Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is causing severe losses in cassava production in Kenya, Tanzania and Uganda. Two real-time RT-PCR assays based on TaqMan chemistry capable of detecting and distinguishing these two viruses are described. These assays were used to screen 493 cassava samples collected from western and coastal Kenya, the main cassava regions of Uganda and inland Tanzania. Both viruses were found in all three countries and across regions therein. Association of CBSD leaf symptom status with CBSV and UCBSV assay results was weak, confirming the need for a diagnostic assay. For leaf samples that were observed with CBSD-like leaf symptoms but shown as CBSV and UCBSV negative by the RT-PCR assay, deep sequencing using a Roche 454 GS-FLX was used to provide additional evidence for the absence of the viruses. The probability of the CBSD associated diagnostics detecting a single CBSV or UCBSV positive sample amongst other non-CBSD samples was modelled. The results of this study are discussed in the context of the application of diagnostics of CBSD-associated viruses under the Great Lakes Cassava Initiative and the need to minimize the risk of further spread of the viruses with cassava multiplication material. It is shown that high throughput testing undertaken at Fera of 300 cassava leaves taken from fields for seed multiplication, when analysed in pools of 10, has given a 95% probability of detecting 1% infected plants in the field.

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From 2000-2003 a range of Farm Scale Evaluation (FSE) trials were established in the UK to assess the effect of the release and management of herbicide tolerant (HT) crops on the abundance and diversity of farmland wildlife compared with their conventionally managed non-GM-equivalents. The objective of this research project was to investigate gene flow within the winter (WOSR) and spring oilseed rape (SOSR) FSE trials and to develop a statistical model for the prediction of cross-pollination frequency that can be used to evaluate current separation distance guidelines. Seed samples were collected from the non-GM half of the trial sites and were tested for evidence of cross-pollination from the GM HT halves using a quantitative PCR assay specific to the HT (bar) gene. Rates of cross-pollination were found to decrease rapidly with increasing distance from the GM source. The quantitative data were subjected to statistical analysis and a two-step model was found to provide the best fit for the data. Significant differences were found between the results for WOSR, SOSR and varietal association (VA) crops. The model predicted that the %GM content (including upper 95% confidence limits) of a sample taken at a distance of 50 m away from the GM source would be 0.04% (0.84%) for WOSR, 0.02% (0.39%) for SOSR, 0.77% (21.72%) for WOSR VA and 0.37% (5.18%) for SOSR VA. The data and models presented here are discussed in the context of necessary separation distances to meet various possible thresholds for adventitious presence of GM in OSR.

From 2000 to 2003 a range of Farm Scale Evaluation (FSE) trials were established in the UK to assess the effect of the release and management of herbicide tolerant (HT) crops on arable weeds and invertebrates. The FSE trials for maize were also used to investigate crop-to-crop gene flow and to develop a statistical model for the prediction of gene flow frequency that can be used to evaluate current separation distance guidelines for GM crops. Seed samples were collected from the non-GM half of 55 trial sites and 1,055 were tested for evidence of gene flow from the GM HT halves using a quantitative PCR assay specific to the HT (pat) gene. Rates of gene flow were found to decrease rapidly with increasing distance from the GM source. Gene flow was detected in 30% of the samples (40 out of 135) at 150 m from the GM source and events of GM to non-GM gene flow were detected at distances up to and including 200 m from the GM source. The quantitative data were subjected to statistical analysis and a two-step model was found to provide the best fit for the data. A dynamic whole field model predicted that a square field (150 m x 150 m in size) of grain maize would require a separation distance of 3 m for the adjacent crop to be below a 0.9% threshold (with <2% probability of exceeding the threshold). The data and models presented here are discussed in the context of necessary separation distances to achieve various possible thresholds for adventitious presence of GM in maize.