Temporal dynamics and population genetic structure of Fusarium graminearum in the upper Midwestern United States

• Population structure has persisted in sympatry for over 15 years in F. graminearum.
• Frequency of 3ADON chemotype strains increased over the last 15 years.
• NX-2 isolates have been present at low frequency at least since the year 2000.
• Further testing may show that NX-2 isolates constitute a distinct population.

Fusarium graminearum sensu stricto causes Fusarium head blight (FHB) in wheat and barley, and contaminates grains with several trichothecene mycotoxins, causing destructive yield losses and economic impact in the United States. Recently, a F. graminearum strain collected from Minnesota (MN) was determined to produce a novel trichothecene toxin, called NX-2. In order to determine the spatial and temporal dynamics of NX-2 producing strains in MN, North Dakota (ND) and South Dakota (SD), a total of 463 F. graminearum strains were collected from three sampling periods, 1999–2000, 2006–2007 and 2011–2013. A PCR-RFLP based diagnostic test was developed and validated for NX-2 producing strains based on polymorphisms in the Tri1 gene. Trichothecene biosynthesis gene (Tri gene)-based polymerase chain reaction (PCR) assays and ten PCR-restriction fragment length polymorphism (RFLP) markers were used to genotype all strains. NX-2 strains were detected in each sampling period but with a very low overall frequency (2.8%) and were mainly collected near the borders of MN, ND and SD. Strains with the 3ADON chemotype were relatively infrequent in 1999–2000 (4.5%) but increased to 29.4% in 2006–2007 and 17.2% in 2011–2013. The distribution of 3ADON producing strains also expanded from a few border counties between ND and MN in 1999–2000, southward toward the border between SD and MN in 2006–2007 and westward in 2011–2013. Genetic differentiation between 2006–2007 and 2011–2013 populations (3%) was much lower than that between 1999–2000 and 2006–2007 (22%) or 1999–2000 and 2011–2013 (20%) suggesting that most change to population genetic structure of F. graminearum occurred between 1999–2000 and 2006–2007. This change was associated with the emergence of a new population consisting largely of individuals with a 3ADON chemotype. A Bayesian clustering analysis suggested that NX-2 chemotype strains are part of a previously described Upper Midwestern population. However, these analyses also suggest that the NX-2 isolates could represent a distinct population, but that interpretations of population assignment are influenced by the small number of NX-2 strains available for analysis.