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. 2023 May 26;12(11):2117.
doi: 10.3390/plants12112117.

Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses

Leela Chandra Manozna Nidumolu  1 , Kristina Mae Lorilla  1 , Indrani Chakravarty  1 , Claudia Uhde-Stone  1
Affiliations

Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses

Leela Chandra Manozna Nidumolu et al. Plants (Basel). .

Abstract

Soybean (Glycine max) is an important agricultural crop, but nutrient deficiencies frequently limit soybean production. While research has advanced our understanding of plant responses to long-term nutrient deficiencies, less is known about the signaling pathways and immediate responses to certain nutrient deficiencies, such as Pi and Fe deficiencies. Recent studies have shown that sucrose acts as a long-distance signal that is sent in increased concentrations from the shoot to the root in response to various nutrient deficiencies. Here, we mimicked nutrient deficiency-induced sucrose signaling by adding sucrose directly to the roots. To unravel transcriptomic responses to sucrose acting as a signal, we performed Illumina RNA-sequencing of soybean roots treated with sucrose for 20 min and 40 min, compared to non-sucrose-treated controls. We obtained a total of 260 million paired-end reads, mapping to 61,675 soybean genes, some of which are novel (not yet annotated) transcripts. Of these, 358 genes were upregulated after 20 min, and 2416 were upregulated after 40 min of sucrose exposure. GO (gene ontology) analysis revealed a high proportion of sucrose-induced genes involved in signal transduction, particularly hormone, ROS (reactive oxygen species), and calcium signaling, in addition to regulation of transcription. In addition, GO enrichment analysis indicates that sucrose triggers crosstalk between biotic and abiotic stress responses.

Keywords: crosstalk; nutrient deficiency; sucrose signaling; transcriptome.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
(a) MA (mean average) plot of log2 FC against normalized sequence counts at 20 min (t20) and 40 min (t40) of sucrose treatment, each compared to t0 (no-sucrose control). To reduce background noise, shrinkage of the effect size was applied before visualization. Values of padj (adjusted p-value) ≤0.01 in the DESeq2 gene expression analysis are shown in blue. (b) PCA plot of the three biological replications representing differences between both time points (20 min, 40 min) and control (t0). (c) Venn diagram: significantly up-regulated DEGs in t20 and t40 with a p-value < 0.05 and a log2 FC ≥ 1 are represented on top (green), and significantly down-regulated genes in t20 and t40 with a p-value < 0.05 and a log2 FC ≤ 1 are represented on the bottom (blue).
Figure 2
Figure 2
Heatmap of the top 40 up-regulated genes in both t20 and t40 (sorted for t20) across biological replications. Shown are the relative numbers of normalized reads in FPKM for the three biological replications: t0 (control), t20, and t40.
Figure 3
Figure 3
GO analysis of biological processes (a) and molecular functions (b) among highly upregulated genes (Log2FC > 3, p-value < 0.05) at t40.
Figure 3
Figure 3
GO analysis of biological processes (a) and molecular functions (b) among highly upregulated genes (Log2FC > 3, p-value < 0.05) at t40.
See this image and copyright information in PMC

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