Currently, software-intensive systems have become larger and complex, resulting from the interoperability of several sometimes distributed, independent systems so that emergent, broader missions can be performed. So referred as Systems-of-Systems (SoS), this new class of systems has emerged in special in critical application domains. In another perspective, reference architecture is a special type of software architecture that has provided a considerable support to the development, evolution, and also standardization of systems of given application domains. Considering their usefulness, reference architectures are even more important to SoS than they have been today, by making it possible to mainly promote interoperability among constituent systems of SoS. Adequate interoperability in SoS has been still a great challenge to the community. In this scenario, this foreword arises challenges in this new research topic of reference architectures for SoS. As a result, we intend to open a discussion around SoS and reference architectures and research lines as well.