Scholarlink

Background <p>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.</p> Results <p>Here, we used RNA sequencing of wild-type (WT) and <i>TaNPF6.2-</i>overexpressing plants (<i>TaNPF6.2-OE</i>) 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 <i>trans-</i>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 <i>cis</i>-regulated genes analysis. Gene Ontology (GO) analyses revealed that the potential <i>cis</i>-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.</p> Conclusions <p>This study identifies lncRNA candidates that could play a role in improving NUE, providing a basis for future functional investigations.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月4日

查看全文
  • Huanhuan Wang,
  • Kaifeng Zheng,
  • Qinyue Min,
  • Yanrong Pang,
  • Xiuhua Xue,
  • Wanjie Li,
  • Fanfan Zhang,
  • Lichao Zhang,
  • Shengcheng Han

摘要

Background

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.

Results

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.

Conclusions

This study identifies lncRNA candidates that could play a role in improving NUE, providing a basis for future functional investigations.