Disclosed herein is a transport software defined networking (SDN) controller, comprising a receiver configured to receive advertisement messages from physical layer NEs, each advertisement message indicating a mapping between a physical layer network elements (NE) port and an adjacent network layer NE, and a processor coupled to the receiver. The SDC controller is configured to determine a relationship between a logical topology and a physical topology, inspect a network layer link aggregation group (LAG) request, the request indicating a first network layer NE is requesting modification of a LAG with a second network layer NE, and modify a physical layer connection between a physical layer NE adjacent to the first network layer NE and a second physical layer NE adjacent to the second network layer NE to implement the LAG modification based on the relationship between the physical topology and the logical topology.