Co-expression network analysis reveals early molecular signatures of nitrate foraging by poplar roots

Abstract

Nitrogen is an important macronutrient that is essential for plant growth and acts as a signaling molecule. The amount of nitrogen obtained from soil is often insufficient to satisfy plant demands. To cope with nitrogen deficiency, crops use root elongation to expand the available soil space and obtain more nitrogen resources; however, the regulatory mechanism underlying this important adaptation strategy remains unclear. In this study, phenotypic and physiological changes in poplar roots in response to different nitrogen concentrations were monitored. Poplar root elongation was observed under low nitrogen conditions, and physiological indexes related to nitrogen assimilation changed within 2 h. A dynamic transcriptome analysis revealed significant differences at the early stage of nitrogen treatment based on nitrogen availability. According to K-means testing, these differences mainly involved the duration and degree of enrichment of some primary metabolites, consistent with the results of a weighted correlation network analysis. Several TFs, such as MYB2/73/111/116/123, bZIP42/53/60, and NAC083/104, may play important roles in this early response to variation in nitrogen availability. Transcriptional regulatory networks were constructed, and key regulatory elements were identified, such as MYB3, E2F, and DRE-like at 30 min, and ARF, T-box, and SBP-box at 90 min pxMYB56, a TF closely related to a 90-min element, was identified, and root suppression was observed in pxMYB56-overexpressing plants. These results can serve as a valuable resource for dissecting the role of candidate genes promoting root elongation in poplar under low nitrogen concentrations.