What made you decide to focus on Crop Protection Genetics as a line of work?
Since high school, I was interested in the diversity in biology, what was going on in the natural world, and how humans were affecting their environment. I became more interested in agriculture and The Land Institute in college, when I had an internship here. I was in an Environmental Studies program that knew about The Land Institute. We talked extensively about issues in agriculture, sustainability, and the need for people to maintain natural resources. I liked the experimentation of coming up with questions that you could then test and figure out the answers to, and the creativity of that process – using observations to answer those questions. I became interested in crop protection as a way to maintain the yield in agriculture. Controlling disease is one of the most important factors in maintaining yield. I also like exploring the diversity of pathogens and trying to solve the puzzle of what pathogen is causing a particular symptom. It’s interesting to know about the bad guys in the system and learn more about how they interact with the plants.
So, you came to The Land Institute as an intern – how did you end up working here as a staff member?
I started as an intern working with Lee (De Haan) and David (Van Tassel). I had a small independent project and presented some of the breeding research at the lunch forum at Austin College. I was impressed how much progress could be made in the crops over such a small number of generations and short amount of time. It was more interesting me than a lot of other biology research projects that I was exposed to – understanding how something worked but not necessarily having a practical application like creating a new food crop.
Of all the different types of science that I was exposed to in college, I kept coming back to the work that The Land Institute was doing and how practical and exciting it was. I talked to Lee about what types of projects I could work with, what schools might be a good fit, and finding an advisor who might be interested in working on something related to The Land Institute. He initially connected me with Don Wyse in Minnesota, and then I met Jim Anderson, a wheat breeder with an interest in perennial wheat. I received funding through the Growers Association of Minnesota working on a disease resistance project, and then worked with The Land Institute germplasm that was my master’s thesis material. I went on to get a PhD to gain more experience learning types of techniques and more of the innovation that was happening in the field of genetics at the time. After that, I came to The Land Institute for a postdoc and worked with Shuwen (Wang) on perennial wheat and genotyping.
And now you have your own program?
I started working more in some of my areas of focus in graduate school, specifically in controlling disease, because that seems to be a big issue for any crop that’s domesticated. I am working especially with silphium and Kernza® because Kernza is already being produced as a crop and silphium is faced with especially severe disease pressure. Silphium is a uniquely challenging crop because it is native compared to our other grain crops, which are all exotic. They were all domesticated somewhere else, but silphium has all the native pests and diseases here in Kansas where it evolved.
Are you working on pathogens for all The Land Institute’s crops?
Right now, it’s mainly silphium and Kernza. I did an initial assessment of what I could see in the field last year for all our main crops and some of the candidate species like Brandon’s (Schlautman) alfalfa and Kura clover. I wanted to see what diseases were affecting our crops and to get a baseline level of infection to see if there are severe diseases that we need to start working to control. I did a broad general assessment and will meet with each of the programs about what I found and whether it’s worth looking for resistance or another management approach to control those diseases, or if the diseases are likely to be minor and not cause large problems for breeding or production. Some disease might look horrible on the leaves, but if they don’t affect the yield very much or produce a toxin which would drastically reduce the ability for us to consume the crop, they might not be very important.
I saw fusarium and silphium rust mentioned on your webpage – are those the main pathogens you are working on?
Those are two specific pathogens that I’m working with quite a bit. The silphium rust is the most consistent and damaging foliar fungal disease of silphium, but last year we found another disease with the capacity to be severe in some years, so we might need to divert some attention to that disease also. And fusarium is probably the most concerning disease of wheatgrass, though wheatgrass is much more resistant to the disease than wheat or barley are. Although fusarium is not particularly severe, it does produce a toxin in the grain. Fusarium resistance is something we can select for in our breeding program and toxin in the grain is something we need to monitor for food safety.
How would the management strategies that you are looking at for controlling diseases differ from what is conventionally used?
Right now, I’m mainly focused on using disease resistance, which is a conventional strategy, but our crops have a much greater diversity of genes and alleles for resistance than conventional crops. So, we could build much more robust disease controls as we are domesticating our crops. In conventional crops like corn, wheat, and soybeans – the genetic diversity pools are much smaller, so the number of resistance genes is not nearly as large. In those crops, there are cases where resistance is broken down because it’s only controlled by one gene.
It sounds challenging to select so many kinds of genes for different things and get them to all match up.
It is hard to select for a lot of traits at one time, because you need to have good combinations in the same plant. It can be easier to select some plants that have some of the genes that you need and another plant that has a different set, and eventually by intercrossing get the optimal combinations. Kernza and silphium are outcrossing species and no two individuals in the field are genetically the same. While they are selected to be a uniform crop, there is still opportunity for different plants to have different resistance genes, so we don’t have or even want every plant in the field to have exactly the same type of defense genes.
Does much of your work take place in the lab, in the field, or both?
Both. There are things that we need to do in the lab to identify the pathogens that might be problematic, but there’s also quite a bit of surveying and looking at the plants themselves. We also grow the inoculum in the lab in a controlled environment. Once we’ve identified more of the important pathogens, we’ll do more work in the greenhouse and growth chambers. We would like to develop methods to screen seedlings in a consistent environment for disease so we can make the selections in a quicker and more uniform way than we can in the field.
What is inoculum?
Inoculum contains active pathogen propagules that are capable of infecting the host plant. We inoculate our plants by putting them in close proximity to inoculum or other plants which are infected that can spread the disease or by injecting a pathenogenic solution into the plant tissue. The concentration of pathogen is often higher than the plant would be exposed to naturally to ensure the plant has had adequate exposure to become infected. Under environmental conditions suitable for infection, it makes the plant sick unless their immune systems can fight it off.
So, it’s seeing how much they can take to see which ones survive best?
Yes. We are looking for the ones with the most resistance. A lot of the diseases aren’t killing the plants, but they prevent them from uptaking nutrients. Some pathogens damage the leaves and prevent photosynthesis, which reduces food yield. We might select for resistance that reduces damage to the leaves or reduces toxins in our food product.
What would you consider some of your biggest challenges currently?
Identifying and ranking the various pathogens for different environments. We need to build a better network for what’s happening in other places too and get more researchers involved everywhere our crops are being grown and in every area that we’re interested in like management, diseases, pests, or food quality.
Have you made any important discoveries in the past year or two that have helped the research move forward or in a new direction?
We identified the rust species that infects silphium in Kansas and the Midwest through sequencing. That allowed us to learn a little about its life cycle, how we might be able to grow it in the lab, and what strategies could be used to control it. I really want to be able to grow the silphium rust in the lab, but we can’t figure out how to get the next stage of the pathogen’s life cycle to be completed in a controlled environment. So, something isn’t right: temperature, humidity, the length of time, the day length, or something else.
So, you need to see the full life cycle?
We need to see it to be able to study it, so we know more about rate-limiting steps in its life cycle, but also so we can replicate it and use inoculum in the greenhouse. We need to be able to reproduce it ourselves without waiting for the right time of year and the right environmental conditions, which don’t happen every year, for infection in the field.
Do weather patterns and climate change effect your diseases?
Yes, quite a bit. Most diseases are highly dependent on moisture, temperature, and humidity. Moisture is probably the most variable, at least in a single environment. If we have a wet year, especially a cold, wet year, we’ll see more fungal pathogens. If it’s a hot, dry spring with late season moisture, maybe more bacterial diseases. That’s why field research must be done over multiple years and why greenhouses and controlled environments are very useful. Even irrigating in the field is extremely helpful. The fusarium trial we set up is in an irrigated area so it helps to ensure that we’ll have good (high) disease levels so that we can test all the plants in a consistent way.
What are your 5-10-year goals for your program?
I would like to figure out which diseases we need to work on as priorities. We have a couple figured out but need to know more about diseases that are harder to see. We haven’t looked at viruses at all, and we haven’t looked belowground unless something is completely killing the plant. There are a couple additional areas to go into.
I would also like to become more integrated with the breeding programs to give the breeders tools that they can use to quantify disease and disease resistance so they can make their own selections. I’d also like to help them with their selection process by either setting up seedling screening or disease nurseries in the field to accelerate the breeding progress.
The other big area of interest is finding out how we should be controlling diseases in perennial systems. I have a long-term project on disease accumulation that I hope will be able to address some management questions. For example, are there other management strategies that we should be looking at like fire or biomass removal? Which pathogens are more likely to accumulate over time? Or is that something that’s really an issue?
It sounds like to develop some of those tools that you need more communication between a larger number of researchers. Does the Global Inventory Project help inform your work?
That project currently focuses on what plants could be domesticated as crops. But the type of data I need may exist for pathogens of some of the plants we work on. There are records of disease data that herbariums collect also. Most of the archived data is presence/absence, so we could figure out which diseases are where (to some extent) but wouldn’t know the severity or anything about diseases that haven’t been characterized or studied. Probably more archival information is available for fungi, and not as much for viruses and bacteria. Right now, we want to work with other pathologists and our collaborators to get them to help us identify pathogens, collect data to see what management strategies can reduce disease, and maybe send in samples.
So, you need a World Health Organization for plants?
That would be great!
Why have people studied fungus more than viruses and bacteria?
Fungi are more prevalent, they cause more of the plant diseases in the crops that we eat, and they’re also much easier to work with. Many times, with fungi you can see a spot on a leaf, collect that spot, get part of the fungus (the fungal hyphae and the reproductive spores), and store inoculum relatively easily. Then you can grow them in the lab, characterize, and reproduce them easily. Bacteria fragments are smaller, so it took a lot longer to visually identify them microscopically, and they are less resilient to harsh environments. Then, viruses are even smaller and require extremely high-powered microscopes to study and are often vectored by other organisms, making it more complicated to study and replicate disease.
Viruses can be systemic and move to other parts of the plant, but they’re also often seed born, so they can be passed on to the next generation. Once you have viruses in the seed, they can be difficult to get rid of. And they frequently don’t exhibit symptoms as consistently. If it’s very hot, the symptoms can disappear, and you don’t see them. So, they’re harder to screen for, to reproduce, and to inoculate with to get a consistent evaluation.
With the bacteria and fungi, do you have “medicine” for the plants, or is it more of growing strategies that help deal with them?
For something like viruses or bacteria, it could be that management techniques like prevention are even better than a cure. Management could be not mowing through a field because cutting an infected plant would spread it to the next injured plant and then the virus or bacteria could get in. There’s resistance as well for those diseases and chemical treatments that might be similar to medicines. Chemical treatments like fungicides can be effective if treated early in the infection but have an additional cost for growers. There are some organic forms of chemicals as well.
Any other breakthroughs?
Identifying the silphium rust was exciting. There’s little literature available, but we were able to confirm it through sequencing and learn something about its life cycle. We think it will be a good candidate to breed for resistance. Resistance is highly heritable, so that is pretty useful!
Is part of your role putting together strategies on avoiding diseases and the care of diseased plants for farmers and growers?
So far, it hasn’t included that. I’ve been working more on breeding projects and information for other researchers, graduate students doing projects, and people wanting to measure some of these disease traits in their populations and maybe map some of the disease traits. I’ve been doing more extension for researchers than growers, but that could change in the future.
The only crop that we’ve started doing extension on is Kernza, and most of this information has been compiled by Green Lands Blue Waters. Since Kernza is infected by some of the same significant diseases as wheat, there is some knowledge about management, though genetic resistance is preferred. Then there are diseases in silphium that don’t exist in any other conventional crop. So, when silphium gets to the point where farmers are growing it, we would probably be the ones to develop strategies. As we advance in growing our crops for many consecutive years, managing a perennial grain system is going to be different than an annual system. No one else has done it so we will be heavily involved in this area in the future.
That sounds challenging, but exciting too!
Yes, it is. We’re not going to work on every possible disease out there, just the ones that are the most important initially and the ones that other research groups won’t study. It’s kind of like breeding for many different traits at the same time. Breeders must have a selection index and weight some things more strongly than others. We have to decide how much research intensity to invest into each disease and as we are going, we’ll keep having to re-assess the strategy and take into account new diseases. But fortunately, we have a growing team of collaborators who are interested in helping us develop these crops.
Check out the other interviews in the series!
Interview with a Plant Scientist: Brandon Schlautman, Perennial Legumes
Interview with a Plant Scientist: Stan Cox, Perennial Sorghum
Interview with a Plant Scientist: David Van Tassel, Perennial Oilseeds
Interview with a Plant Scientist: Shuwen Wang, Perennial Wheat
Interview with a Plant Scientist: Lee De Haan, Kernza®
Support the work of Kathryn and other plant breeders at The Land Institute.