Transcriptome Profiling Reveals the Gene Network Responding to Low Nitrogen Stress in Wheat

Yiwei Wang; Pengfeng Li; Yiwang Zhu; Yuping Shang; Zhiqiang Wu; Yongfu Tao; Hongru Wang; Dongxi Li; Cuijun Zhang

doi:10.3390/plants13030371

Transcriptome Profiling Reveals the Gene Network Responding to Low Nitrogen Stress in Wheat

Plants (Basel). 2024 Jan 26;13(3):371. doi: 10.3390/plants13030371.

Authors

Yiwei Wang^{1

2}, Pengfeng Li^{2

3}, Yiwang Zhu², Yuping Shang^{2

4}, Zhiqiang Wu², Yongfu Tao², Hongru Wang², Dongxi Li¹, Cuijun Zhang²

Affiliations

¹ College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan 030024, China.
² Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
³ College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
⁴ College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China.

Abstract

As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, understanding the response mechanisms to low N (LN) stress is essential for the regulation of NUE in wheat. In this study, LN stress significantly accelerated wheat root growth, but inhibited shoot growth. Further transcriptome analysis showed that 8468 differentially expressed genes (DEGs) responded to LN stress. The roots and shoots displayed opposite response patterns, of which the majority of DEGs in roots were up-regulated (66.15%; 2955/4467), but the majority of DEGs in shoots were down-regulated (71.62%; 3274/4565). GO and KEGG analyses showed that nitrate reductase activity, nitrate assimilation, and N metabolism were significantly enriched in both the roots and shoots. Transcription factor (TF) and protein kinase analysis showed that genes such as MYB-related (38/38 genes) may function in a tissue-specific manner to respond to LN stress. Moreover, 20 out of 107 N signaling homologous genes were differentially expressed in wheat. A total of 47 transcriptome datasets were used for weighted gene co-expression network analysis (17,840 genes), and five TFs were identified as the potential hub regulatory genes involved in the response to LN stress in wheat. Our findings provide insight into the functional mechanisms in response to LN stress and five candidate regulatory genes in wheat. These results will provide a basis for further research on promoting NUE in wheat.

Keywords: RNA-seq; low nitrogen; nitrogen signaling network; wheat.

Grants and funding

This work was supported by the Elite Young Scientists Program of CAAS, and Science, Technology and Innovation Commission of Shenzhen Municipality; Basic Research Programs of Shanxi Province (202303021211069).