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

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

PROVIDER: PRJNA951790 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24058176_1.fastq.gz	Fastqsanger.gz
	SRR24058176_2.fastq.gz	Fastqsanger.gz
	SRR24058177_1.fastq.gz	Fastqsanger.gz
	SRR24058177_2.fastq.gz	Fastqsanger.gz
	SRR24058178_1.fastq.gz	Fastqsanger.gz

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

Project description: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.

2023-05-05 | GSE228888 | GEO

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

| S-EPMC10255639 | biostudies-literature

RNA-seq Provides Insights into Sucrose Signaling Re-sponses in White Lupin Roots

Project description:White lupin (Lupinus albus) has become a model plant for understanding plant adapta-tions to phosphorus (P) and iron (Fe) deficiency, two major limiting factors for plant productivity. In response to both nutrient deficiencies, white lupin forms cluster roots, bottle-brush-like root structures that aid in P and Fe acquisition from soil. While cluster root function is well studied, not much is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose has been identified as a long-distance signal sent in increased concentrations from shoot to root in response to both P and Fe deficiency. Thus, sucrose plays a dual role both as a signal and as a major source of energy for the root. To unravel the responses to sucrose as a signal, we performed Illumina paired-end cDNA sequencing of white lupin roots treated with sucrose for 20, 40 or 80 minutes, compared to untreated controls. We identified 634 up-regulated and 956 down-regulated genes in response to sucrose. Twenty minutes of sucrose treatment showed the most responses, with the ethylene-activated signaling pathway as the most enriched GO (Gene Ontology) category. The number of up-regulated genes went down at 40 min and 80 minutes, and protein dephosphorylation became the most enriched category. Taken together, our findings indicate active responses to sucrose as a signal at 20 minutes after sucrose addition, but fewer responses and potential re-setting of signal transduction pathways by dephosphorylation of proteins at 40 and 80 minutes.

2025-01-25 | GSE283515 | GEO

Transcription profiling of Arabidopsis roots from plants grown in nutrient solutions with various concentrations of nitrate and sucrose

Project description:We used Arabidopsis thaliana Col-0 for all experiments. The plants were grown hydroponically on nutrient solution as described previously [Plant J 1999, 18(5):509-519]. Briefly, plants were grown on sand, placed in custom-designed styrofoam rafts, in a growth chamber (EGC, Chagrin Falls, OH, USA) at 22°C with 60 mmol photons m-2s-1 light intensity and 8 h/16 h light/dark cycles. The seeds were initially germinated in tap water. After one week, the water was replaced with a complete nutrient solution [Plant J 1999, 18(5):509-519]. All the experiments were performed with 6 week old plants. Nutrient solutions were renewed weekly and on the day before the experiments. For treatments, individual rafts were transferred to containers with 300mL of nutrient solution supplemented with various concentrations of nitrate (as a mix of 2/1 KNO3/Ca(NO3)2) and/or sucrose. The N-free nutrient solutions contained 0.25 mM K2SO4 and 0.25 mM CaCl2 instead of KNO3 and Ca(NO3)2. Plants were transferred to treatments media at the beginning of the light period and were harvested 8h afterwards. Roots and leaves were harvested separately and quickly frozen in liquid N2.

2006-11-30 | E-MEXP-828 | biostudies-arrayexpress

Transcriptomics Provide Insights into Early Responses to Sucrose Signaling in Lupinus albus.

Project description:Phosphorus (P) and iron (Fe) deficiency are major limiting factors for plant productivity worldwide. White lupin (Lupinus albus L.) has become a model plant for understanding plant adaptations to P and Fe deficiency, because of its ability to form cluster roots, bottle-brush-like root structures that play an important role in the uptake of P and Fe from soil. However, little is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose, sent in increased concentrations from the shoot to the root, has been identified as a long- distance signal of P and Fe deficiencies. To unravel responses to sucrose as a signal, we performed Oxford Nanopore cDNA sequencing of white lupin roots treated with sucrose for 10 min, 15 min, and 20 min, compared to untreated controls. We identified a set of 17 genes, including two bHLH transcription factors, that were upregulated at all three time points of sucrose treatment. GO (gene ontology) analysis revealed enrichment of auxin- and gibberellin-responses as early as 10 min after sucrose addition, and the emerging of ethanol-responses at 20 min of sucrose treatment, indicating a sequential involvement of these hormones in plant responses to sucrose.

2024-05-27 | GSE268152 | GEO

Transcriptomic profile of Sbash and Crossroads actinobacteriophages during various stages of growth.

Project description:The goal of this sequencing project was to measure transcription levels of Sbash and Crossroads actinobacteriophages during different stages of their lifecycle, including lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes), in order to study which genes contribute to superinfection exclusion.

2019-02-18 | GSE121829 | GEO

Bradyzoite subtypes rule the crossroads of Toxoplasma development

Project description:Bradyzoite subtypes rule the crossroads of Toxoplasma development

| PRJNA1370100 | ENA

Iron Therapy in Colo-Rectal Neoplasm and Iron Deficiency Anemia: Intravenous Iron Sucrose Versus Oral Ferrous Sulphate.

Project description:The main objective of this study is to evaluate the efficacy of intravenous iron sucrose in increasing preoperative haemoglobin values in patients with colo-rectal neoplasm and iron deficiency anemia, compared to the standard treatment with oral iron. It will also determine whether intravenous iron sucrose administration improves outcomes such as postoperative haemoglobin values, serum ferritin values, transfusional needs, postoperative complications, or length of hospital stay.

| 2019445 | ecrin-mdr-crc

Nutritional Status and Nutrient Supply in Hospitalised Surgical Patients

Project description:Prospective single arm, single center observational study to assess the nutritional status and the nutrient supply during hospitalization for elective gastrointestinal surgery.

| 2293083 | ecrin-mdr-crc

Effects of anoxia and sucrose on seedling growth

Project description:Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark without added sucrose. Samples were subsequently kept for 6h either [1] under aerobic conditions, [2] under anoxia in absence of sucrose or [3] under anoxia in presence of sucrose. Keywords: other

2005-01-10 | GSE2133 | GEO

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