Genome-Wide Association Studies Identify OsNLP6 as a Key Regulator of Nitrogen Use Efficiency in Rice

Nitrogen (N) is the mineral element with the largest demand for crops, contributing up to 40% to 50% to the final yield. There is an increasing demand for breeding high N use efficiency (NUE) cultivars using high NUE genes due to the urgent requirements for sustainable agricultural development. Here, GWAS was conducted and OsNLP6 was identified, which encodes a NIN-like protein (NLP) transcription factor, as a key regulatory gene which was highly expressed in roots for rice NUE and yield formation. OsNLP6 positively regulates N uptake by activating the transcription of OsPTR2.4, which affects the nitrate transporter. The expression of this molecular module was significantly induced by low N stress. OsNLP6^HapII was identified as an elite haplotype with high-NUE, which was mainly found in the Xian rice subgroup derived from Southeast Asia, and could enhance N uptake and effective panicle number per plant, thereby boosting rice yield and NUE. Introducing OsNLP6^HapII into the Geng rice subgroup can be a potential strategy for marker-assisted selection breeding in rice. Overall, the present study highlights that the OsNLP6-OsPTR2.4 molecular module can be used to breed rice cultivars with higher NUE in order to achieve agricultural sustainability.