Toxigenicity and pathogenicity of <Emphasis Type="Italic">Fusarium poae</Emphasis> and <Emphasis Type="Italic">Fusarium avenaceum</Emphasis> on wheat

In a field experiment between 2004 and 2006, 14 winter wheat varieties were inoculated with either a mixture of three isolates of F. poae or a mixture of three isolates of F. avenaceum. In a subsequent climate chamber experiment, the wheat variety Apogee was inoculated with individual single conidium isolates derived from the original poly conidium isolates used in the field. Disease symptoms on wheat heads were visually assessed, and the yield as well as the fungal incidence on harvested grains (field only) was determined. Furthermore, grains were analysed using LC-MS/MS to determine the content of Fusarium mycotoxins. In samples from field and climate chamber experiments, 60 to 4,860 μg kg⁻¹ nivalenol and 2,400 to 17,000 μg kg⁻¹ moniliformin were detected in grains infected with F. poae and F. avenaceum, respectively. Overall, isolate mixtures and individual isolates of F. avenaceum proved to be more pathogenic than those of F. poae, leading to a higher disease level, yield reductions up to 25%, and greater toxin contamination. For F. poae, all variables except for yield were strongly influenced by variety (field) and by isolate (climate chamber). For F. avenaceum, variety had a strong effect on all variables, but isolate effects on visual disease were not reflected in toxin production. Correlations between visual symptoms, fungal incidence, and toxin accumulation in grains are discussed.     

Characterization of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">melongenae</Emphasis> isolates from Turkey with ISSR markers and DNA sequence analyses

Fusarium oxysporum f. sp. melongenae (Fomg), causal agent of Fusarium wilt of eggplant, is a serious pathogen in open fields and greenhouses. Inter-simple sequence repeat (ISSR) banding profiles, sequence analyses of inter-transcribed-spacer (ITS), translation elongation factor 1-alpha (TEF-1α), and actin (actA) DNA regions were employed in this study to determine genetic diversity and population structure of Fomg isolates obtained from Turkey. For ISSR study, (ACTG)₅, (GACAC)₃, (GACA)₄, (GATA)₄, HVH(TG)₇ and (CA)₈RG primers were selected from a set of 16. Discriminative ability of the primers revealed with various indices including polymorphic information content (PIC), and mean PIC value was calculated as 0.26. The ISSR data revealed 31 loci belonging to 202 Fomg isolates and 14 of them were found to be polymorphic. The isolates on neighbor joining ISSR tree were grouped into two major clusters which separated Fomg and outgroup isolates. Population structure was investigated based on bayesian modeling and results indicated five subpopulations (K = 5, ?K = 205.42). Mean genetic and geographical distances among sampling locations revealed only a weak and insignificant correlation (r = 0.583, P = 0.06). Phylogenetic analyses were carried out with ITS, TEF-1α and actA DNA regions with a selected subset of 30 Fomg, along with one non-host and one outgroup isolates. Since ITS region were not able to provide a meaningful separation, TEF-1α and actA sequences of each organism were concatenated individually to build a dendrogram. The clustering tree successfully separated the Fomg, non-host and outgroup isolates in which all Fomg were located on the same branch, forming a monophyletic group in the dendrogram.     

Genetic variation among <Emphasis Type="Italic">Fusarium</Emphasis> isolates from onion,and resistance to <Emphasis Type="Italic">Fusarium</Emphasis> basal rot in related <Emphasis Type="Italic">Allium</Emphasis> species

The aim of this research was to study levels of resistance to Fusarium basal rot in onion cultivars and related Allium species, by using genetically different Fusarium isolates. In order to select genetically different isolates for disease testing, a collection of 61 Fusarium isolates, 43 of them from onion (Allium cepa), was analysed using amplified fragment length polymorphism (AFLP) markers. Onion isolates were collected in The Netherlands (15 isolates) and Uruguay (9 isolates), and received from other countries and fungal collections (19 isolates). From these isolates, 29 were identified as F. oxysporum, 10 as F. proliferatum, whereas the remaining four isolates belonged to F. avenaceum and F. culmorum. The taxonomic status of the species was confirmed by morphological examination, by DNA sequencing of the elongation factor 1-α gene, and by the use of species-specific primers for Fusarium oxysporum, F. proliferatum, and F. culmorum. Within F. oxysporum, isolates clustered in two clades suggesting different origins of F. oxysporum forms pathogenic to onion. These clades were present in each sampled region. Onion and six related Allium species were screened for resistance to Fusarium basal rot using one F. oxysporum isolate from each clade, and one F. proliferatum isolate. High levels of resistance to each isolate were found in Allium fistulosum and A. schoenoprasum accessions, whereas A. pskemense, A. roylei and A. galanthum showed intermediate levels of resistance. Among five A. cepa cultivars, ‘Rossa Savonese’ was also intermediately resistant. Regarding the current feasibility for introgression, A. fistulosum, A. roylei and A. galanthum were identified as potential sources for the transfer of resistance to Fusarium into onion.     

Trichothecene genotype and genetic variability of <Emphasis Type="Italic">Fusarium graminearum</Emphasis> and <Emphasis Type="Italic">F. cerealis</Emphasis> isolated from durum wheat in Argentina

Fusarium head blight (FHB) is one of the most important fungal diseases affecting wheat worldwide and it is caused mainly by species within the Fusarium graminearum species complex (FGSC). This study evaluated the presence of FGSC in durum wheat from the main growing area in Argentina and analyzed the trichothecene genotype and chemotype of the strains isolated. Also, the genetic variability of the strains was assayed using ISSR markers. Molecular analysis revealed that among the strains isolated and identified morphologically as F. graminearum, there were 14 strains identified as F. cerealis. Also, it revealed that durum wheat grains were mostly contaminated by F. graminearum, being this the only species reported so far, within the FGSC, affecting durum wheat in Argentina. Analysis of molecular variance (AMOVA) indicated a high genetic variability within rather than between F. graminearum populations. All F. graminearum strains presented 15ADON genotype and were able to produce DON while all F. cerealis strains presented the NIV genotype and most of them were able to produce this toxin. The finding of F. cerealis in durum wheat grains indicates the need for investigating if this fungus is the responsible for the NIV contamination found in wheat in Argentina.     

Characterisation of novel <Emphasis Type="Italic">Fusarium graminearum</Emphasis> microsatellite markers in different <Emphasis Type="Italic">Fusarium</Emphasis> species from various countries

Fifteen novel microsatellite markers were isolated from Fusarium graminearum. The level of polymorphism at these novel and 13 previously published microsatellite markers was analysed in 33 F. graminearum strains from Europe, North America, and Nepal. The number of alleles for each of the novel markers ranged from 4 to 20 and gene diversity from 0.417 to 0.962. In comparison with the previously published markers, the resolution for distinguishing among different strains was slightly increased. Twenty-seven markers were also detectable in three F. culmorum strains and one F. crookwellense strain. None of the markers was detected in three F. avenaceum and four F. poae strains, underlining the potential use of these microsatellite markers for species differentiation.     

<Emphasis Type="Italic">Fusarium oxysporum</Emphasis> and <Emphasis Type="Italic">Fusarium avenaceum</Emphasis> associated with yield-decline of pyrethrum in Australia

Fusarium wilt, one of the destructive diseases of cucumber can be effectively controlled by using biocontrol agents such as Trichoderma harzianum. However, the mechanisms controlling T. harzianum-induced enhanced resistance remain largely unknown in cucumber plants. Here we screened the potent T. harzianum isolate TH58 that could effectively control F. oxysporum (FO). Glasshouse efficacy trials also showed that TH58 decreased disease incidence by 69.7 %. FO induced ROS over accumulation, while TH58 inoculation suppressed ROS over accumulation and improved root cell viability under F. oxysporum infection. TH58 inoculation could reverse the FO-induced cell division block and regulate the proportional distribution of nuclear DNA content through inducing 2C fraction. Moreover, the expression levels of cell cycle-related genes such as CDKA, CDKB, CycA, CycB, CycD3;1 and CycD3;2 in TH58 - pre-inoculated seedlings were up-regulated compared with those infected with FO alone. Taken together, these results suggest that T. harzianum improved plant resistance against Fusarium wilt disease via alterations in nuclear DNA content and cell cycle-related genes expression that might maintain a lower ROS accumulation and higher root cell viability in cucumber seedlings.     

Pathogenic variation in poplar rust <Emphasis Type="Italic">Melampsora larici-populina</Emphasis> from England

Using a leaf disc method, 19 isolates of the poplar rust, Melampsora larici-populina , and one isolate of M.populnea from England were inoculated on to 25 poplar clones belonging to Populus nigra and P.trichocarpa, and hybrids between P. deltoides and P. nigra, P. deltoidesand P. trichocarpa, P.tacamahaca and P.trichocarpa, and P. alba and P. tremula. Disease was scored based on the pustule area and inoculum density. In terms of whether sporulating uredinia formed, the 19 isolates showed seven different patterns to the tested poplar clones. The majority of the rust isolates infected P. nigra P3090 and Vereecken, P.nigra×P. deltoides Casale and Tasman, P. tacamahaca×trichocarpa 36 and Balsam Spire, and P.trichocarpa Blom. Populus trichocarpa×P. deltoides 69039/4 was infected by only three isolates collected from southern England. No visible symptoms appeared on P. alba ×P. tremulaTower and P.trichcarpa×P. deltoides×P. deltoides76028/5 in inoculations with M. larici-populina isolates. Populus alba×P.tremula Tower was infected only by M. populnea. When M. larici-populina isolates were tested using AFLP, no differences were found either between isolates from different geographical regions or between those having narrow spectrum of virulence and those showing wide spectrum of virulence on the tested clones. The results suggest that the UK rust populations possess virulences which were found in races E1, E2, E3 and E4 in continental Europe and that rust having virulence patterns similar to race E4 has occurred in UK poplar plantations since 1996.     

<Emphasis Type="Italic">Fusarium ershadii</Emphasis> sp. nov., a Pathogen on <Emphasis Type="Italic">Asparagus officinalis</Emphasis> and <Emphasis Type="Italic">Musa acuminata</Emphasis>

Two Fusarium strains, isolated from Asparagus in Italy and Musa in Vietnam respectively, proved to be members of an undescribed clade within the Fusarium solani species complex based on phylogenetic species recognition on ITS, partial RPB2 and EF-1α gene fragments. Macro- and micro-morphological investigations followed with physiological studies done on this new species: Fusarium ershadii sp. nov can be distinguished by its conidial morphology. Both isolates of Fusarium ershadii were shown to be pathogenic to the monocot Asparagus officinalis when inoculated on roots and induced hollow root symptoms within two weeks in Asparagus officinalis seedlings. In comparison mild disease symptoms were observed by the same strains on Musa acuminata seedlings.     

Fusarium rot of hyacinth caused by <Emphasis Type="Italic">Gibberella zeae</Emphasis> (anamorph: <Emphasis Type="Italic">Fusarium</Emphasis><Emphasis Type="Italic"> graminearum</Emphasis>)

Severe rot of leaves, peduncles and flowers caused by Gibberella zeae (anamorph: Fusarium graminearum) was found on potted plants of hyacinth (Hyacinthus orientalis), a liliaceous ornamental, in greenhouses in Kagawa Prefecture, Japan, in January 2001. This disease was named “Fusarium rot of hyacinth” as a new disease because only the anamorph, F. graminearum, was identified on the diseased host plant. The authors contributed equally to this work. The fungal isolate and its nucleotide sequence data obtained in this study were deposited in the Genebank, National Institute of Agrobiological Sciences and the DDBJ/EMBL/GenBank databases under the accession numbers MAFF239499 and AB366161, respectively.     

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.     

Cloning of the pathogenicity-related gene <Emphasis Type="Italic">FPD1</Emphasis> in <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">lycopersici</Emphasis>

We selected a reduced-pathogenicity mutant of Fusarium oxysporum f. sp. lycopersici, a tomato wilt pathogen, from the transformants generated by restriction enzyme-mediated integration (REMI) transformation. The gene tagged with the plasmid in the mutant was predicted to encode a protein of 321 amino acids and was designated FPD1. Homology search showed its partial similarity to a chloride conductance regulatory protein of Xenopus, suggesting that FPD1 is a transmembrane protein. Although the function of FPD1 has not been identified, it does participate in the pathogenicity of F. oxysporum f. sp. lycopersici because FPD1-deficient mutants reproduced the reduced pathogenicity on tomato.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number AB110097     

Relationships between aflatoxin production and sclerotia formation among isolates of <Emphasis Type="Italic">Aspergillus</Emphasis> section <Emphasis Type="Italic">Flavi</Emphasis> from the Mississippi Delta

Aspergillus section Flavi isolates, predominately A. flavus, from different crops and soils differed significantly in production of aflatoxin and sclerotia. About 50% of the isolates from corn, soil and peanut produced large sclerotia, while only 20% of the rice isolates produced large sclerotia. There was a higher frequency of small sclerotia-producing isolates from rice compared to the other sources and isolates that did not produce sclerotia were significantly less likely to be toxigenic than strains that produced large sclerotia.     

Genetic structure of <Emphasis Type="Italic">Pyrenophora teres</Emphasis> f. <Emphasis Type="Italic">teres</Emphasis> and <Emphasis Type="Italic">P. teres</Emphasis> f. <Emphasis Type="Italic">maculata</Emphasis> populations from western Canada

Infection by Pyrenophora teres f. teres (Ptt) or P. teres f. maculata (Ptm), the causal agents of the net and spot forms of net blotch of barley, respectively, can result in significant yield losses. The genetic structure of a collection of 128 Ptt and 92 Ptm isolates from the western Canadian provinces of Alberta (55 Ptt, 27 Ptm), Saskatchewan (58 Ptt, 46 Ptm) and Manitoba (15 Ptt, 19 Ptm) were analyzed by simple sequence repeat (SSR) marker analysis. Thirteen SSR loci were examined and found to be polymorphic within both Ptt and Ptm populations. In total, 110 distinct alleles were identified, with 19 of these shared between Ptt and Ptm, 75 specific to Ptt, and 16 specific to Ptm. Genotypic diversity was relatively high, with a clonal fraction of approximately 10 % within Ptt and Ptm populations. Significant genetic differentiation (PhiPT = 0.230, P = 0.001) was found among all populations; 77 % of genetic variation occurred within populations and 23 % between populations. Lower, but still significant genetic differentiation (PhiPT = 0.038, P = 0.001) was detected in Ptt, with 96 % of genetic variation occurring within populations. No significant genetic differentiation (PhiPT = 0.010, P = 0.177) was observed among Ptm populations. Isolates clustered in two distinct groups conforming to Ptt or Ptm, with no intermediate cluster. The high number of haplotypes observed, combined with an equal mating type ratio for both forms of the fungus, suggests that P. teres goes through regular cycles of sexual recombination in western Canada.     

Characterization of <Emphasis Type="Italic">Inago1</Emphasis> and <Emphasis Type="Italic">Inago2</Emphasis> retrotransposons in <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis>

From the genome of a Japanese field isolate of the rice blast fungus, Magnaporthe oryzae, we newly identified Inago1 and Inago2 LTR retrotransposons. Both elements were found to be Ty3/gypsy-like elements whose copies were dispersed within the genome of Magnaporthe spp. isolates infecting rice and other monocot plants. Southern hybridization patterns of nine re-isolates derived from conidia of the strain Ina168 produced after a methyl viologen treatment were not changed, indicating that the insertion pattern of Inago elements is relatively stable.     

First report of blueberry red ringspot disease caused by <Emphasis Type="Italic">Blueberry</Emphasis><Emphasis Type="Italic">red</Emphasis><Emphasis Type="Italic">ringspot</Emphasis><Emphasis Type="Italic">virus</Emphasis> in Japan

Virus-like symptoms—red ringspots on stems and leaves, circular blotches or pale spots on fruit—were found on commercial highbush blueberry (Vaccinium corymbosum) cultivars Blueray, Weymouth, Duke and Sierra in Japan. In PCR testing, single DNA fragments were amplified from total nucleic acid samples of the diseased blueberry bushes using primers specific to Blueberry red ringspot virus (BRRV). Sequencing analysis of the amplified products revealed 95.7–97.7% nucleotide sequence identity with the BRRV genome. This paper is the first report of blueberry red ringspot disease caused by BRRV in Japan. The nucleotide sequence data reported in this paper are available in the GenBank/EMBL/DDBJ database as accessions AB469884 to AB469893 for BRRV isolates from Japan.     

Morphological,pathological and genetic variations among isolates of <Emphasis Type="Italic">Cochliobolus sativus</Emphasis> from Nepal

Spot blotch, caused by Cochliobolus sativus (Ito & Kuribayashi) Drechs. ex Dastur, is one of the important diseases of wheat worldwide. The main objective of this study was to investigate the phenotypic and genotypic variability among C. sativus isolates from the hills and plains in Nepal. A total of 48 monoconidial isolates of C. sativus from the hills (n = 24 isolates) and plains (n = 24 isolates) in Nepal were analyzed for morphology, aggressiveness and genetic structure. C. sativus isolates were grouped into three categories on the basis of their colony texture and mycelia colour. Thirteen isolates from the hills and plains belonging to three morphological groups were randomly selected and evaluated for aggressiveness on eight wheat cultivars (Chirya 1, Chirya 7, Milan/Shanghai 7, SW 89–5422, PBW 343, BL 1473, BL 3036, and RR 21) at the seedling stage. Nonparametric analysis revealed that the isolates from the plains (median disease rating of 5) were significantly (P = 0.0001) more aggressive than the isolates from the hills (median disease rating of 3). A significant (P = 0.0001) isolate by cultivar interaction was demonstrated and the isolates from the same geographic region and morphological group displayed different degrees of aggressiveness on wheat cultivars tested. Combined IS-PCR and rep-PCR analyses revealed moderate gene diversity (H = 0.24 and 0.25 for the hills and plains, respectively). Low linkage disequilibrium (LD) value and non-significant (P = 0.001) population differentiation (G″_ST = 0.05) were detected, indicating that isolates of C. sativus from the hills and plains in Nepal were genetically similar. Analysis of molecular variation (AMOVA) revealed low (7%) levels of genetic variation between the hill and plain populations, whereas >93% of genetic variation was found within populations. Overall, C. sativus isolates from Nepal are pathologically and genetically diverse, and such information will be useful in developing wheat cultivars resistant to C. sativus.     

Natural phenolic acids from wheat bran inhibit <Emphasis Type="Italic">Fusarium culmorum</Emphasis> trichothecene biosynthesis <Emphasis Type="Italic">in vitro</Emphasis> by repressing <Emphasis Type="Italic">Tri</Emphasis> gene expression

The effect of natural phenolic acids from wheat bran on type B trichothecene biosynthesis by Fusarium culmorum was investigated in vitro. Durum wheat bran contained various monomeric forms of phenolic acids, with ferulic acid being the most abundant. In addition, various oligomeric forms of ferulic acid and mainly dimeric forms were also detected. When liquid cultures of F. culmorum were supplemented with a natural wheat bran extract, trichothecene production was fully inhibited. The exact mechanism by which toxin synthesis is repressed remains to be clarified but we showed that the phenolic acid treatment resulted in a drastic reduction in the expression level of structural trichothecene biosynthetic genes. The inhibitory efficiency of the natural phenolic acid extract was significantly higher than that of a reconstituted mixture containing similar concentrations of monomeric forms. Thus, to elucidate the full repression of type B trichothecene production induced by the natural phenolic acid extract from wheat bran, two hypotheses can be raised: (i) a synergistic impact of monomeric and dimeric forms of phenolic acids, (ii) the occurrence of an unidentified oligomeric form able to efficiently repress toxin yield. As a first attempt to investigate the effect of oligomeric forms, one of the most abundant dimer of ferulic acid, the 8-5′-benzofuran dimer, has been synthesized in vitro and was shown to inhibit trichothecene biosynthesis to the same extent than the monomer of ferulic acid.     

Pathogenicity of morphologically different isolates of <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> with <Emphasis Type="Italic">Brassica napus</Emphasis> and <Emphasis Type="Italic">B. juncea</Emphasis> genotypes

Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a serious threat to oilseed production in Australia. Eight isolates of S. sclerotiorum were collected from Mount Barker and Walkway regions of Western Australia in 2004. Comparisons of colony characteristics on potato dextrose agar (PDA) as well as pathogenicity studies of these isolates were conducted on selected genotypes of Brassica napus and B. juncea. Three darkly-pigmented isolates (WW-1, WW-2 and WW-4) were identified and this is the first report of the occurrence of such isolates in Australia. There was, however, no correlation between pigmentation or colony diameter on PDA with the pathogenicity of different isolates of this pathogen as measured by diameter of cotyledon lesion on the host genotypes. Significant differences were observed between different isolates (P ≤ 0.001) in two separate experiments in relation to pathogenicity. Differences were also observed between the different Brassica genotypes (P ≤ 0.001) in their responses to different isolates of S. sclerotiorum and there was also a significant host × pathogen interaction (P ≤ 0.001) in both experiments. Responses between the two experiments were significantly correlated in relation to diameter of cotyledon lesions caused by selected isolates (r = 0.79; P < 0.001, n = 48). Responses of some genotypes (e.g., cv. Charlton) were relatively consistent irrespective of the isolates of the pathogen tested, whereas highly variable responses were observed in some other genotypes (e.g., Zhongyou-ang No. 4, Purler) against the same isolates. Results indicate that, ideally, more than one S. sclerotiorum isolate should be included in any screening programme to identify host resistance. Unique genotypes which show relatively consistent resistant reactions (e.g., cv. Charlton) across different isolates are the best for commercial exploitation of this resistance in oilseed Brassica breeding programmes.     

Diverse <Emphasis Type="Italic">Fusarium solani</Emphasis> isolates colonise agricultural environments in Ethiopia

Fusarium solani is a fungal pathogen that infects many different genera of plants. It represents one of the two Fusarium spp. commonly isolated from agricultural soils and plant tissues in Ethiopia. To determine the diversity of F. solani in Ethiopia, we studied 43 isolates using Amplified Fragment Length Polymorphism (AFLP) and nucleotide sequences of the Translation Elongation Factor 1α (TEF-1α) and β-tubulin genes. TEF-1α sequences from GenBank, representing previously described species and clades of the F. solani-Haematonectria haematococca complex, were also included for comparative purposes. Phylogenetic analyses of the TEF-1α data separated the isolates into three groups corresponding with the three previously described clades (Clades 1–3) for this fungus. The Ethiopian isolates aggregated into one group corresponding to Clade 3. TEF-1α, β-tubulin and AFLPs further separated the Ethiopian isolates into a number of clusters and apparently novel phylogenetic lineages. Although the biological and ecological significance of these lineages and clusters is unclear, our data show that the Ethiopian agricultural environment is rich in species and lineages of the F. solani-H. haematococca complex.     

Host resistance mediated inter-genotype competition and temporal variation in <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">vasinfectum</Emphasis>

Temporal variation in Fusarium oxysporum f. sp. vasinfectum (Fov) populations was determined by comparing the genetic diversity of pathogen isolates recovered from three consecutive cotton crops (2002, 2004 and 2006) in the Boggabilla area of New South Wales, Australia. A total of 288 isolates were collected, among which 25 distinct AFLP genotypes were identified. These genotypes were classified into two main groups corresponding to known vegetative compatibility groups (VCG)—01111 and 01112. The Fov populations were dominated by four genotypes (I-A, I-B, II-A, II-B) that accounted for 87.5% of the isolates. Significant temporal variation was observed in both sampled fields with 6.8% and 10.7% of total genetic variation being attributed to differences among collections in different years. Genetic diversity based on Nei’s gene diversity and the Shannon-Wiener index increased over time. Significant changes in the frequency of the dominant Fov genotypes were observed in one field, where genotype I-A declined from 84.8% to 40.0% over the study period (2002–2006), while genotype I-B increased from 7.6% to 35.4%. Strong inter-genotype competition was detected in glasshouse bioassays with 93.4% of symptomatic plants sampled from dual inoculation trials being infected by single genotypes. Competition was differentially mediated by cotton cultivars as the competitive ability of pathogen genotype I-B was enhanced on the resistant cultivar Sicot 189 relative to the susceptible cultivar Siokra 1–4. This suggests that host-mediated inter-genotype competition may play an important role in temporal variation in Fov populations in the field.