Circadian clock controlled gene expression in soybean seeds
Ontology highlight
ABSTRACT:
ORGANISM(S): Glycine max
PROVIDER: GSE18827 | GEO | 2010/06/21
SECONDARY ACCESSION(S): PRJNA121159
REPOSITORIES: GEO
Similar Datasets
Project description:Microarray expression profiling was used to identify genes expressed in developing soybean (Glycine max) seeds that are controlled by the circadian clock. Plants with developing seeds were entrained to 12hour light: 12 hour dark cycles and sampled in constant light conditions. Soybean seeds entrained to 12 hour-light:12 hour dark photocycles were harvested after 24 hours of constant light and temperature conditions. Timepoint 24h represents subjective dawn. To minimize developmental variation, flowers were marked as they opened and seeds were harvested from marked pods after 5 weeks. There are two replicate samples at each time point, and each sample consists of 8 seeds collected from three diffferent plants.
2010-07-08 | E-GEOD-18827 | biostudies-arrayexpress
Project description:Purpose: A time-course transcriptome study to identify probable GA-responsive genes in soybean embryonic axes during seed germination. Methods: Seeds were germinated in the presence or absence of 200 µM PBZ. Seeds were germinated in 28°C temperature and 12/12h photoperiod (dark/light) and harvested at 12, 24 and 36 hours after imbibition (HAI). Three biological replicates were performed. Results: Identification of GA-responsive genes during germination in Glycine max.
2019-07-26 | GSE112872 | 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:To understand the molecular events underlying seed maturation, quiescence and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at four seed developmental stages (cotyledon, early, mid and late maturation), mature dry seeds, and seedlings, eight days after seed sowing.
2017-07-12 | GSE99571 | GEO
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds. MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).
2015-05-25 | E-GEOD-38373 | biostudies-arrayexpress
Project description:Soybean (Glycine max) is one of the most important economic crops. The protein and oil content traits in its seeds usually show a negative correlation, which is worthy of further study. Compared mature seeds of the high-protein soybean Tokachi long-leaf and high-oil soybean Zhonghuang 35, as well as the recombinant inbred lines of high-protein/low-oil populations and high-oil/ low-protein populations by proteomic analysis, it was found that there is a good repeatability and clear separation of proteomes with protein or oil content traits
2021-05-10 | PXD025909 | iProX
Project description:Soybean (Glycine max L. cv Enrei) seeds were sterilized with 2% sodium hypochlorite solution and then thoroughly rinsed in water. The sterilized seeds were sown 4 cm inside surface of sand in 450 mL of quartz seedling cases wetted with 150 mL water and grown at 25°C and 70% humidity in a growth chamber (Sanyo, Tokyo, Japan) under white fluorescent light (160 μmol m-2 s-1, 16 h light period/day). Two-day-old soybeans were flooded for 2 days and hypocotyl samples were collected at the day of removal of flooding and then at 2 more points during the 4-day recovery period.
2015-05-26 | PXD001567 | Pride
Project description:Transformation of Glycine max with seed-targeted expression vectors via Agrobacterium causes measurable unscripted gene expression changes in the seed transcriptome Overall design: mRNA was sequenced from three transgenic events expressing three different recombinant proteins in soybean seeds. Three plants were chosen from each as group replicates, and three seeds from each plant as individual biological replicates.
2015-10-06 | E-MTAB-4317 | biostudies-arrayexpress
Project description:Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production. Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits.
2015-04-29 | GSE21598 | GEO
Project description:Purpose: Comprehensive comparison of gene-expression profiles between 3mlpa (mutant with low phytic acid) and 3MWT (non-mutant with normal phyic acid) soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. Methods: mRNA sequencing reads (101SE) were generated in triplicate from five seed developmental stages of 3mlpa and 3MWT soybean line using Illumina HiSeq 2000. Results: A total of 4235 differentially expressed genes, including 512-transcription factor genes were identified. Eighteen biological processes such as apoptosis, glucan metabolism, cellular transport, photosynthesis and 9 transcription factor families including WRKY, CAMTA3 and SNF2 were enriched during seed development. Genes associated with apoptosis, glucan metabolism, and cellular transport showed enhanced expression in early stages of lpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. Conclusion: This study provides a global perspective of transcriptomal changes during soybean seed development in 3mlpa mutant. The results suggest that low phtic acid-causing mutations in 3mlpa play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively. RNA-Seq of five seed developing soybean seeds from mips1/mrp-l/mrp-n triple mutant line (with low phytic acid) and MIPS1/MRP-L/MRP-N non-mutant line (with normal phytic acid). The mRNA libraries from three biological replicates of each sample were sequenced as 101 SE using Illumina HiSeq 2000.
2016-01-15 | E-GEOD-75575 | biostudies-arrayexpress