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Series GSE228888 Query DataSets for GSE228888
Status Public on May 05, 2023
Title Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses
Organism Glycine max
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design Comparative gene expression profiling analysis of RNA-seq data from soybean roots exposed to 0 (control), 20 min and 40 min of 10 mM sucrose in 3 biological replications
Contributor(s) Uhde-Stone C, Manozna Nidumolu LC, Lorilla KM, Chakravarti I
Citation(s) 37299096
Submission date Apr 03, 2023
Last update date Aug 04, 2023
Contact name Claudia Uhde-Stone
Organization name California State University, East Bay
Department Biological Sciences
Lab Stone lab
Street address 25800 Carlos Bee Blvd
City Hayward
State/province CA
ZIP/Postal code 94542
Country USA
Platforms (1)
GPL28801 Illumina NovaSeq 6000 (Glycine max)
Samples (9)
GSM7142249 soybean-root_t0-control_biol-rep1
GSM7142250 soybean-root_t0-control_biol-rep2
GSM7142251 soybean-root_t0-control_biol-rep3
BioProject PRJNA951790

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Supplementary file Size Download File type/resource
GSE228888_FPKM_all_samples.csv.gz 9.4 Mb (ftp)(http) CSV
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