Cross-infectivity, Genomic Analysis, and Transcriptomic Profiling of Fusarium graminearum in Artificial Barley-Broadleaf Crop Rotation

Commodities

Practices

Crop rotation is a critical strategy for managing pests and pathogens. This practice is widely adopted in North Dakota, aiming to maximize profit by best-utilizing crops with complementary effects (NDSU Extension Service). It has certain benefits to the soil, particularly improving soil health and nutrient management. However, crop residues can harbor soil-borne fungal pathogens, such as Fusarium graminearum, and serve as inoculum sources for the next crop. F. graminearum primarily causes the devastating head blight disease in barley and wheat but has also been reported to cause disease in potatoes and soybeans, among other crops (Ali et al., 2005; Okello et al., 2020). Our initial experiments show that F. graminearum isolates collected from potatoes and barley can infect and cause discoloration to barley heads and lentil roots, respectively. These results add to the growing evidence of the ability of this fungus to cross-infect, along with its possible influence on crop rotation's success in managing the disease.

Crop rotation can be an effective tool for managing F. graminearum. Although several studies have been conducted in this area, genomic and transcriptomic aspects are limited. Compartalized or two-speed genomes have been described in some fungi, including F. graminearum (Dong et al., 2015; Wang et al., 2017). The fast sub-genome is a site for evolution, contains fewer genes, and is rich in repeat elements (Wang et al., 2017). Changes in the genome and transcriptome of F. graminearum in a barley-mediated crop rotation have not been documented. Our research specifically focuses on the ability of F. graminearum to change its genomic and transcriptomic landscape in response to a barley-broadleaf crop rotation. This will entail sequencing and screening of isolates based on their ability to infect barley, potatoes, and soybeans and then followed by an artificial crop rotation in the greenhouse where barley is the first crop, followed by a broadleaf (soybean or potato) or another cereal (barley or wheat) to serve as a comparison, using F. graminearum in a single or mixed population. We will do sequencing to determine the genomic and transcriptomic changes of each pair. The direct outcomes of this project will improve crop rotation strategies through a deeper understanding of these biological mechanisms. We intend to inform growers about our findings by attending field days and presenting our results to symposiums, forums, and conferences. We expect that farmers will consider changing their crop rotation sequence relative to the results of our study. 

Our proposal is a novel study linking the genomic and transcriptomic aspects to the well-known practice of crop rotation. For this reason, most of our outcomes will be on the learning side as we introduce these concepts to farmers and researchers alike. In this study, we will elucidate the changes in the genomic and transcriptomic landscape of F. graminearum in response to crops in rotation. A learning outcome from this project is knowing that F. graminearum present in barley crop residues poses a threat to the next crop in rotation. Another learning outcome is a better understanding by the farmers and fellow researchers about how genomic changes in F. graminearum, in single or mixed populations, allow it to infect several crops. Introducing genome compartmentalization or two-speed genome concept in F. graminearum is also a learning outcome for the farmers and stakeholders. An action outcome is for farmers to consider or change the crops they plant next to barley, considering the results of this project. Another action outcome is identifying potential avenues suitable for a follow-up project or even a collaboration with farmers and stakeholders to further the cause of the current study. The incorporation of results of our project to the existing extension materials covering crop rotation and crop production is also one of the action outcomes.