Glycine max
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PROVIDER: PRJNA304631 | ENA |
REPOSITORIES: ENA
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Project description:Inference of transcription regulatory network in low phytic acid soybean seeds
| PRJNA395215 | ENA
Project description:The low phytic acid trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ABC transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the low phytic acid trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with low phytic acid and better germination rate. The gene regulatory network for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. Gene regulatory networks were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of low phytic acid soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that low phytic acid seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid signaling candidate transcription factors putatively regulating genes in this process were identified as well. Analysis of the gene regulatory networks reveal altered regulation in processes that may be affecting the germination of low phytic acid soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of low phytic acid crops, understanding of which is necessary in order to mitigate these problems.
2021-06-17 | GSE172018 | 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
Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.]
2011-11-22 | GSE33395 | GEO
Project description:A transcriptome analysis of soybean seeds harvested at different developing stages (between stage 7.1 and stage 9) was carried out to understand the molecular events occuring during the acquisition of seed longevity during maturation.
2017-05-01 | GSE98199 | GEO
Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.] genotype: M955 LPA sib-selection - year: 2003(2-replications); genotype: M955 LPA sib-selection - year: 2004(2-replications); genotype: M955 WT sib-selection - year: 2003(3-replications); genotype: M955 WT sib-selection - year: 2004(2-replications)
2011-11-22 | E-GEOD-33395 | biostudies-arrayexpress
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:A dominant loss of function mutation in myo-inositol phosphate synthase gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified several transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling and seed dormancy. We validated the predicted regulatory network by comparing it with published regulatory interactions in Arabidopsis. Some regulatory interactions were found in the low phytic acid mutants but not in non-mutant plants. These findings provide important hypotheses on expression regulation of myo-inositol metabolism, and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at https://lilabatvt.github.io/LPANetwork/.
2018-01-12 | GSE101692 | 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:Large-Scale Gene Expression Profiling of Developing Soybean Seeds of Evans
| PRJNA260822 | ENA