OsNPF3.1, a member of the NRT1/PTR family, increases nitrogen use efficiency and biomass production in rice

The overuse of nitrogen (N) fertilizer in fields has increased production costs and raised environmental concerns. Increasing the N use efficiency (NUE) of rice varieties is crucial for sustainable agriculture. Here we report the cloning and characterization of OsNPF3.1, a gene that controls rice NUE. An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice. OsNPF3.1, which is expressed mainly in the aerial parts of rice, also affects rice plant height, heading date, and thousand-grain weight. The OsNPF3.1 protein is located in the plasma membrane. When OsNPF3.1 was subjected to artificial selection, two naturally varying loci were associated with NUE, of which OsNPF3.1Chr6_8741040 differed between indica and japonica rice. OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.