This study examines the CO 2 -mediated influence of plant resistance on crown rot dynamics under continuous cropping of partially resistant wheat line 249 and the susceptible cultivar Tamaroi. Disease incidence, severity, deoxynivalenol and Fusarium biomass were assessed after each cycle in microcosms established at ambient and 700 mg kg À1 CO 2 using soil and stubble of these wheat lines from a field experiment with free to air CO 2 enrichment. Monoconidial isolates from wheat stubble were collected initially, and after five cropping cycles, to compare the frequency and aggressiveness of Fusarium species in the two populations. Aggressiveness was measured using a high-throughput seedling bioassay. At elevated CO 2 , the higher initial incidence in Tamaroi increased with cropping cycles, but incidence in 249 remained unchanged. Incidence at ambient CO 2 did not change for either line. Elevated CO 2 induced partial resistance in Tamaroi, but not in 249. Increased Fusarium biomass in wheat tissue at elevated CO 2 matched raised deoxynivalenol of the stem base in both lines. After five cycles of continuous wheat cropping, aggressiveness increased in pathogenic F. culmorum and F. pseudograminearum by 110%, but decreased in weakly pathogenic F. equiseti and F. oxysporum by 50%. CO 2 and host resistance interactively influenced species frequency, and the highly aggressive F. pseudograminearum became dominant on Tamaroi irrespective of CO 2 concentration, while its frequency declined on 249. This study shows that induced resistance at elevated CO 2 will not reduce crown rot severity, or impede the selection and enrichment of Fusarium populations with increased aggressiveness.

Fusarium crown rot (FCR), caused predominantly by Fusarium pseudograminearum (Fp) in Australia, is an important fungal disease of wheat and barley. FCR causes significant yield losses and reduced grain quality worldwide. This study investigated the population dynamics of FCR‐causing F. pseudograminearum isolates from Western Australia (WA), a major wheat‐growing region. Wheat samples were collected from a total of seven different sites in 2008 and 2015. Two sites, Tammin and Karlgarin, with moderate to high FCR incidence, were intensively sampled in both years. The results revealed significant increase in Fp isolation frequency between 2008 and 2015. Over 86% of 1100 Fusarium isolates were Fp in 2015 compared with 59% of 639 isolates from 2008. Mating type idiomorphs, toxin chemotypes and population genetic structures were determined for a subset of 279 Fp isolates (132 isolates from 2008 and 165 from 2015). Mating type analysis revealed differences in MAT1‐1 and MAT1‐2 distributions between Tammin and Karlgarin for both years. Results also showed that 97.6% of Fp isolates analysed had the 3‐ADON trichothecene chemotype. Additionally, for the first time in Australia, the 15‐ADON chemotype was identified in 2.3% and 2.4% of Fp isolates from 2008 and 2015, respectively. The genetic structure of Fp population determined using 21 cleaved amplified polymorphic sequence (CAPS) markers revealed a high level of genetic variation within and between populations. In addition, 2015 isolates from Tammin and Karlgarin were significantly more aggressive (P < 0.0001) than 2008 isolates. This finding may have implications in managing this significant fungal disease.