A network of genes associated with poplar root development in response to low nitrogen

Abstract

Deployment of the root system is highly sensitive to the levels and spatial distribution of nutrients like nitrogen. However, the genetic determinants of these sensing and deployment mechanisms are still poorly understood. Previously, using system approaches based on temporal changes in root transcriptome in relation to low nitrogen (LN), we have been able to identify a module that activates root production in poplar in response to LN conditions. Here, using comparative, gene ontology and expression analyses, we provide further evidence that the genes in this module are indeed involved in regulation of root development under LN. Better understanding of these modules will enable approaches for breeding for better nitrogen use efficiency through development of a more sensitive and plastic root system.

Keywords: Gene network; Populus tremula x P. alba; hubs; lateral root growth; nitrogen stress.

Figure 1.

Gene regulatory network (GRN) associated with the 3 superhubs. Superhubs are represented square whereas hub and other terminal genes are represented as circle and triangles. Hubs connected to only one superhub are presented in the same color as the corresponding superhub (purple for PtaNAC1, blue for PtaRAP2.11 and orange for PtaHWS). The hubs connected to all the 3 superhubs are presented as green triangle. The hubs connected to both PtaNAC1 and PtaRAP2.11 are presented as green circle whereas those connected to both PtaRAP2.11 and PtaHWS are presented as yellow circles. Abbreviations for the hub genes are provided in Table 1. The gene regulatory network is constructed based on previously-described transcription profiling or co-expression data of poplar roots grown under normal and LN conditions using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE). The the expression profiles of 9,198 differentially expressed genes (DEGs) of the 6 time-point data as well as an additional list of 424 differentially expressed transcription factors were used as input for the ARACNE. Rank product was used for identifying DEGs.

Figure 2.

Effect of PtaRAP2.11 and PtaHWS overexpression on the expression of connected hubs under normal and LN conditions. Expression was analyzed in root of WT-717, oe-PtaRAP2.11 and oe-PtaHWS plants after 40 d under control and LN. Primers used for the above hub genes are provided in Table S1. oe = overexpression using Camv35S promoter. Values show mean ± standard error of the mean (SEM) (n = 3). Asterisk represent significant difference between WT-717 and transgenic for a given treatment (P < 0.05) as determined by Student's t-test.