The external application of nitrogen (N) fertilizers is an important practice for increasing crop production. However, the excessive use of fertilizers significantly increases production costs and causes environmental problems, making the improvement of crop N-use efficiency (NUE) crucial for sustainable agriculture in the future. Here we show that the rice (Oryza sativa) NUE quantitative trait locus DULL NITROGEN RESPONSE1 (qDNR1), which is involved in auxin homeostasis, reflects the differences in nitrate (⁠ $NO3−$⁠) uptake, N assimilation, and yield enhancement between indica and japonica rice varieties. Rice plants carrying the DNR1^indica allele exhibit reduced N-responsive transcription and protein abundance of DNR1. This, in turn, promotes auxin biosynthesis, thereby inducing AUXIN RESPONSE FACTOR-mediated activation of $NO3−$ transporter and N-metabolism genes, resulting in improved NUE and grain yield. We also show that a loss-of-function mutation at the DNR1 locus is associated with increased N uptake and assimilation, resulting in improved rice yield under moderate levels of N fertilizer input. Therefore, modulating the DNR1-mediated auxin response represents a promising strategy for achieving environmentally sustainable improvements in rice yield.

Between the two major rice subspecies, indica varieties generally exhibit higher nitrate (NO₃^‒) uptake and nitrogen (N)-use efficiency (NUE) than japonica varieties. Introducing efficient NO₃^‒ utilization alleles from indica into japonica could improve NUE, and at the same time uncover unknown regulators of NO₃^‒ metabolism. Here, we identify OsWRKY23 as a key regulator of NO₃^‒ uptake and NUE differences between indica and japonica rice. The OsWRKY23^indica allele exhibits reduced transcriptional activation of a negative regulator of auxin accumulation, DULL NITROGEN RESPONSE1 (DNR1). The resultant increase in auxin level improves NO₃^‒ uptake and assimilation, which ultimately enhances grain yield. Geographical and evolutionary analyses reveal overlapping distribution of OsWRKY23^indica and DNR1^indica, particularly in low-fertility soils, suggesting their involvement in the adaptation to low N conditions to improve NUE and grain yield. Incorporating the OsWRKY23-DNR1 module from indica rice represents a promising strategy to enhance japonica NUE, which is crucial for sustainable agriculture.

Nitrogen (N) deficiency–induced increases in the root-to-shoot biomass ratio in plants are adaptive in nature but suboptimal for agriculture. Understanding the regulatory mechanisms governing this developmental plasticity could help improve crop performance while reducing fertilizer application. We identified OsWRI1a (WRINKLED1a) as a regulatory hub coordinating rice root and shoot growth in response to external N supply, thereby stabilizing the root-to-shoot ratio. In roots, OsWRI1a enhances N-responsive development by promoting auxin accumulation. Meanwhile, shoot OsWRI1a stimulates tiller development and therefore shoot growth. We identified an elite OsWRI1a haplotype that minimizes root-to-shoot ratio fluctuation under N deficiency, improving N-use efficiency and grain yield. Our findings reveal a central mechanism coordinating N-responsive growth allocation for sustainable agriculture.