Genetic diversity of Australian Fusarium graminearum and F. pseudograminearum

Genotypic diversity in Fusarium pseudograminearum and F. graminearum from Australia and the relationship between diversity and pathogen aggressiveness for head blight and/or crown rot of wheat were examined. Amplified fragment length polymorphism (AFLP) analysis revealed a high level of genotypic diversity within each species. Sixty-three of the 149 AFLP loci were significantly different between the two species and 70 of 72 F. pseudograminearum and 56 of 59 F. graminearum isolates had distinct haplotypes. When head blight and crown rot severity data from a recently published work on isolates representing the entire range of aggressiveness were used, only the genotypic diversity of F. pseudograminearum was significantly associated with its aggressiveness for the two diseases. Cluster analyses clearly demonstrated the polyphyletic structures that exist in both pathogen populations. The spatial diversity within F. graminearum was high within a single field, while frequent gene flow ( N _m ∼ 14) and a low fixation index ( G _st = 0·03) were recorded among F. pseudograminearum isolates from the adjacent states of New South Wales and Queensland. The differences in population structure between the heterothallic F. pseudograminearum (teleomorph G. coronicola ) and the homothallic F. graminearum (teleomorph G. zeae ) were not as pronounced as expected given their contrasting mating systems. Neither species was panmictic or strictly clonal. This points to sexual recombination in F. pseudograminearum , suggesting that ascospores of G. coronicola may also play a role in its biology and epidemiology.     

Genotypic diversity in Fusarium pseudograminearum populations in Australian wheat fields

Despite being closely related to Fusarium graminearum, which has been extensively characterized in many countries around the world, the population biology of Fusarium pseudograminearum, the main causal agent of crown rot of wheat in Australia and many other wheat‐growing regions, has been comparatively poorly studied to date. A simple sequence repeat analysis of 163 F. pseudograminearum isolates from three field sites in NSW, Australia identified 128 distinct multilocus genotypes. Observed genetic diversity within fields was high, whilst genetic variation between fields was low. Across all fields genetic linkage disequilibrium was detected, but of the three individual fields, only one also displayed linkage disequilibrium. These results indicate that the isolates obtained were part of the same, highly diverse, population. However, this population may not be freely interbreeding. Whilst isolation incidence of F. pseudograminearum was found to be spatially aggregated within fields, spatial aggregation of genotypes within fields was weak. The study suggests that processes influencing population dynamics may operate at a scale larger than the narrow geographical scale covered in the fields sampled.     

Mycelial compatibility reactions of Australian Fusarium graminearum and F. pseudograminearum isolates compared with AFLP groupings

Using the mycelial reactions of 435 combinations of 14 Fusarium pseudograminearum and 15 F. graminearum isolates, it was demonstrated for the first time that mycelial reactions/barrage formation cannot be clearly used to distinguish F. graminearum and F. pseudograminearum. Mutually compatible isolates produced very different patterns of compatibility with other isolates. However, about 60% of pairings between F. graminearum and F. pseudograminearum isolates were compatible, indicating common ancestry. The Mantel tests used to determine any possible associations between mycelial compatibility reactions and AFLP genotypic diversity data revealed no association between the two systems in either species. In addition, no association was found between mycelial compatibility reactions and sexual reproduction in the two species. Implications of the higher frequency of mycelial compatibility reactions observed in F. pseudograminearum than in F. graminearum are discussed.     

Genetic structure of Fusarium pseudograminearum populations from the Australian grain belt

Crown rot, caused by the fungus Fusarium pseudograminearum (teleomorph Gibberella coronicola) is a major disease of wheat in the Australian grain belt. However, there is little information available on the population structure of this pathogen. We measured genetic diversity as assessed with amplified fragment length polymorphism (AFLP) analysis within and between populations of F. pseudograminearum from northeastern, south central, and southwestern regions of the Australian grain belt. Amongst the 217 isolates, 176 haplotypes were identified and grouped into two main clusters. One cluster contained isolates from populations in northeastern Australia, and the other cluster contained isolates from populations in south central and southwestern Australia. The southern populations were distinguished from the northeastern populations by higher levels of population differentiation (Gst) between them and genetic identity amongst the regional populations. We hypothesize that the F. pseudograminearum populations from northeastern and southern Australia are independent, which could result from different founding events or from geographic isolation and the accumulation of genetic differences due to genetic drift and/or selection.     

Phenotypic and molecular characterization of the resistance to azoxystrobin and pyraclostrobin in Fusarium graminearum populations from Brazil

Wheat farmers rely on fungicides to protect fields against several foliar and flowering diseases, including Fusarium head blight (FHB). A range of active ingredients is used in isolation or in dual premixes that include a dimethylation inhibitor (DMI) or a quinone outside inhibitor (QoI) fungicide. Comprehensive information about fungicide resistance in F. graminearum is available for DMIs, while for QoIs the data are scarce. We characterized 225 strains obtained from two states in southern Brazil, Rio Grande do Sul (RS) and Paraná (PR), in relation to their response to two QoIs. The median EC₅₀ (effective concentration leading to 50% inhibition of conidial germination) value for azoxystrobin (n = 25 isolates) was 2.20 μg/ml in the PR population and 4.04 μg/ml in the RS population. For pyraclostrobin (n = 50), the median EC₅₀ was 0.28 μg/ml in the PR population and 0.24 μg/ml in the RS population. Evidence of cross-resistance could not be detected. Screening using a discriminatory dose (DD) for azoxystrobin in a larger number of isolates from PR (n = 75) and RS (n = 100) states allowed the detection of 50% and 28% sensitive strains, respectively. Using the DD for pyraclostrobin, 33% and 18.8% were classified as less sensitive in the PR and RS isolates, respectively. In RS, the frequency of less-sensitive isolates increased over time (2007–2011). No point mutation at any of the target spots (F129L, G137R, G143A) was detected. Our results represent an important step towards the establishment of a sensitivity profile for two of the most commonly used QoIs in commercial premixes targeting FHB control.     

Fusarium graminearum and Fusarium pseudograminearum caused the 2010 head blight epidemics in Australia

Wheat crops in southeast Queensland (Qld) and northern New South Wales (NSW) were infected with fusarium head blight (FHB)‐like symptoms during the 2010–11 wheat growing season. Wheat crops in this region were surveyed at soft dough or early maturity stage to determine the distribution, severity, aetiology and toxigenicity of FHB. FHB was widespread on bread wheat and durum, and Fusarium graminearum and/or F. pseudograminearum were diagnosed from 42 of the 44 sites using species‐specific PCR primers directly on spikelets or from monoconidial cultures obtained from spikelets. Stem base browning due to crown rot (CR) was also evident in some samples from both states. The overall FHB and CR severity was higher for NSW than Qld. Deoxynivalenol (DON) concentration of immature grains was more than 1 mg kg^?1 in samples from 11 Qld and 14 NSW sites, but only 13 of 498 mature grain samples sourced from the affected areas had more than 1 mg kg^?1 DON. DON concentration in straw also exceeded 1 mg kg^?1 in eight Qld and all but one NSW sites but this was not linked to DON concentration of immature grains. The proportion of spikelets with positive diagnosis for F. graminearum and/or F. pseudograminearum and weather‐related factors influenced DON levels in immature grains. The average monthly rainfall for August–November during crop anthesis and maturation exceeded the long‐term monthly average by 10–150%. Weather played a critical role in FHB epidemics for Qld sites but this was not apparent for the NSW sites, as weather was generally favourable at all sites.     

Comparative analysis of genetic structures and aggressiveness of Fusarium pseudograminearum populations from two surveys undertaken in 2008 and 2015 at two sites in the wheat belt of Western Australia

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.     

Fusarium pseudograminearum as an emerging pathogen of crown rot of wheat in eastern China

Fusarium crown rot of wheat has been spreading in the Huanghuai wheat-growing area in China since 2010, leading to a potential yield loss. To investigate the pathogens associated with this disease in Jiangsu and Shandong provinces in recent years, 617 Fusarium isolates were isolated from nine sites in these two provinces between 2014 and 2016. Of these isolates, 372 were identified as Fusarium pseudograminearum, and the remaining isolates were identified as F. asiaticum and F. graminearum, suggesting that F. pseudograminearum is becoming a predominant causative pathogen of crown rot of wheat in eastern China. Trichothecene gene detection and chemical analyses of trichothecenes indicated that the F. pseudograminearum isolates belonged to the 3-ADON or 15-ADON chemotype, and one isolate had the NIV genotype but produced no detectable NIV. 3-ADON isolates were predominant in Jiangsu, whereas 15-ADON isolates were prevalent in Shandong. The mating type of the F. pseudograminearum isolates were identified. MAT-1 and MAT-2 existed, but in most collections, particularly those in Jiangsu, the ratios of the two mating types deviated significantly from an expected 1:1 ratio. The reason for the occurrence of F. pseudograminearum is hypothesized, and the chemotype and mating type distribution of this species in these two provinces are analysed.     

Genetic population structure and trichothecene genotypes of Fusarium graminearum isolated from wheat in southern Brazil

A sample of 140 Fusarium graminearum isolates from Rio Grande do Sul, Brazil, representing three populations at least 150 km from one another, were examined for trichothecene genotype based on PCR amplification of portions of the Tri3 and Tri12 genes and a species‐specific (Fg16F/R) primer pair. Genetic diversity was assessed in a sample of 103 F. graminearum lineage 7 (F. graminearum sensu stricto) isolates using amplified fragment length polymorphism (AFLP) markers. The 15‐ADON genotype was dominant, followed by the NIV genotype (2–18% prevalence), across all three populations. All NIV‐type isolates were in lineage 2 (F. meridionale) and all 15‐ADON‐type isolates were in lineage 7. Isolates with the same haplotype were rare and genotypic diversity was uniformly high (≥98% of the count), suggesting that recombination has played a significant role. The number of migrants (N_m) was estimated between 5 and 6 across all loci and all populations, but the high frequency of private alleles (up to 30%) suggests a historical, rather than contemporary, gene flow. Regarding linkage disequilibrium, 0·8, 1·5 and 2·2% of the locus pairs from the three populations were in disequilibrium, which is lower than values reported in other locations. Thus, Brazilian populations differ from those found in Europe, North America and most of Asia in the presence of a significant frequency (7·8%) of isolates of the NIV genotype in lineage 2.     

Genetic structure of <Emphasis Type="Italic">Fusarium verticillioides</Emphasis> populations isolated from maize in Argentina

Fusarium verticillioides (sexual stage Gibberella moniliformis) is a common fungal pathogen of maize worldwide that also produces fumonisin mycotoxins. Populations of this fungus can be diverse with respect to neutral and selectable genetic markers. We used vegetative compatibility groups (VCGs) and amplified fragment length polymorphisms (AFLPs) to evaluate the genetic structure of three F. verticillioides populations from commercial maize fields in Argentina. Based on work with similar populations from outside South America, we expected individuals within the populations to be genetically diverse, that genotypic variation would be distributed in a manner consistent with random mating, and that populations from different locations would be genetically indistinguishable from one another. We analysed 62 AFLP loci for 133 fungal isolates. All three populations were genotypically diverse but genetically similar and potentially part of a larger, randomly mating population, with significant genetic exchange occurring between the three subpopulations. There was no evidence for linkage disequilibrium at P = 0.05. The low values of G _ST , the lack of frequent private alleles, and the lack of a systemic pattern of linkage disequilibrium all suggest that sexual reproduction is sufficiently common in F. verticillioides and that the dispersal of strains is sufficiently efficient for the population of F. verticillioides in the main maize growing region to be a single randomly mating population with no detectable genetic subdivision. Thus differences in disease and/or toxin production observed in this region are best attributed to differences other than the genetic composition of the population.     

Vegetative compatibility grouping in Fusarium oxysporum f.sp. radicis-lycopersici from the UK, the Netherlands, Belgium and France

The population structure of Fusarium oxysporum f.sp. radicis-lycopersici ( F.o.r.l .), the causal agent of crown and root rot disease in tomato, was studied using the vegetative compatibility grouping approach. Four vegetative compatibility groups (VCGs) were identified among 37 isolates from the UK, the Netherlands, Belgium and France. Three of these VCGs (0090, 0091, 0094) had already been described, whereas VCG 0097 was new. VCG 0094 was dominant in the UK, the Netherlands and Belgium, but not in France. The opposite was true for the cosmopolitan VCG 0091, while the cosmopolitan VCG 0090 was only found in France. Based on hyphal interactions, VCG 0094 was divided into three subgroups, each comprising isolates from at least two countries. One isolate of VCG 0094 did not belong to any of these subgroups, suggesting further variability in this VCG. Isolate FORL-19R from France, previously assigned to VCG 0090 I, was reassigned to VCG 0090 III, a new subgroup of VCG 0090 found in Israel. FORL-19R and additional members of its subgroup manifest cross-VCG compatibility between VCG 0090 and VCG 0092. Along with previous studies, the multiple VCGs and subgroups found among F.o.r.l . in western Europe demonstrate a high level of genetic diversity in this pathogen.