Large scale analysis of leaf gene expression upon infection of susceptible or resistant apple varietes with different strains of Erwinia amylovora

Investigation of whole genome gene expression level changes in leaves of susceptible (MM106) or resistant (ME010) apple genotypes either non-inoculated, inoculated with the wild type strain of Erwinia amylovora (CFBP1430) or the non-pathogenic mutant strain PMV6023. The mutant strain PMV6023 is affected in the biosynthesis of the type 3 secretion system delivering bacterial effectors into apple cells. Leaves were harvested for RNA extraction before inoculation, 6 hours and 24 hours after inoculation. A total of 28 samples were associatied as pairs to perform 14 competitive hybridisations. Biological replicates are from 2 independantly grown grafted apple scions series, leading to 7 swaps. Three swaps including dye switch were associated to compare leaf samples from susceptible and resistant varieties either before inoculation, 6 or 24 hours after inoculation with the wild type strain CFBP1430. Four additional swaps including dye switch were associated to compare leaf samples harvested within each apple variety, either 6 or 24 hours after inoculation with CFBP1430 or PMV6023 bacterial strains. These latter swaps allowed to determine the impact of type III effector delivery on host gene expression either for susceptible or resistant genotypes, at 6 or 24 hours after inoculation.