Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.

Raphanus raphanistrum L. (wild radish) is a major problematic weed worldwide. Random amplified polymorphic DNA (RAPD) was used to estimate the degree of genetic diversity between and within 2 populations of wild radish (WARR 5 and WARR 6), found to exhibit multiple herbicide resistance compared with a susceptible population (WARR 7). It is believed that weed species with high degrees of genetic variation show potential for developing resistance to herbicides. Of the 13 RAPD primers screened, 9 primers generated 97 polymorphic bands concomitant with a high level of polymorphism (82%) between the wild radish populations, characteristics of an outbreeding species. Analysis of molecular variance (AMOVA) showed a markedly higher proportion of diversity within populations (87%) as opposed to between populations (13%). Principal component analysis (PCA) further highlighted the large amount of variation between individuals within populations. Only one marker, OPC19–8, was found to be unique to the WARR 7 population but absent in WARR 5 and in most individuals of the WARR 6 populations. This marker may potentially be correlated with herbicide susceptibility. The 2 resistant wild radish populations were found to be closely related (0.7% dissimilar) to each other, whereas the susceptible population was genetically dissimilar to them by 2.3%. This higher level of dissimilarity between the susceptible and resistant populations may be explained by limited gene flow between them since the susceptible population is geographically located further away from the resistant populations. Hence, it may be concluded that the underlying genetic structure of the 3 wild radish populations seems to be similar despite WARR 6 and WARR 5 having been exposed to mixed herbicide usage for over 17 years.

Herbicides provide growers with the means to chemically manage weeds; surfactants are often an effective way of improving the performance of these herbicides. However, the mode of action of surfactants at the molecular level is not well understood. As a preliminary step towards understanding the molecular mechanism of action of an etheramine surfactant, plant gene expression in response to foliar application of surfactant NUL1026 was analysed in Arabidopsis thaliana, using the commercially available Affymetrix ATH1-121501 chip. One hundred and ninety-six genes were found to be significantly altered 1 h after plants were treated with 0.2% (V/V) of surfactant NUL1026. Functional category analysis of these genes revealed that the largest categories included metabolism, physiological processes, transport, protein metabolism, response to stimulus and transcription. A number of genes encoding detoxification proteins, such as cytochrome P450, glutathione Stransferase and members of the multidrug-resistance associated proteins, were upregulated. Interestingly, microarray results showed a number of genes encoding enzymes involved in the jasmonic acid biosynthesis pathway and also the 1-aminocyclopropane-1-carboxylate synthase gene for ethylene production were upregulated, indicating that treatment with surfactant NUL1026 affects the expression of a number of genes involved in the detoxification and signalling pathways.