NCCC307: Biochemistry and Genetics of Plant-Fungal Interactions

(Multistate Research Coordinating Committee and Information Exchange Group)

Status: Active

NCCC307: Biochemistry and Genetics of Plant-Fungal Interactions

Duration: 10/01/2023 to 09/30/2028

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Fungi cause severe diseases on diverse crops leading to billion dollars losses to agriculture production each year.  In addition to less plant yield, many fungi produce chemicals that are threats to food and feed safety because of their frequent toxicity and occurrence in crops.  The management of fungal disease relies primarily on the breeding of host resistance, the application of fungicides, and the use of cultural practices such as crop rotation. Although these control strategies do mitigate losses, the yearly persistence of plant disease epidemics, due increasingly to general increases in elevated temperatures and drought conditions, necessitate the development of novel control measures that are economically sound and environmentally sustainable.  The biological understanding of fungal pathogens and their host-pathogen interactions is critical for this discovery process. Unfortunately, our understanding of the biochemical and genetic basis of fungal pathogenicity is limited, which has hindered fundamental advances in disease control strategies. 

It is critical to the development of effective and long-term control measures that we better understand plant-fungal interactions and the response of plants to pathogens and other plant microbiota. Appreciating the complexity of these interactions begins with the knowledge that phytopathogenic fungi express several different pathogenic lifestyles including biotrophy, hemibiotrophy, and necrotrophy, and may show tissue specificity or microhabitat preferences. Within each of these lifestyles, pathogenesis may be correlated to toxin synthesis, production of extracellular enzymes or effectors that modulate plant defense, specific developmental programs, or detoxification activities. Under some conditions, fungi may even grow as an endophyte (asymptomatic) in planta.  The level of complexity surrounding pathogenesis studies is increased due to the potential co-occurrence of numerous plant pathogenic fungi of agricultural importance. Superimposed on this complexity are the effects of changing climate conditions and the introduction of non-native pathogens into naïve host populations. Current modeling projects an increase in pathogen epidemics and mycotoxin levels in the future. In order to realistically make advances in understanding pathogenesis and hence, provide insightful information for the development of management tools, the multi-disciplinary complexities involved in host-pathogen interactions must be simultaneously studied with several fungal genera and even other microbiota. If granted a renewal, the NCCC-307 committee will conduct meetings in which individuals from diverse disciplines, working with diverse fungal systems will interact, exchange knowledge, and thus better understand host-fungal interactions and identify the outstanding questions of fundamental value to mitigating losses from fungal pathogens.

This multistate group was initiated in 1991 (first meeting - January 1992) as NCR-173, renewed in 1994, 1998, 2003 as NCCC-173, renewed in 2008 as NCCC-207 and renewed in 2013 and 2018 as NCCC-307. This group began by focusing on the genetics and biochemistry of host-fungal interactions in the genus Colletotrichum, as it was a model fungal system for the study of phytopathogenesis. Collectively, Colletotrichum species are easy to maintain and manipulate in culture, numerous research laboratories worldwide study this genus, and plant bioassays, biochemical, molecular, and genetic protocols have been optimized. By focusing our efforts on a single genus, an enormous amount of information was quickly obtained from the various labs. The exchange of ideas and results in subsequent meetings allowed us to begin building the foundation for understanding the basis of plant-fungal interactions. Through collaborative interactions made possible by this NCCC committee, understanding the genetic and molecular basis of pathogenicity in the fungal genus Colletotrichum has been advanced significantly. The emphasis on Colletotrichum pathogens was expanded to other fungal genera in the early 2000s. Members of the group have active research programs on several different pathogenic fungal genera including Alternaria, Fusarium, Magnaporthe, Sclerotinia, Aspergillus, Cochliobolus, Pyrenophera, Monilinia, and Ustilago. As a result of this increasing scientific diversity in our membership, we have increased the level and caliber of scientific exchange. Major areas of research focus on intercellular communication between fungal and plant cells, classical genetic analysis of quantitative traits, molecular systematics, chromosome evolution, molecular transformation and reporter gene tool development, functional gene analysis, and genetic aspects of host-pathogen compatibility.

The group has increasingly challenged itself with understanding fundamental concepts and the underlying processes governing compatibility in fungal-plant interactions. We have met annually, and these sessions have fostered scientific information exchange and coordination of research efforts and management strategies concerning fungal diseases. Examples of collaborative projects (funded and unfunded) and publications involving members of the group and meeting participants are included here:


Representative Grants:

The Role of Mating-type Genes in Pathogenicity of Fusarium graminearum to Wheat.  US Wheat and Barley Scab Initiative Project ID FY18-VA-005.  2018 and 2019 for $86,286.  PI Lisa Vaillancourt, University of Kentucky and CoPI Frances Trail, Michigan State University.

Cloning and validation of new Parastagonospora nodorum necrotrophic effectors and further characterization of SnTox1 and the SnTox1-Snn1 interaction, Agriculture and Food Research Initiative Competitive Grant no. 2016-67013-24813 from the USDA National Institute of Food and Agriculture.” 2016-2019, $472,400 PD – Tim Friesen USDA, CoPI - Zhaohui Liu North Dakota State University


Representative Informal collaborations:

During the informal portion of our yearly meetings, participants describe their insights and experiences on the “subtleties” of working with fungi, resulting in the sharing of strains, plasmids, and protocols.

Former NCCC307 members and current guest attendees R. Redman and R. Rodriguez, Adaptive Symbiotic Technologies, provided fungal cultures free of charge to J. Lorang for field trials and use in University classroom demonstrations.

J. Slot provided advice on horizontal gene transfer to R. Todd which led to a substantial savings in effort to Dr. Todd and a formal acknowledgment in the published manuscript.

Guest Patricia Santos received fungal transformation plasmids constructed in former NCCC307 member L. Ciuffettii’s lab, published by J. Lorang et. al.

Despite the emphasis on host-pathogen interactions, the NCCC-307 group has continually stressed interdisciplinary activities that are clearly reflected in the makeup of our participants. NCCC-307 members include classical geneticists, population biologists, evolutionary biologists, molecular biologists, physiologists, mycotoxicologists, plant molecular biologists, field epidemiologists, and pest management research and extension scientists. Thus, this is an exceptional collaborative interaction between a blend of basic and applied scientists representing land grant universities, private industry, and government. We also have guest attendees from throughout the region, the country, and internationally. Guest attendees include members of fungal-based industries engaged in translational research developing microbial products for agriculture. The interdisciplinary nature of the NCCC-307 members has allowed several laboratories to make greater advances than if the group were restricted to specific labs or systems. The inclusion of scientists studying host-parasite interactions in other fungal systems has proven to be of tremendous value. Collectively, these fungi express several different pathogenic lifestyles (biotrophy, hemibiotrophy, and necrotrophy) and show tissue specificity or microhabitat preferences. In addition, classical genetic analysis, biochemical, molecular, and applied field studies addressing plant-fungal interactions are presently being addressed in these systems. By widening our scope from a single model system to encompass several model systems, the information shared allows us to compile and analyze a great deal of information regarding the universal similarities and unique differences involved in pathogenesis. In so doing, NCCC-307 has broadened its scope and generated new synergisms. In this renewal, we propose to maintain the scientific diversity of the committee and bring focused attention to identifying the most significant outstanding questions concerning fungal-host interactions, identifying approaches to answering these questions, and communicating these ideas to USDA national program leaders and funding directors.  Collectively, the knowledge generated by member labs will help guide plant breeding and engineering efforts, as well as biological control and cultural methods, to reduce plant diseases and toxin contamination, especially in the face of a changing climate.


  1. Bring together scientists that study the genetics and biochemistry of fungal-plant interactions in several different economically important fungal genera having different trophic interactions with plants. These genera include Alternaria, Aspergillus, Cochliobolus, Colletotrichum, Fusarium, Magnaporthe, Monilinia, Pyrenophora, Sclerotinia and Ustilago.
  2. Continue the coordination of common and unique genetic and/or biochemical research on the economically important fungal genera named in Objective 1.
  3. As a logical extension of Objective 2, identify common and unique genetic and/or biochemical components of plant hosts and their microbiomes that facilitate or deter diverse fungal-plant associations of the economically important fungal genera named in Objective 1.
  4. Integrate research findings concerning the biology and genomics of plant-fungal interactions with new information about resistance mechanisms in host plants and plant microbiomes (integrate Objectives 2 and 3), thereby providing field pathologists and agronomists with improved management strategies against plant pathogens.
  5. Explore new and collaborative funding possibilities to enhance activities.

Procedures and Activities

Researchers studying the genetics, molecular biology and biochemistry host-fungal interactions are brought together annually to meet to share research and discuss coordinated research among participants. These meetings facilitate new research and funding collaborations, the standardization of research protocols, and the advancement of fundamental ideas concerning fungal-plant interactions. Members of the committee routinely publish in peer-reviewed journals including several joint, collaborative publications.

Expected Outcomes and Impacts

  • Exchange of ideas/information/data/resources Comments: This committee seeks to provide and encourage an open, critical, and accessible platform for the discussion of the Biochemistry and Genetics of Plant-Fungal Interactions via an annual meeting. This meeting will enhance productivity and save time and money by sharing the most recent resources and ideas. The makeup of the committee and the atmosphere created at the meetings is meant to encourage discussion of unpublished results in the context of the latest data and concepts of fungal-plant interactions. As such, the meeting must maintain and foster a noncompetitive, mutually beneficial and collaborative environment. This has in the past stimulated participants to refine hypotheses and pursue novel research approaches to address outstanding and long-term problems associated with fungal diseases of plants. The impact of this research has been a clearer understanding of basic factors and mechanisms underlying host-pathogen interactions which directly impacts the strategies breeders, chemical companies and other researchers use to select, screen and manage diseases.
  • Coordination of specific laboratory and field research Comments: Streamline experimental designs to address hypothesis driven questions applicable to all systems. Enhance data collection, analysis, and interpretation utilizing a multi-disciplinary approach. Coordination of studies and communication through collaboration has resulted in rapid accumulation and sharing of information to better understand processes involved in plant-fungal interactions. This coordination will continue to positively impact the rate of discovery in fundamental and field-based research on fungal-plant interactions.
  • Publication of both individual and joint research/review articles Comments: Enhance the available information base allowing for the better understanding of plant-fungal interactions. This information has been and will continue to be utilized to provide guidance for the development of management tools to enhance economic productivity and promote environmental stewardship.

Projected Participation

View Appendix E: Participation

Educational Plan

Research relevant to NCC307 objectives is communicated to the public by our members through publication in journal articles and presentations at national and international scientific meetings. Members' graduate students and post-doctoral associates are encouraged to present their research projects at our annual meetings and typically comprise 80% of the speakers.  This gives them a unique opportunity to present research to a friendly but rigorous audience and helps to foster future collaborations.  Annual meetings are conducted during the Fungal Genetics Conference, to encourage wide participation, but also in different states on alternate years, so that travel to the meeting will be advantageous for different subsets of members.


There will be two officers for this committee. A secretary will be elected every three years at the appropriate annual meeting. The secretary records and distributes minutes of the annual meeting, and then becomes chair of the committee for the following two years. The chair directs the activities of the committee, serves as the liaison between the committee and the administrative advisor, and makes arrangements for the next annual meeting. In addition, a local host will be selected each year who will be responsible for choosing the location for the next meeting and coordinating local arrangements with the chair.

Literature Cited

Representative Publications

Thapa, V., Keller, N. P., Roossinck, M. J., 2022. Evaluation of virus-free and wild-type isolates of Pseudogymnoascus destructans using a porcine ear model. mSphere. 7, e0102221.

Richards, J. K., Kariyawasam, G. K., Seneviratne, S., Wyatt, N. A., Xu, S. S., Liu, Z., Faris, J. D., Friesen, T. L., 2022. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. New Phytol. 233, 427-442.

Won, T. H., Bok, J. W., Nadig, N., Venkatesh, N., Nickles, G., Greco, C., Lim, F. Y., Gonzalez, J. B., Turgeon, B. G., Keller, N. P., Schroeder, F. C., 2022. Copper starvation induces antimicrobial isocyanide integrated into two distinct biosynthetic pathways in fungi. Nat Commun. 13, 4828.

Geiser, D. M., Al-Hatmi, A., Aoki, T., Arie, T., Balmas, V., Barnes, I., Bergstrom, G. C., Bhattacharyya, M. K. K., Blomquist, C. L., Bowden, R., Brankovics, B., Brown, D. W., Burgess, L. W., Bushley, K., Busman, M., Cano-Lira, J. F., Carrillo, J. D., Chang, H. X., Chen, C. Y., Chen, W., Chilvers, M. I., Chulze, S. N., Coleman, J. J., Cuomo, C. A., de Beer, Z. W., de Hoog, G. S., Del Castillo-Munera, J., Del Ponte, E., Dieguez-Uribeondo, J., Di Pietro, A., Edel-Hermann, V., Elmer, W. H., Epstein, L., Eskalen, A., Esposto, M. C., Everts, K. L., Fernandez-Pavia, S. P., da Silva, G. F., Foroud, N. A., Fourie, G., Frandsen, R. J. N., Freeman, S., Freitag, M., Frenkel, O., Fuller, K. K., Gagkaeva, T., Gardiner, D. M., Glenn, A. E., Gold, S., Gordon, T., Gregory, N. F., Gryzenhout, M., Guarro, J., Gugino, B., Gutierrez, S., Hammond-Kosack, K., Harris, L. J., Homa, M., Hong, C. F., Hornok, L., Huang, J. W., Ilkit, M., Jacobs, A., Jacobs, K., Jiang, C., Jimenez-Gasco, M. D. M., Kang, S., Kasson, M. T., Kazan, K., Kennell, J. C., Kim, H., Kistler, H. C., Kuldau, G. A., Kulik, T., Kurzai, O., Laraba, I., Laurence, M. H., Lee, T. Y., Lee, Y. W., Lee, Y. H., Leslie, J. F., Liew, E. C. Y., Lofton, L. W., Logrieco, A., Sanchez Lopez-Berges, M., Luque, A. G., Lysoe, E., Ma, L. J., Marra, R. E., Martin, F. N., May, S. R., McCormick, S., McGee, C. T., Meis, J. F., Migheli, Q., Mohamed Nor, N. M. I., Monod, M., Moretti, A., Mostert, D., Mule, G., Munaut, F., Munkvold, G. P., Nicholson, P., Nucci, M., O'Donnell, K., Pasquali, M., Pfenning, L. H., Prigitano, A., Proctor, R., Ranque, S., Rehner, S., Rep, M., Rodriguez-Alvarado, G., Rose, L. J., Roth, M. G., Ruiz-Roldan, C., Saleh, A. A., Salleh, B., Sang, H., Scandiani, M., Scauflaire, J., Schmale, D., 3rd, Short, D. P., Sisic, A., Smith, J., Smyth, C. W., Son, H., Spahr, E., Stajich, J. E., Steenkamp, E., Steinberg, C., Subramaniam, R., Suga, H., Summerell, B. A., Susca, A., Swett, C. L., Toomajian, C., Torres-Cruz, T. J., Tortorano, A. M., Urban, M., Vaillancourt, L. J., Vallad, G. E., van der Lee, T., Vanderpool, D., van Diepeningen, A. D., Vaughan, M., Venter, E., Vermeulen, M., Verweij, P. E., Viljoen, A., Waalwijk, C., Wallace, E. C., Walther, G., Wang, J., Ward, T., Wickes, B., Wiederhold, N. P., Wingfield, M. J., Wood, A. K. M., Xu, J. R., Yang, X. B., Yli-Matilla, T., Yun, S. H., Zakaria, L., Zhang, H., Zhang, N., Zhang, S., Zhang, X., 2021. Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani species complex. Phytopathology. 111, 1064-1079.

Mínguez, J. M., Donofrio, N. M., Espeso, E., Fernandes, T. R., Goldman, G. H., Judelson, H., Nordzieke, D., Di Pietro, A., Sionov, E., Sukno, S. A., Thon, M. R., Todd, R. B., Voll, L., Xu, J. R., Horwitz, B. A., Wilson, R. A., 2020. Nutritional factors modulating plant and fruit susceptibility to pathogens: BARD workshop, Haifa, Israel, February 25–26, 2018. Phytoparasitica. 48, 317-333.

Reynolds, H. T., Slot, J. C., Divon, H. H., Lysoe, E., Proctor, R. H., Brown, D. W., 2017. Differential retention of gene functions in a secondary metabolite cluster. Mol Biol Evol. 34, 2002-2015.



Land Grant Participating States/Institutions


Non Land Grant Participating States/Institutions

Oregon State University, USDA-ARS Red River Agricultural Research Center, USDA-ARS/Georgia, USDA-ARS/Illinois
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