# Analysis of the Transcriptome Response to Low Nitrogen in Populus ussuriensis

## TL;DR

This study explores how Populus ussuriensis plants respond to low nitrogen by analyzing gene activity in roots, revealing thousands of genes involved in stress adaptation.

## Contribution

The study identifies a gene regulatory network and over 8000 differentially expressed genes in Populus ussuriensis roots under nitrogen stress.

## Key findings

- Low nitrogen conditions increased root biomass but suppressed shoot growth in Populus ussuriensis.
- 8289 genes showed altered expression, focusing on nitrogen metabolism, antioxidant defense, and hormone regulation.
- A regulatory network of 60 nitrogen-metabolism-related genes was constructed to explain stress responses.

## Abstract

Nitrogen is a vital nutrient that forest trees absorb from the soil through their roots. A lack of nitrogen greatly reduces the growth of forest trees. In this study, we aim to understand how wild-type Populus ussuriensis plantlets grown in vitro respond to low-nitrogen conditions at the molecular level. We grew Populus ussuriensis under both normal and low-nitrogen conditions and observed how they developed over time. Our results showed that when nitrogen was limited, Populus ussuriensis grew more roots but produced less shoot tissue. Bioinformatics analyses of root gene activity revealed over 8000 genes that exhibited altered expression patterns under nitrogen stress. These genes primarily regulate nitrogen uptake and utilization, antioxidant defense, root development, and internal hormone regulation. Among them, 443 transcription factors (mainly of the MYB and AP2/ERF types) were identified among all differentially expressed genes. Additionally, we constructed a regulatory network comprising 60 nitrogen-metabolism-related genes that collectively coordinate the nitrogen stress response in Populus ussuriensis. This study establishes a systematic foundation for investigating molecular adaptation mechanisms in Populus ussuriensis roots under nitrogen stress.

(1) Background: Nitrogen is a key element that is essential for plant growth, and it is absorbed by roots from the soil. Nitrogen stress severely limits forest tree productivity; therefore, elucidating the molecular mechanisms underlying nitrogen stress tolerance in forest trees is critical for sustainable forestry. (2) Methods: Phenotypic analyses of wild-type (WT) Populus ussuriensis (P. ussuriensis) plantlets grown in vitro were carried out at different time points under both normal and low-nitrogen conditions. Transcriptome analyses of roots were performed at 0, 12, 24, 48, 96, and 336 h under low-nitrogen stress via RNA-seq. A gene regulatory network (GRN) for nitrogen-metabolism-associated DEGs was constructed using a three-gene module framework and a bottom-up Gaussian Graphical Model algorithm. (3) Results: WT P. ussuriensis plantlets grown in vitro exhibited a synergistic response characterized by increased root biomass and suppressed shoot growth. Transcriptome analyses identified 8289 DEGs enriched in nitrogen metabolism, ROS scavenging, root development, and phytohormone signaling. A total of 443 differentially expressed transcription factors (TFs) (mainly MYB, AP2/ERF, and bHLH) were detected. A nitrogen-metabolism-associated GRN comprising 60 nodes was established. (4) Conclusions: Transcriptomic data and nitrogen metabolism pathway predictions from this study establish a systematic foundation for investigating molecular adaptation mechanisms in P. ussuriensis roots under nitrogen stress.