Ontology highlight
ABSTRACT:
PROVIDER: PRJNA662977 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12626432.fastq.gz | Fastqsanger.gz | |||
| SRR12626433.fastq.gz | Fastqsanger.gz | |||
| SRR12626434.fastq.gz | Fastqsanger.gz | |||
| SRR12626435.fastq.gz | Fastqsanger.gz | |||
| SRR12626436.fastq.gz | Fastqsanger.gz |
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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
Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used.
2015-07-02 | GSE65553 | GEO
Project description:Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.
2019-06-24 | GSE129320 | GEO
Project description:We generated a comprehensive RNAseq expression atlas for several stress conditions in order to analyze changes in the gene expression during adaptation to mild stresses. The stresses are divided into two main groups: the “nutrient stresses” and the “environmental stresses”. Nutrient stresses include nutrient depletion (-N, -P, -S, -micronutrients), salt stress (+NaCl), osmotic stress (+mannitol) and control. The environmental stresses consist of high light, prolonged darkness, heat, cold and control.
2020-01-21 | E-MTAB-7822 | biostudies-arrayexpress
Project description:To decipher stress responses under flooding and drought as well as flooding-tolerant mechanisms in soybean, the mathematic biological approach of simulation model was applied. Furthermore, wild-type soybean with ABA treatment and flooding-tolerant mutant line, which displayed flooding tolerance, were used as the flooding-tolerant materials. Proteins acquired by gel-free/label-free proteomic technique were used for simulation model of responses under different stresses and flooding tolerant.
2018-10-26 | PXD005680 | Pride
Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used. The Williams 82 and DT2008 soybean plants were grown for 14 days in the vermiculite soil under greenhouse conditions. The whole plants of 14-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 10 h. All roots of independent 14-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.
2015-07-02 | E-GEOD-65553 | biostudies-arrayexpress
Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop.Whole genome DNA microarrays were used to compare the nodule transcriptome profiling of soybean ‘Williams 82’ grown in vermiculite and subjected to low (0.1 mM; LP) or adequate (2.0 mM; HP) Pi levels. Plants were inoculated with two Bradyrhizobium diazoefficiens strains (USDA110 vs. CB1809), which exhibited contrasting growth and nodulation patterns under LP conditions, with the former model strain displaying a lower Pi-stress acclimatization in combination with the model Williams 82. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used. Microarrays were used to compare the nodule transcriptomes of the model soybean ‘Williams 82’ plants grown in vermiculite and subjected to low (0.1 mM) or sufficient (2.0 mM) inorganic phosphate levels
2025-10-01 | GSE244933 | GEO
Project description:Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate(Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated.Taken together, identification of differential phosphoproteins not only reveled complex regulatory pathways in soybean adaptation to Pi starvation through reversible protein phosphorylation.
2021-06-13 | PXD025771 | Pride
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.
2014-11-01 | GSE57252 | GEO