Transcriptome and gene co-expression network analysis revealed a putative regulatory mechanism of low nitrogen response in rice seedlings

TL;DR

This study explores how rice seedlings respond to low nitrogen by analyzing gene expression and co-expression networks, identifying key genes and pathways involved in nitrogen tolerance.

Contribution

The study identifies a putative regulatory mechanism for low nitrogen response in rice seedlings using transcriptome and co-expression network analysis.

Findings

RNA-Seq analysis revealed significant changes in gene expression related to nitrogen and carbon metabolism under low nitrogen conditions.

WGCNA identified gene modules and hub genes, including those involved in ion transport and root development, which may facilitate nitrogen acquisition under low N.

Cell activity and cell wall modification modules were found to be coordinated by OsLBD3-1, promoting root development under low nitrogen.

Abstract

In rice, nitrate (NO3
−) and ammonium (NH4
+) are the main sources of inorganic nitrogen (N) for growth, which also serve as signaling molecules. Depending on the N status, plants modulate their physiological traits such as root system architecture (RSA) and transcriptome makeup, including N uptake and assimilation genes, to adapt to the amount of N available in the growth medium. In this study, time-course hydroponic experiment under low N (0.4 mM NH4
+) and sufficient N (1.6 mM NH4
+) was performed using low N tolerant introgression lines, KRIL8 and KRIL37, which carry a small region of the wild rice Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari background. RNA-Seq analysis was used to profile changes in gene expression related to N and carbon metabolism which varied significantly and identified the accumulation of transcripts involved in secondary metabolite synthesis at the peak of low N stress. Weighted gene co-expression network analysis (WGCNA) identified several gene modules and their hub genes, including ion transport related modules consisting of genes that negatively regulate N uptake including OsHHO3, OsBT, and OsACTPK1 in all the lines. The repression of these genes under low N could be a basic mechanism to facilitate N acquisition in rice roots. The network analysis also identified cell activity and cell wall modification modules in the introgression lines which could be coordinated by OsLBD3-1, a paralogue of the Crown rootless1 gene for the promotion of root development to enhance N acquisition under low N conditions. The present analysis revealed the involvement of major pathways for low nitrogen tolerance of the selected lines.

Figures