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Two Brassica lines derived from an interspecific cross between Brassica napus and B. carinata were evaluated for tolerance to the fungal pathogen Alternaria brassicae. Pathogen-induced chlorosis and necrosis spread significantly in one line whereas it remained localized in the other. Proteome-level changes in response to the fungal pathogen were investigated using two-dimensional electrophoresis. Levels of 48 proteins were significantly affected at various time points in the tolerant line (41 up-regulated and 7 down-regulated). In contrast, in the susceptible line, we observed the levels of 23 proteins to be significantly affected with 4 increasing and 19 decreasing. We were successful in establishing the identities of 38 proteins and those identified from the tolerant line included enzymes involved in the generation of reactive oxygen species (ROS), ROS mediated signaling, auxin signal transduction and metabolic …