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In a cooperative relay network, a relay (R) node may facilitate data transmission to the destination (D) node when the latter node cannot correctly decode the source (S) node data. This paper considers such a system model and presents a cross-layer approach to jointly design adaptive modulation and coding (AMC) at the physical layer and the truncated cooperative automatic repeat request (C-ARQ) protocol at the data-link layer for quality-of-service (QoS)-constrained applications. The average spectral efficiency and packet loss rate of the joint C-ARQ and AMC scheme are first derived in closed form. Aiming to maximize the system spectral efficiency, AMC schemes for the S-D and R-D links are optimized, whereas a prescribed packet-loss-rate constraint is satisfied. As an interesting application, joint link adaptation and blockage mitigation in land mobile satellite communications (LMSC) with temporally correlated channels is then investigated. In LMSC, the S node data can be delivered to the D node when the S-D is in the outage, therefore provisioning the QoS requirements. For applications without instantaneous feedback, an optimized rate selection scheme based on the channel statistics is also devised. Detailed and insightful numerical results are presented, which indicate the superior performance of the proposed joint AMC and C-ARQ schemes over their optimized joint AMC and traditional ARQ counterparts.