Cross-Species Root Transcriptional Network Analysis Highlights Conserved Modules in Response to Nitrate between Maize and Sorghum

Abstract

Plants have evolved complex mechanisms to respond to the fluctuation of available nitrogen (N) in soil, but the genetic mechanisms underlying the N response in crops are not well-documented. In this study, we generated a time series of NO3−-mediated transcriptional profiles in roots of maize and sorghum, respectively. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes that related to NO3− treatments. A cross-species comparison revealed 22 conserved modules, of which four were related to hormone signaling, suggesting that hormones participate in the early nitrate response. Three other modules are composed of genes that are mainly upregulated by NO3− and involved in nitrogen and carbohydrate metabolism, including NRT, NIR, NIA, FNR, and G6PD2. Two G2-like transcription factors (ZmNIGT1 and SbNIGT1), induced by NO3− stimulation, were identified as hub transcription factors (TFs) in the modules. Transient assays demonstrated that ZmNIGT1 and SbNIGT1 are transcriptional repressors. We identified the target genes of ZmNIGT1 by DNA affinity-purification sequencing (DAP-Seq) and found that they were significantly enriched in catalytic activity, including carbon, nitrogen, and other nutrient metabolism. A set of ZmNIGT1 targets encode transcription factors (ERF, ARF, and AGL) that are involved in hormone signaling and root development. We propose that ZmNIGT1 and SbNIGT1 are negative regulators of nitrate responses that play an important role in optimizing nutrition metabolism and root morphogenesis. Together with conserved N responsive modules, our study indicated that, to encounter N variation in soil, maize and sorghum have evolved an NO3−-regulatory network containing a set of conserved modules and transcription factors.

Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with different rooting depth responses to drought stress in potato

“…In Arabidopsis thaliana , root regulatory gene circuits in response to drought stress have been elucidated based on comprehensive transcriptome mapping of roots ( Rasheed et al., 2016 ; Bashir et al., 2018 ). Transcriptional module discovery can identify coexpression networks that control biological processes associated with root development ( Du et al., 2020 ; Wang et al., 2021b ). Therefore, we generated transcriptional modules of nuclear genes for potato root development and co-expressed target genes in C16 and C119 that could determine the differences in root development and rooting depth between the two potato cultivars.…”

Nitrogen-dependent binding of the transcription factor PBF1 contributes to the balance of protein and carbohydrate storage in maize endosperm

“…RR047A). Quantitative RT-PCR (RT-qPCR) was performed on a Roche Light Cycler 2.0 with Light Cycler software (build 4.1.1.21) as described previously ( Du et al, 2020 ). Briefly, 1 μL of cDNA was added to 5 μL of SYBR Premix Ex TaqTM (TaKaRa Bio Inc., Japan), together with 0.8 μL of each gene-specific primer (forward and reverse, at 10 mM), and the final volume was brought to 10 μL with DNase-free water.…”

Nitrogen sensing and regulatory networks: it's about time and space

“…Another widely used approach to uncover gene-to-trait relations from the network perspective is by associating co-expression network modules with either functional information or phenotypes. Cross-species weighted gene co-expression network analysis (WGCNA; Langfelder and Horvath 2008 ) has identified an N-regulatory network conserved between maize and sorghum, despite the difference in genome size and phylogenetic distance between these two species ( Du et al 2020 ). Notably, ZmHPP, a top-ranked TF in regulating the conserved N-regulatory modules, has an Arabidopsis homolog ATNITR2;2 (AT3G47980) that is also a hub gene (nodes with the most edges) in another co-expression network module for nitrogen signaling ( Canales et al 2014 ).…”