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Department of Plant Pathology

Research & Extension Experiences for UndergraduatesResearch & Extension Experiences for UndergraduatesResearch & Extension Experiences for UndergraduatesResearch & Extension Experiences for UndergraduatesResearch & Extension Experiences for Undergraduates
Department of Plant Pathology
Kansas State University
1712 Claflin Road
4024 Throckmorton PSC
Manhattan, KS 66506

Ph: +1-785-532-6176
Fx: +1-785-532-5692

2022 Projects 

Projects may be subject to change. 

The program is subject to cancellation or change due to the covid19 pandemic. We are monitoring the situation and coordinating with various KSU partners to guide our decisions and planning. If we need to make major changes or cancellations we will let selected participants know as soon as possible. 

You will list three projects on your APPLICATION FORM. We cannot guarantee that you will be placed in one of your top three selections, but your selections will help us place students in projects that are a good match for their interests.

You do not need to already have the skills mentioned in the project descriptions, just an interest to learn. You will gain hands-on training during the program.

Gene editing to develop improved wheat varieties

CRISPR/CAS9 technology can be used to rapidly generate new variants of genes with improved function. We use CAS9 technology to edit wheat genes that can increase yield and disease resistance, and improve nutritional quality. Intern will be involved in selecting genes that affect positively these traits in wheat, designing CRISPR/CAS9 reagents for gene editing using bioinformatical tools, and testing these reagents using next-generation sequencing (NGS) technologies available at the KSU Integrated Genomics Facility. The student will conduct these experiments as part of the gene editing projects aimed at improving wheat traits.

60% lab, 40% computer.

Mentors:Wei Wang and Eduard Akhunov


Wheat extension, diagnostics, and pathogen surveillance

So you want to be a plant doctor? Plants get sick too! This REEU internship will be focused on plant disease diagnostics and extension, with many hands-on opportunities to be a plant disease detective. Come learn techniques for diagnosing sick plants, characterizing and managing pathogen isolates, and reporting findings back to growers. Additionally, students will have the opportunity to shadow extension agents and develop video and print extension materials to directly help growers manage disease problems on their farms. The isolate characterization component of this project will be focused on the yield-limiting pathogen that causes Fusarium head blight of wheat, Fusarium graminearum.

60% lab, 40% field

Mentors: Kelsey Andersen Onofre and Jessica Rupp


Genome Engineering in fungi using CRISPR-Casdavid-cook

Have you heard about Genome Engineering or CRISPR-Cas and want to learn more? Maybe you know the basics details and you want to get some hands-on experience creating targeted DNA alterations to a genome. Complete an internship in the Cook lab as part of the K-State REEU program and you'll have the opportunity to learn out this exciting new technology and a whole lot more. You will learn basic microbiology techniques, some mycology, molecular biology, and about genetically modified organisms. You will leave with proficiency and knowledge about DNA editing using CRISPR and be on your way to changing the future!

Areas: Genome engineering, mycology, molecular-biology, CRISPR-Cas, plant pathology

MentorDavid Cook


Synthetic Biology to Make Super Seeds

 Seeds function as powerful biosynthetic factories that convert photosynthetically derived sugars into storage lipids, proteins and carbohydrates. My research group uses synthetic biology approaches to genetically modify metabolism so that seeds can produce novel compounds with functionalities useful for different applications. One particular focus involves modifying the chemical structure of vegetable oil to make a better, low-viscosity biofuel. You will have the opportunity to learn a variety of synthetic biology methods, including rapid assembly of gene constructs, CRISPR/Cas9 genome editing and plant transformation, as well as different biochemical methods to quantify lipids and amino acids in the modified seeds.

 Lab 100%

Mentor:Tim Durrett


Let’s Make Better Wheat 

Let’s help wheat fight off pests! Come help screen wheat breeding populations for pathogen and disease resistance to find the genetic factors that help produce our favorite breads and cereals. The intern will select resistant wheat to certain wheat pathogens, and using high throughput sequencing and genotyping techniques identify genetic regions involved in plant resistance using current bioinformatics tools. These genetic factors will be transferred into our breeding programs for improved wheat for future deployment and development. 

Greenhouse 20%, Lab 30%, Computer 50% 

Mentor:Katherine Jordan

tania kim

Crop diversity effects on pest and beneficial insects

Crop plants are vulnerable to pest infestation. As such, the US spends $12.5 billion/year for pesticides, however, more sustainable measures are needed to control pest outbreak.  For example, planting different crop types or varieties can reduce the likelihood of damage to target crop plants. For this project, we will examine how crop diversity (monocultures versus polycultures, annual versus perennial crop species) affects the likelihood of infestation and damage by pests such as aphids.  We will also examine how crop diversity affects the likelihood of colonization of important predatory insects (e.g. lady beetles) that naturally feed on aphids and pollinators.

Field 50%/Greenhouse 25%/Lab 25%.

Mentor: Tania Kim

dal hoe

Cytogenetics of alien gene transfer in wild wheat

Just like we all have some interesting relatives, wheat has some wild in-laws of its own! Bread wheat was domesticated in Central Asia around Iran and Iraq and the wild relatives can still be found there today. Though they don’t really even look like wheat and aren’t any good for making bread, the wild relatives have important genes for disease resistance. Using chromosome engineering and bioinformatics, we are transferring these useful genes into wheat to make stronger wheat plants that are resistant to disease and other stress.

Areas: genetics and genomics, plant breeding, plant pathology, cytogenetics.

Greenhouse 25%/Lab 75%.

MentorDal-Hoe Koo 


Weed Management

 Weeds are one of the greatest challenges farmers have. Weed scientists work to find effective and economical soluweedtions to farmers’ weed management challenges and share that information with farmers and agribusinesses. In this internship, students will have the opportunity to work in the field on projects related to herbicide evaluation as well as nonchemical weed management practices. In addition, students will have the opportunity to participate in Extension-related activities, including summarizing data. If you enjoy biology or chemistry, gathering information, working outdoors, and helping people, this internship might be for you!

80% Field, 20% Lab + Greenhouse


Mentor:Sarah Lancaster


Biology of sorghum and soybean diseases

Sorghum and soybean are major crops in Kansas. My lab studies fungal disease of both crops, including characterizing seedborne fungi, mechanisms of resistance to stalk rot in sorghum, and working with crop breeders to identify resistance to diseases. Students in my lab will learn how to isolate and culture diverse fungi, microscopic techniques, and greenhouse inoculation assays.

Lab 50%/Greenhouse 50%

Mentor:Chris Little

s liu

What makes plants resistant to diseases?

Plants do not have immune systems like ours, but they fight off pathogens. Some plants have a strong capability to fight against diseases but some do not. In this project you will inoculate plant pathogenic bacteria on plants (e.g. wheat and corn), observe symptom developing through time-lapse imaging, and quantify disease resistant levels among plant individuals.  You will also use DNA technologies to find genomic regions causing resistance.You will learn basic programming, cutting-edge computation techniques for data processing and visualization, and knowledge in plant diseases, genetics, and genomics.

Lab 60%/Greenhouse 30%/Field 10%.

Mentor: Sanzhen Liu


New insect-associated viruses: Friends or Foes?

Many plant pathogens rely on insect vectors for their transmission. Insects are occupied by native resident microorganisms from diverse groups ranging from bacteria to fungi to viruses, together called microbiome. Many of these microbes are not pathogen but they might be beneficial. We recently discovered/identified new insect-specific viruses associated with important insect vectors of plant pathogens. We consider the new viruses as natural components of the insect host`s microbiome. Join host-virus-vector interactions research team to explore the molecular interaction between the insect and its new viruses.

Areas: Virology, molecular biology, vector biology, and bioinformatics.

MentorShahideh Nouri


Establishing a high-throughput transformation platform for crop genome-phenome cause-effect studies

Functional genome analysis through genetic transformation and plant regeneration processes must enter the high-throughput stage in order to determine how these genome sequences generate crop phenotypes. However, functional genomics researches in most crops are constrained by low transformation efficiency. Establishment of a robust, reliable crop transformation and regeneration system for the use of ectopic overexpression, RNAi, and CRISPR/Cas9 gene editing approaches is crucial for understanding of the relationship between genomes and phenomes in the crops. You will learn crop (e.g., rice, maize, sorghum, tomato, lettuce, etc.) tissue culture, gene transformation, and genome editing technology.

MentorSanghun Park

y park

Insect hormone disruptors

Park team focuses on the development of new tools to disrupt insect endocrine system based on the knowledge of hormone receptors revealed in comparative genomics. Current project includes high throughput screening of chemical compounds that act on insect specific ecdysis triggering hormone receptor and mite specific neuropeptide receptors. Students will be trained for molecular biology and data analyses of bioassay depending on the background and the interests of the students assigned. Most of all, the students will have opportunities to play with arthropods, learn the fun biology, and perform modern molecular techniques to solve the problems in pest control.

MentorYoonseong Park

jesse poland

An eye in the sky...

Unmanned aerial vehicles (UAVs), sometimes called ‘drones’, are more than just fun toys to make cool videos. They are also powerful research tools that can help us quickly measure field experiments and farmer’s fields to measure plant growth and plant diseases. Join our research team to use UAVs for rapid measurements of plant traits and explore how this high-resolution data can be used for different analysis to understand plants.

Areas: physiology, engineering, genetics and genomics, high-throughput phenotyping.

Mentor: tbd

deann presley

Going undercover

Cover crops are used to prevent erosion and improve soil structure and have the added benefit of increasing the plant biodiversity of a cropping system. Does increasing biodiversity aboveground lead to increased biodiversity belowground, and if so, how does it affect the plant pathogenic organisms? In this project, you will collect measurements in the field and soil sample experiments with and without cover crops to determine if there are any effects of cover crops on soil health.

50%, Field, 50% Lab.

MentorDeAnn Presley


My feet hurt! Investigating root rots in diversified cropping systems of wheat

Once upon a time, farmers used to grow wheat, followed by a year of giving the field a rest, called a fallow period. Fallow was meant to recharge the soil with moisture and fertility that could be used in the following cropping cycle. However, with the population growing and farming becoming an economic challenge, wheat growers are looking for new rotations that can make a profit. Peas are now being grown in place of fallow in many regions, including northern KS. While they do use the moisture saved for the wheat crop, their Rhizobia fix nitrogen to improve fertility. But, it may come with a cost. During this project, you will investigate if root rot pathogens that affect both wheat and pea are building up in the soil due to these cropping systems. This will include trips to sample wheat and pea across northern KS and culturing these pathogens in the lab. The pathogen communities will then be compared to wheat-fallow systems. Could we be driving a system we can't control?

Field 50%, Lab 50%

MentorJessica Rupp


Squish that bug! Improving insect pest control methods with molecular biology

Insect pests cause direct damage to crops and livestock and also vector pathogens that can cause serious veterinary and medical health problems. Typical management practices involve use of conventional chemical insecticides but increasing reports of resistance to these insecticides as well as increasing concern over their environmental impact are driving the development of novel strategies for insect pest control. The Silver laboratory is interested in understanding the molecular interactions of insecticides with their target sites as well as identifying new physiological mechanisms that can be exploited for insect pest control. Current projects include analyzing the effects of arbovirus infection on feeding and host-seeking behavior in mosquitoes and biting midges and understanding the mechanisms of RNA interference for development as a tool for controlling biting midge larvae and other insect pests. Interns will have the opportunity to learn molecular biology techniques, live cell imaging, cell culture, RNA interference, and/or insect behavioral assays while working alongside lab personnel and will develop independent research projects depending on their research interests.

100% Lab

MentorKristopher Silver


Pollinator ecology and machine learning

Pollinators are important components of our ecosystem that help provide us with much of the food we eat, maintain diverse natural plant communities, and make for enjoyable creatures to observe in our gardens. Our lab studies the ecology of pollinator communities in grassland habitats and surrounding landscapes. Machine learning and computer vision are emerging technologies in our field that will help remove the bottleneck associated with sampling, processing, and identifying pollinators in the field. Students will have the opportunity to participate in our experiments on these topics by gathering pollinator specimens and images in the field and processing them in the lab for ecological analysis and incorporation into our deep learning models for bee identification and detection. We will work with students to develop independent research projects based on their particular interests in pollinator ecology, which may or may not feed into our ongoing research.

50% lab, 50% field

Mentor:Brian Spiesman


The genetic basis of fungal pathogen diversity

Fusarium is a genus of filamentous fungi that contains many plant pathogens causing diseases on major crops. My lab studies the variability in important pathogen traits due to natural genetic differences among isolates from the same Fusarium species. The traits we study include fungicide sensitivity, the amount of mycotoxin produced, the number of spores produced when an isolate sexually reproduces, and the rate of growth at different temperatures. In this project, you may: collect data on the variability of the above pathogen traits; use DNA sequence from samples to analyze genetic diversity; and associate genetic markers with trait variability. This project will expand your knowledge of: microbiological techniques such as culturing fungal isolates and measuring traits; molecular techniques such as DNA extraction and amplification, and DNA sequencing; and bioinformatics techniques such as next-generation DNA sequence processing, comparative genomics, and analysis of genetic diversity. 

Lab: 60% Computer: 40%

MentorChristopher Toomajian


Help Control a Cereal Killer

A fungus, called Magnaporthe oryzae, causes blast disease that destroys enough rice every year to feed 60 million people.  This fungus adapted to infect wheat in the 1980s, and now threatens global wheat production as well.  Have a blast understanding how the fungus kills cereal crops at the molecular and cellular level.  You will learn live cell imaging using confocal and fluorescence microscopy to observe the fungus invading rice cells.  Learn to document locations and dynamics of fluorescently labeled fungal effector proteins, critical tools the fungus uses to hijack host cells and cause disease.  You will also gain skills in molecular biology, construction of fluorescent fungal strains, and rice infection assays. 

Lab 100% 

MentorBarbara Valent