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Take-all is a disease in wheat which can cause significant yield losses. If it was possible to predict these losses, by competitive PCR, agronomic decisions could be made to reduce them. As the causal agent, Gaeumannomyces graminis, is found in the soil organic matter, soil DNA extraction methods were tested for their efficacy. An inhibition assay was designed to test the level of inhibition present in DNA extracted from soil. Of the extractions tested the CTAB extraction was the most successful at removing inhibitors and the commercially available Soil DNA Isolation Kit ™ was the least successful. All extraction methods tested required some dilution to enable the amplification of the inhibition standard. Soil DNA extraction was found to be time consuming so stem bases and roots were used with the competitive PCR assay. To create a quantitative competitive PCR assay published primers were amplified with known G. graminis isolates. They produced unexpected results which meant that they were unsuitable for use in a competitive PCR assay. Consequently HAGG primers were designed and successfully amplified known G. graminis var. tritici and var. avenae isolates, and isolated G. graminis from take-all infected wheat plants. The HAGG competitive PCR assay was used to quantify the presence of the take-all pathogen in a large number of plant samples ranging in age. Regressions of DNA concentration and visual symptoms or yield did not result in strong correlations. Analysis suggested the variability between the fields explained a large proportion of variability. A large scale experiment was completed to compare the impact of various seed treatments on pathogen DNA concentration, visual disease assessment, grain quality and yield. Early assessment of the plant material demonstrated the heterogeneous nature of this disease. When taking the pathogen DNA concentration at stubble into account a Latitude® (silthiofam) seed treatment achieved the greatest yield; Baytan® (triadimenol and fuberidazole) resulted in the lowest yield. The experiment demonstrated that this competitive PCR assay has the potential in field experiments to take account of the initial inoculum load.

Field experiments (2000-2002) were carried out to determine the effect of eyespot caused by Oculimacula yallundae and O. acuformis (formerly known as W-type and R-type, respectively) on yield or lodging resistance of winter wheat and to identify any differences in the development of the two pathogens throughout the season. A field experiment on artificially inoculated wheat was designed to clarify the effects of the two Oculimacula spp. on plant characteristics associated with lodging resistance and on yield of individual shoots and whole crop. Overall yield of winter wheat in the absence of lodging was reduced by 11% and 6% by eyespot caused by O. acuformis and O. yallundae respectively. Both species reduced the stem safety factor associated with lodging resistance, indicating their ability to cause lodging in winter wheat by reducing stem-bending strength. The ability of O. acuformis to cause significant yield loss was demonstrated in a series of fungicide efficacy experiments in early-drilled winter wheat. Oculimacula acuformis developed more and caused greater yield loss in the first winter wheat in which other stem-base pathogens were absent in the early growth stages of the crop. Fungicide mixtures containing cyprodinil were consistently more effective in controlling eyespot caused by O. acuformis in first, second and third winter wheat crops. Positive relationships were observed between DNA concentrations of O. acuformis, O. yallundae and M. nivale throughout the growing season, indicating that these species co-existed within the crop. While the DNA of M. nivale consistently increased more up to GS 39 in different field experiments, DNA of Oculimacula spp. increased at different times in the growing season and these increases were sometimes associated with the relative quantities of DNA of M. nivale at the early growth stages.

In order to determine the effect of a range of fungicide products, dose rate and time of application on the development of Fusarium head blight (FHB) and mycotoxin contamination of winter wheat, a series of field experiments (1998-2001) were carried out. A mixture of the fungicides metconazole+azoxystrobin provided the most significant reduction of (FHB) severity (63%) in comparison with control treatments followed by mectonazole (39%) and tebuconazole (45%) applied at both full and half the manufacturers recommended dose rate. Quantification of Tri5 DNA and deoxynivalenol (DON) concentration in harvested grain indicated that metconazole and tebuconazole were the most efficacious fungicides at reducing colonisation of grain by trichothecene-producing Fusarium species and DON content. Azoxystrobin had no effect on Tri5 DNA and DON concentration in grain, but significantly reduced the incidence of Microdochium nivale infected wheat grain. Fungicides applied early in the growing season (GS 31 and 39) were less effective at controlling disease than those applied later in the season (GS 39 and 59). Indeed, it was evident that the timing of fungicides was critical for the effective control of FHB and DON with the best control achieved when fungicides were applied either two days before or two days after the artificial inoculation of wheat ears with FHB causing pathogens. Regression analysis on field trial data revealed that fungicides were able to influence DON content in harvested wheat grain by affecting the extent of grain colonisation by mycotoxin producing species. Since published literature has suggested that fungicides can directly influence DON contamination by imparting a stress influence on FHB pathogens, glasshouse studies were undertaken to determine the effect of a range of dose rates of the fungicides azoxystrobin and metconazole against FHB and DON in wheat plants inoculated with either Fusarium culmorum or F. graminearum. Results revealed that metconazole was effective at reducing FHB, Tri5 DNA and DON and that a rate response was observed as dose rate was increased from one quarter to double the manufacturer's recommended dose rate. Although azoxystrobin reduced FHB, Tri5 DNA and DON content compared to untreated controls, no dose rate response was observed. Regression analysis of glasshouse data supported those obtained from field studies, suggesting that fungicides are able to influence DON content indirectly by affecting the extent of grain colonisation by F. culmorum and F. graminearum. Further glasshouse studies were conducted to determine the interactions between Alternaria tenuissima, Cladosporium herbarum, M. nivale and F. culmorum and the effect of fungicides on these interactions. Introducing C. herbarum or M. nivale to wheat ears at GS 57, before inoculation with F. culmorum at GS 65, resulted in a significant increase in FHB severity, Tri5 DNA and DON concentration in grain. Applying azoxystrobin to wheat ears after the introduction of M. nivale at GS 57, increased DON concentration in grain by 56%. The significance of interactions between saprophytic fungi, M. nivale and Fusarium species on fungicides efficacy against FHB and DON is discussed.

Fusarium seedling blight is an important disease of wheat caused primarily by seed-borne Microdochium nivale of which there are two sub-species; var. nivale and var. majus. Though important pathogens of UK wheat crops, little is known about the relationship between seed-borne inoculum of each sub-species and subsequent disease, annual and regional distributions of inoculum, their pathogenicity as seed-borne pathogens or the relative effectiveness of the main method used to control seedling blight (seed treatments). This investigation aims to answer questions relating to these important factors of M. nivale as a seed-bome pathogen. Nucleotide sequences for the elongation factor 1-a gene were used to produce primers specific to Microdochium nivale var. nivale and var. majus. Internal standards were constructed and quantitative PGR assays developed using standard assay curves. Microdochium nivale var. nivale and var. majus inoculum was quantified on seed harvested in 1997, 1998 and 1999. Total M. nivale DNA was significantly related to the determination of M. nivale contamination using standard agar plate counts in each year, both estimates of M. nivale contamination were significantly related to seedling blight disease symptoms. A positive correlation was observed between fungal biomass of M. nivale var. nivale and var. majus in each year. Microdochium nivale var. majus was the dominant sub-species present in Scottish samples from each year though only in English samples from 1999. Microdochium nivale var. majus was the more pathogenic seedling blight pathogen as either inoculated surface-borne or natural seed-bome inoculum. Beret Gold was most active of six fungicide seed treatments towards isolates of each sub-species in vitro. Field trials showed that the amount of M. nivale DNA quantified in seed was reflected in the amount present in the resultant seedlings. This was reduced significantly through the use of the seed treatments Beret Gold or Sibutol. Significant differences between the treatments were evident when disease pressure was high.Microdochium nivale var. majus was the most effective coloniser at the seedling stage whereas var. nivale predominated prior to flowering. These results show that (i) PCR assays are a useful determinant of M. nivale contamination of wheat seed and seedling blight symptoms, (ii) seasonal and regional fluctuations occur in sub-species predominance on seed samples (iii) M. nivalevar. majus is a more pathogenic seedling blight pathogen than var. nivale (iv) Sibutol and Beret Gold are effective against both sub-species at the seedling stages of crop development.