Transcriptome profiling of Arabidopsis thaliana leaves infected with Botrytis cinerea at different times of the day

Arabidopsis thaliana exhibits differential susceptibility to the fungal pathogen Botrytis cinerea depending on the time of day that infection occurs. We hypothesised that this is driven by teh circadian clock and that differences in the amplitude or speed of the plant defence response will underlie the difference in susceptiblity. A major component of the defence response is transcriptional reprogramming, hence we investigated whether the transcriptional response to B. cinerea infection differs following inoculation at subjective dawn or night (the points of greatest difference in susceptiblity) under constant light conditions. Arabidopsis thaliana (ecotype Col-0) plants were grown for four weeks under 16h:8h light:dark conditions and then moved into constant light 24 hours prior to infection. Detached leaves were inoculated with Botrytis cinerea spores (5 x 104 spores mL-1) or mock-inoculated at subjective dawn or subjective night. Leaves were harvested for transcriptome profiling at 18 and 22 hours after inoculation. Four individual leaves were pooled for one sample. Two technical replicates were carried out for each sample. Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Data was normalised using the Robust Multichip Averaging algorithm.