Lifecycle transcriptomics of field-droughted sorghum reveals rapid biotic and metabolic responses
Ontology highlight
ABSTRACT:
ORGANISM(S): Sorghum bicolor
PROVIDER: GSE128441 | GEO | 2019/11/13
REPOSITORIES: GEO
Similar Datasets
Project description:Lifecycle transcriptomics of field-droughted sorghum reveals rapid biotic and metabolic responses
| PRJNA527782 | ENA
Project description:Two cultivars of sorghum were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. These data are the methanol/water metabolite fraction obtained from a Folsh extraction from Sorghum bicolor leaves and roots. The metabolites were derivatized and analyzed via GC-MS at PNNL. Analyses represent the metabolite profile collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought.
2017-10-23 | MSV000081639 | MassIVE
Project description:Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analysis of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020.
2017-08-17 | GSE98817 | GEO
Project description:Sorghum plants (Btx623 background) were grown in a glasshouse between March and May 2014. At panicle emergence, two biological replicates of flag leaf tissue and two biological replicates of emerging panicle tissue were harvested and used for RNA extraction. Btx623 is a non-shattering Sorghum accession, thus in the future we would like to add additional samples from accessions with varying degrees of seed shattering. This dataset will be useful for future comparisons of 1) shattering individuals at these stages and 2) additional flowering developmental time points in a variety of accessions (http://www.rnaseqforthenextgeneration.org/profiles/carrie-thurber.html#research)
2015-08-19 | E-MTAB-4203 | biostudies-arrayexpress
Project description:Our study provides the first comprehensive insight into the comparative transcriptome between shoot and rhizome in sorghum propinquum. Using the deep RNA sequencing technique, more than 70% of genes were identified to be expressed. Comparative analysis revealed that a strong difference in gene expression patterns between shoot and rhizome organs, especially a set of organ-specific TF genes and cis-elements were determined, implying a unique complicated molecular network controlling shoot or rhizome growth and development. Furthermore, this data set including a deep coverage of the subterranean rhizome transcriptome, provided essential information for future molecular genetic dissection of rhizome formation.
2013-12-31 | GSE43999 | GEO
Project description:Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or “vegetable oils”) in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating “sweet” (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems. We initially tested several gene combinations for a “push-pull-protect" strategy. The top TAG-yielding constructs contained five oil transgenes for a sorghum Wrinkled1 transcription factor (“push”), a Cuphea viscosissima diacylglycerol acyltransferase (DGAT; "pull"), a modified sesame oleosin (“protect”) and two combinations of specialized Cuphea lysophosphatidic acid acyltransferases and medium-chain acyl-acyl carrier protein thioesterases. Though intended to generate oils with medium-chain fatty acids, engineered lines accumulated oleic acid-rich oil to amounts of up to 2.5% DW in leaves and 2.0% DW in stems in the greenhouse, 36-fold and 49-fold increases relative to wild-type plants, respectively. Under field conditions, the top-performing event accumulated TAG to amount of up to 5.5% DW in leaves and 3.5% DW in stems, 78-fold and 58-fold increases, respectively, relative to wild-type TX430. Transcriptomic and fluxomic analyses revealed potential bottlenecks for increased TAG accumulation. Overall, our studies highlight the utility of a lab-to-field pipeline coupled with systems biology studies to deliver high vegetative oil sorghum for SAF and renewable diesel production.
2024-07-31 | GSE272636 | GEO
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).
2014-05-01 | GSE54705 | GEO
Project description:Our study provides the first comprehensive insight into the comparative transcriptome between shoot and rhizome in sorghum propinquum. Using the deep RNA sequencing technique, more than 70% of genes were identified to be expressed. Comparative analysis revealed that a strong difference in gene expression patterns between shoot and rhizome organs, especially a set of organ-specific TF genes and cis-elements were determined, implying a unique complicated molecular network controlling shoot or rhizome growth and development. Furthermore, this data set including a deep coverage of the subterranean rhizome transcriptome, provided essential information for future molecular genetic dissection of rhizome formation. A S. propinquum vegetative clone (unnamed accession) with abundant tillering and strong rhizomes cultured in the greenhouse was used in this experiment. Two organs, shoots and rhizomes, at active tillering stage were collected and flash frozen in liquid nitrogen.
2013-12-31 | E-GEOD-43999 | biostudies-arrayexpress
Project description:Two cultivars of sorghum were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. These data are the methanol/water metabolite fraction obtained from a Folsh extraction from Sorghum bicolor leaves and roots. The metabolites were derivatized and analyzed via GC-MS at PNNL. Analyses represent the metabolite profile collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought.
2017-10-23 | MSV000081639 | GNPS
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). RNAseq deep sequencing
2014-05-01 | E-GEOD-54705 | biostudies-arrayexpress