Glycine max
Ontology highlight
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PROVIDER: PRJNA1057058 | ENA |
REPOSITORIES: ENA
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Project description:Melatonin enhances plant growth and abiotic stress tolerance in soybean plants
| PRJNA248556 | ENA
Project description:Salt stress caused by soil salination inhibits plant growth and development that result in reduction of crop yield and threaten the food security. Several spliceosome components are considered to modify salt stress responses in plants. However, the molecular basis of spliceosome proteins adjustment to salt stress is still unclear. Here we report that an Sm core protein SmEb is required for salt tolerance in Arabidopsis. In addition, SmEb controls alternative splicing of hundreds of pre-mRNA to participate in plant response to salt stress. Our results further reveal that SmEb takes effect on maintain proper ratio of two RCD1 splicing variants to adjust to H2O2 accumulation under salt stress. Together, our findings uncover that proper alternative splicing of pre-mRNAs governed by the spliceosome component SmEb is essential for plant salt stress responses. Salt stress caused by soil salination inhibits plant growth and development that result in reduction of crop yield and threaten the food security. Several spliceosome components are considered to modify salt stress responses in plants. However, the molecular basis of spliceosome proteins adjustment to salt stress is still unclear. Here we report that an Sm core protein SmEb is required for salt tolerance in Arabidopsis. In addition, SmEb controls alternative splicing of hundreds of pre-mRNA to participate in plant response to salt stress. Our results further reveal that SmEb takes effect on maintain proper ratio of two RCD1 splicing variants to adjust to H2O2 accumulation under salt stress. Together, our findings uncover that proper alternative splicing of pre-mRNAs governed by the spliceosome component SmEb is essential for plant salt stress responses.
2023-04-01 | GSE208786 | GEO
Project description:Salinity tolerance is a complex trait and, despite many efforts to obtain rice plants resistant to salt, few results have been achieved since a deeper understanding of the tolerance mechanisms is still needed. We used imaging of photosynthetic parameters, ion analysis and transcriptomic approaches to unveil differences between two rice varieties differing in salt sensitivity. Moreover, we analysed H2O2 production in roots, using a fluorescent probe, and the ensuing gene regulation. Transcriptomic analyses conducted in tolerant plants supported the set-up of an adaptive program consisting of allocating sodium preferentially to roots, restricting it to the oldest leaves and activating regulatory mechanisms of photosynthesis in new leaves. As a consequence, plants resumed growth even under prolonged salt stress. By contrast, in the susceptible variety, RNA profiling unveiled a mis-targeted response, leading to senescence and cell death. In roots of tolerant plants, an increase in H2O2 was observed as early as 5 minutes after treatment. Consequently, the expression of genes involved in perception, signal transduction and response to salt were induced at earlier times when compared to susceptible plant roots. Our results demonstrate that a prompt H2O2 signalling in roots participates to a coordinated response resulting in adaptation instead of senescence in salt treated rice plants.
2018-03-14 | GSE109341 | GEO
Project description:Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Glycine max lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.
2018-05-07 | GSE114074 | GEO
Project description:Ice plant (Mesembryanthemum crystallinum L.) is a halophyte and an inducible CAM plant. Ice plant seedlings exhibit moderate salt tolerance, with root growth unaffected by 200 mM NaCl treatments, while hypocotyl elongation is hindered in salt-stressed etiolated seedlings. Superoxide anion accumulation was prominent in cotyledons and primary leaves but decreased in root tissues over time but was not significantly affected by salt treatment. Hydrogen peroxide (H2O2) levels surged initially in both control and salt-treated seedlings, with higher and more persistent H2O2 levels in salt-treated seedlings, indicating salt-induced ROS accumulation, especially in etiolated seedlings. An RNA-seq analysis of etiolated seedlings revealed 6,326 unigenes (about 8%) showing more than a four-fold change in expression after a 6-h 200 mM NaCl treatment. The top GO terms for 4-fold upregulated DEGs in the Molecular Function category included “cation binding,” “metal ion binding,” “oxidoreductase activity,” “monooxygenase activity,” and “antioxidant activity.” The top GO terms for 4-fold down-regulated DEGs in the Biological Process category included “metabolic process”, “cellular metabolic process”, and “biosynthetic process”. Upregulated genes were primarily linked to ion transport and stress responses and downregulated genes to growth processes like ribosomal protein synthesis and cell wall formation. This indicates that salt stress hinders growth but enhances ion homeostasis and stress response mechanisms. For class III peroxidase family genes, 14 out of 53 identified transcripts met the criteria for differentially expressed genes. Quantitative RT-PCR confirmed that the expression of McPrx4.1, McPrx12.1, and McPrx12.3 increased, while the expression of McPrx60.3 decreased. We suggest distinct roles for individual class III peroxidase members in the trade-offs between plant growth and stress response. Unveiling these responses will advance our understanding of the growth–stress balance in the intrinsic salt tolerance in halophytes.
2025-01-01 | GSE277109 | GEO
Project description:Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on guilt-by-association relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.
2013-12-13 | GSE46153 | GEO
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
Project description:Enterobacter sp. SA187 is a plant growth-promoting bacterium (PGPB) that promotes growth of the crop plant alfalfa under saline irrigation and desert farming conditions. SA187 also enhances salt tolerance of the model plant Arabidopsis thaliana under in vitro conditions. In the present study, we used a transcriptomic approach to elucidate the mechanisms underlying plant growth promotion by SA187 under salt stress. Compared to free-living SA187, a massive metabolic reprogramming of SA187 occurs upon association with Arabidopsis. This effect was largely independent of the plant growth condition (non-salt or salt stress). Our data revealed pronounced changes in gene expression of proteins involved in cell signaling, chemotaxis, flagella biosynthesis, quorum sensing and biofilm formation. Also, upon plant interaction, a complete reprograming of nutrients acquisition and the central carbon metabolism of SA187 was observed. Moreover, in accordance with the previously identified role of bacterially produced 2-keto-4-methylthiobutyric acid (KMBA) in mediating salt stress tolerance, the sulfur metabolism of SA187 was strongly induced. Overall, our results give a deep insight into the metabolic and signaling pathways involved in the transition from free-living to a plant-associated PGPB life style of SA187.
2021-01-04 | GSE124591 | GEO
Project description:Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants. SUBMITTER_CITATION: Biology 2013, 2(4), 1311-1337; doi:10.3390/biology2041311 Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos Delasa Aghamirzaie, Mahdi Nabiyouni, Yihui Fang, Curtis Klumas, Lenwood S. Heath, Ruth Grene and Eva Collakova SUBMITTER_CITATION: Metabolites 2013, 3(2), 347-372; doi:10.3390/metabo3020347 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Eva Collakova, Delasa Aghamirzaie, Yihui Fang, Curtis Klumas, Farzaneh Tabataba, Akshay Kakumanu, Elijah Myers, Lenwood S. Heath and Ruth Grene Total mRNA profiles of 10 time course samples of Soybean developing embryos with three replicates per sample were generated by deep sequencing, using Illumina HiSeq 2000
2013-12-13 | E-GEOD-46153 | biostudies-arrayexpress
Project description:Hydrogen peroxide (H2O2) is an important signaling molecule in plant developmental processes and stress responses. However, whether H2O2-mediated signaling can crosstalk with plant hormone signaling is largely unclear. Here, we show that H2O2 induces oxidation of the BRASSINAZOLE-RESISTANT1 (BZR1) transcription factor, which functions as a master regulator of Brassinosteroid (BR) signaling. Oxidative modification enhances BZR1 transcriptional activity by promoting its interaction with regulators of auxin- and light-signaling, including AUXIN RESPONSE FACTOR6 (ARF6) and PHYTOCHROME INTERACTING FACTOR4 (PIF4). Genome-wide analysis shows that H2O2-dependent regulation of BZR1 activity plays a major role in modifying gene expression related to several BR-mediated biological processes. Furthermore, we show that the thioredoxin TRXh5 can interact with, and catalyze reduction of, BZR1. We conclude that reversible oxidation of BZR1 connects H2O2- and thioredoxin-mediated redox signaling to BR signaling to regulate plant development
2018-03-21 | GSE110488 | GEO