Transcriptome-wide identification and expression analysis of lncRNAs involved in the nitrate response in wheat

Nitrogen (N) fertilizer application increases yield and quality in crops such as wheat, but raises environmental and economic concerns. Long noncoding RNAs (lncRNAs) are emerging as versatile regulators of diverse biological processes. However, the regulatory role of lncRNAs in response to low-N stress and improving nitrogen use efficiency (NUE) remains largely unknown, especially in wheat. Here, we used RNA sequencing of wild-type (WT) and TaNPF6.2-overexpressing plants (TaNPF6.2-OE) under both normal and low-N conditions to create a comprehensive catalog of lncRNAs in wheat roots and investigated their potential regulatory roles in N utilization. In total, 34,612 high-confidence lncRNAs and 131,996 mRNAs were identified, of which 5,008 differentially expressed (DE) lncRNAs and 27,850 DEmRNAs were characterized as responsive to low-N stress. Co-expression analysis suggested that the trans-regulation of lncRNA is associated with C2H2, ERF, MYB, and NAC transcription factors (TFs) in response to low-N stress. Furthermore, we identified 969 DElncRNAs associated with TaNPF6.2 and their ability to sense low-N stress in wheat roots through cis-regulated genes analysis. Gene Ontology (GO) analyses revealed that the potential cis-regulated DEmRNAs were primarily enriched in the “membrane” and “transport” pathways. Finally, 21 DElncRNA-DEmRNA pairs were predicted to participate in the N metabolism regulatory network, and the expression of several critical lncRNAs and their targets was verified by RT-qPCR. This study identifies lncRNA candidates that could play a role in improving NUE, providing a basis for future functional investigations.