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We investigate on the design of modulation schemes suited for two-way wireless relaying systems that apply network coding at the physical layer. We consider network coding based on denoise-and-forward (DNF), which consists of two stages: multiple access (MA) stage and broadcast (BC) stage. For the case of QPSK constellation in the MA stage, we introduce the modulation-related problems in DNF. We propose two approaches to solve those issues. One uses only QPSK constellations at the BC stage. The other allows the use of unconventional 5-ary modulations, optimized according to the channel condition. The performance evaluation shows that a significant improvement in end-to-end throughput can be achieved, in particular for Nakagami-Rice fading channels.