamics of bacterial colonization of plants, and how to evaluate the role of effectors in the development of disease. You will work in a fantastic lab, where the thrill of curiosity drives our research.

  • Lab: 70%, Greenhouse: 30%
  • Faculty: C. Smart

17. Why Light Matters

dinosaur sunriseFungal pathogens have evolved with their hosts over millions of years in repeated cycles of light and darkness.  Over this scale of time, they have developed the means to sense, interpret and use light to direct their development.   We are now discovering ways to use these evolutionary traits against them.  In a number of projects, we use both visible and UV light to suppress plant pathogens with this novel application of photobiology.

  • Lab: 50%, Field: 50%
  • Faculty: Gadoury