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We consider a cognitive wireless relay system that operates on secondary spectrum sharing basis using spectrum pooling. A spectrum pool comprises of a set of available narrowband subchannels over which secondary users may communicate without causing harmful interference to primary users. In the proposed relay system, a source node transmits data symbols on an available spectrum pool to the relay node. At the relay, the received data symbols are amplified, permuted and forwarded to the destination node on an available spectrum pool. The problem of spectrum pool reassignment constitutes the determination of the permutation mapping at the relay node. Our goal is to maximize the ergodic capacity of the relay system, given knowledge of the average signal to noise ratios pertaining to the subchannels in the spectrum pools, by determining the optimum spectrum pool reassignment.