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During early seedling development of oil seed plants, the transition from lipid based heterotrophic to photoautotrophic carbohydrate metabolism is accompanied with a biphasic control of the chloroplast antioxidant system. In continuous light, organellar peroxiredoxins (Prx) and thylakoid-bound ascorbate peroxidase (tAPx) are activated early in seedling development, while stromal ascorbate peroxidase (sAPx), Cu/Zn-superoxide dismutase-2 (Csd2) and monodehydroascorbate reductase (MDHAR) and the cytosolic peroxiredoxins PrxIIB, PrxIIC and PrxIID are fully activated between 2.5 and 3 days after radicle emergence (DARE). Discontinuous light synchronized the expression of chloroplast antioxidant enzymes, but defined diurnally specific typeII-Prx-patterns in the cytosol and initiated chloroplast senescence around 2.5 DARE. Carbohydrate feeding uncoupled sAPx expression from the light pattern. In contrast, sucrose-feeding did not significantly impact on Prx transcript amounts. It is concluded that upon post-germination growth Prxs are activated endogenously to provide early antioxidant protection, which is supported by the Halliwell–Asada-Cycle, whose expressional activation depends on metabolic signals provided only later in development or in day-night-cycles.