9311 allele of OsNAR2.2 enhances nitrate transport to improve rice yield and nitrogen use efficiency.

Improving nitrogen use efficiency (NUE) in rice is a requirement for future sustainable agricultural production. However, key factors and regulatory networks involved in NUE remain unclear. Here, QTL analysis, fine-mapping and functional validation demonstrated that qCR4 encodes a putative high-affinity nitrate transporter-activating protein 2.2 (OsNAR2.2). Located in the endoplasmic reticulum (ER), OsNAR2.2 was confirmed to regulate nitrate transport from root-to-shoot and control panicle number, grain yield and NUE in rice. RNA-seq and RT-qPCR revealed that OsNAR2.2 modulates nitrogen utilization by altering the expressions of some nitrogen metabolism-related genes and auxin signal-related genes. Furthermore, the 9311 allele of OsNAR2.2 significantly enhanced panicle number, grain yield and NUE, which provides a potential target for rice yield and NUE improvement.