Transforming Agriculture, Perennially

Crop Protection Genetics

Disease in plants

Intermediate wheatgrass naturally infected with spot blotch in a nested association mapping population at TLI.

Infections caused by certain bacteria, viruses, and fungi can limit crop yields by reducing nutrient uptake, preventing flowering, or even causing death. Throughout history, diseases have led to major crop epidemics resulting in food shortage and famine. Besides lowering yields, some pathogens produce toxins that make the crop unsuitable for consumption. The Fusarium fungus infects wheatgrass (Kernza®) heads and produces compounds toxic to humans and livestock. But not all microbes negatively affect plants – a few are beneficial and many have no detectable effects.

In 2018, TLI started a program to understand and control the diseases in our perennial crops. In this new program, we first want to identify potential pathogens, develop methods for monitoring their infection rates and measure their damage, and determine which are most problematic. We plan to use sequence and enzyme-based technologies combined with observation to identify the pathogens. Pathogens that do not infect other crops but are specific to our novel crops will require intensive evaluation.   

Fusarium head blight causing pathogen, Fusarium graminearum, macroconidia spores magnified by 40x under a light microscope at TLI.

Crops on the defensive

Plants have many strategies to avoid and limit infection. Structures like thick cell walls, protective leaf cuticles, and seed coats serve as barriers to pathogens. Some plants produce defensive compounds that have antifungal or antibiotic properties that kill or deter microorganisms. Silphium, for example, has high resin content that may deter pests and pathogens from attacking its leaves. Plants have also evolved systems to detect invasion and activate chemical responses to prevent the spread of pathogens. Perennial wheat has genes that are activated when attacked, killing parts of its own leaves around the pathogen to prevent it from spreading. Intermediate wheatgrass (Kernza) has many defense genes that have been used to improve annual wheat varieties against multiple diseases.

After developing ways to measure important diseases, we will search for plants with innate defenses.  If a defense is heritable, breeders can select and cross the resistant individuals that employ different defense strategies to develop disease resistant populations or varieties.

Resting stage teliospores of the fungus Puccinia silphii that causes rust disease in Silphium species, stained with iodine and magnified by 40× at TLI. (Fig. 4 in Vilela et al. 2018 Sustainability)

Fighting on our own turf with reinforcements

As managers of agricultural systems, humans assist crops by controlling weeds, pests, and diseases. We typically use disruptive methods like tillage and chemical control, but in natural grasslands, forces like fire and grazing manage these problems. These strategies can have many beneficial effects in reducing the size of pathogen populations. We plan to test and use strategies such as burning and timing of biomass harvest in developing a natural systems agriculture.

We also plan to incorporate diversity on multiple levels.  We predict that genetic diversity within our crop species can reduce the ability of certain pathogen strains from becoming dominant and causing severe damage. Incorporating diversity at the community level by growing companion plants in polyculture could be structured to physically limit pathogen spread or reduce the humidity required for the reproduction of particular pathogens. To utilize diversity from other kingdoms, we plan to identify potentially pathogenic and beneficial microbes through genetic approaches. After experimentation, we may be able to employ beneficial microbes to deter or compete with pathogens as a biocontrol strategy.

Striving for long-lasting peace (or de-escalation)

Early rust infection in silphium plant at TLI.

We are very interested in studying the long term role of disease in perennial systems and the impact of polyculture.  There is a strong likelihood that some pathogens will persist and may accumulate over time, while other pathogens will diminish due to seasonal variation or competition. We expect some of those pathogens like viruses and belowground microbes may colonize the plants and become very difficult to eliminate. Because plant diversity is unlikely to control these less mobile types of pathogen, avoiding the initial infection through management, using host defense, or employing biocontrol may help to reduce the pathogen population sizes. Our goal is not to completely eliminate all disease. Allowing small levels of infection is not only practical, but can prevent pathogens from evolving to circumvent plant disease resistance genes, which has led to severe epidemics in the past.

Project Team

Kathryn Turner
Research Associate, Crop Protection Genetics

Selected Publications

Abstract: New crops with greater capacity for delivering ecosystem services are needed to increase agricultural sustainability….

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Abstract: Silflower (Silphium integrifolium Michx.) is in the early stages of domestication as a perennial version…

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