Nitrate (N) is an essential macronutrient and a key signalling molecule vital for plant development and production of yield.  Application of excessive N-rich fertilizers has been the hallmark of green revolution and this is not sustainable.  Understanding how plants uptake and metabolize nitrate is essential to design and develop new crops that have enhanced N-use efficiency.  A number of transcription factors, nitrate transporters and nitrate responsive genes and their regulatory modules have been identified and characterized in many model plants.  However, in rice, a monocot crop of immense importance, little is known about the nitrate sensor regulators, metabolites and transcription factors that are involved in N-metabolism and regulation of specific phenotypes.  We identified a miRNA-mediated regulation of a specific class of N-responsive transporters and transcription factors that play crucial roles in root development and architecture. Using whole-genomic, genetic, molecular and biochemical approaches, our results revealed the role of this regulatory module in uptake of N, transport, auxin biosynthesis and transport of auxin.  Our results identified a previously unknown N-dependent regulatory cascade involved in the development of rice roots and paves way for its employment in designing next generation crops.