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Two-way relaying promises considerable improvements on spectral efficiency in wireless relay networks. While most existing works focus on physical layer approaches to exploit its capacity gain, the benefits of two-way relaying on upper layers are much less investigated. In this paper, we study the cross-layer design and optimization for delay quality-of-service (QoS) provisioning in two-way relay systems. Our goal is to find the optimal transmission policy to maximize the weighted sum throughput of the two users in the physical layer while guaranteeing the individual statistical delay-QoS requirement for each user in the datalink layer. This statistical delay-QoS requirement is characterized by the QoS exponent. By integrating the concept of effective capacity, the cross-layer optimization problem is equivalent to a weighted sum effective capacity maximization problem. We derive the jointly optimal power and rate adaptation policies for both three-phase and two-phase two-way relay protocols. Numerical results show that the proposed adaptive transmission policies can efficiently provide QoS guarantees and improve the performance. In addition, the throughput gain obtained by the considered three-phase and two-phase protocols over direct transmission is significant when the delay-QoS requirements are loose, but the gain diminishes at tight delay requirements. It is also found that, in the two-phase protocol, the relay node should be placed closer to the source with more stringent delay requirement.