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Background  Phosphate (Pi) and Nitrogen (N) are essential macronutrients required for plant growth and development. In  Arabidopsis thaliana  (Arabidopsis), the transcription factor  PHR1  acts as a Pi central regulator.  PHL1  is a homolog of  PHR1  and also plays a role in maintaining Pi homeostasis. In rice ( Oryza sativa ),  OsPHR1–4  are the orthologs of  PHR1  and have been implicated in regulating sensing and signaling cascades governing Pi homeostasis.    Results  Here the role of  OsPHR3  was examined in regulating the homeostasis of N under different Pi regimes. Deficiencies of different variants of N exerted attenuating effects on the relative expression levels of  OsPHR3  in a tissue-specific manner .  For the functional characterization of  OsPHR3 , its Tos17 insertion homozygous mutants i.e.,  osphr3–1 ,  osphr3–2,  and  osphr3–3  were compared with the wild-type for various morphophysiological and molecular traits during vegetative (hydroponics with different regimes of N variants) and reproductive (pot soil) growth phases. During vegetative growth phase, compared with the wild-type,  OsPHR3  mutants showed significant variations in the adventitious root development, influx rates of  15 N-NO 3  −  and  15 N-NH 4  + , concentrations of total N, NO 3  −  and NH 4  +  in different tissues, and the relative expression levels of  OsNRT1.1a ,  OsNRT2.4, OsAMT1;1, OsNia1  and  OsNia2.  The effects of the mutation in  OsPHR3  was also explicit on the seed-set and grain yield during growth in a pot soil. Although Pi deficiency affected total N and NO 3  −  concentration, the lateral root development and the relative expression levels of some of the NO 3  −  and NH 4  +  transporter genes, its availability did not exert any notable regulatory influences on the traits governing N homeostasis.    Conclusions   OsPHR3  plays a pivotal role in regulating the homeostasis of N independent of Pi availability.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1462-7) contains supplementary material, which is available to authorized users.

OsPHR3 affects the traits governing nitrogen homeostasis in rice