Transcriptome profiling of switchgrass over expressing Medicago STENOFOLIA (STF) gene
Ontology highlight
ABSTRACT:
ORGANISM(S): Panicum virgatum
SUBMITTER: Yuhong Tang
PROVIDER: E-MTAB-5539 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The most effective method of micro-propagation for clonal replicates for switchgrass seed production is from the axillary buds of the lower nodes. We hypothesized that buds and nodes from low and high tillering lines from an inbred population will aid in identifying genes important for the different tillering habits of these plants. Since tiller number is directly correlated with biomass yields, identifying genes associated with high tillering trait will provide valuable biomarkers for marker-assisted selection and for QTL mapping of tillering trait in switchgrass. First-generation switchgrass inbred lines derived from selfing a parental genotype M-^QNL94 LYE 16x13M-^R, which was selected from the Oklahoma State University northern lowland breeding population in 2007 was used in this study. The NL94/298 inbred line produced fewer tillers than NL94/145. Stems of the high tillering line had 2-3 phytomers, while the low tillering line had 1-2 phytomers. Eight other inbred lines from this population that showed similar phenotypes as NL94/145 or NL94/298 and similar genotypes based on 380 genomic SSR marker profiles were selected for this study. Individual stems from these nine lines each for high and low tillering habit were harvested from field growing plants in the Agronomy field plots, Stillwater. Vegetative buds from first phytomer and node regions from second phytomer were cut out using a sharp scalpel under a dissection scope and immediately frozen in liquid nitrogen for transcriptomics analysis.
2014-01-14 | E-MTAB-1899 | biostudies-arrayexpress
Project description:In this study we were interested in identifying the gene networks that are responsive to chronic heat treatment in a switchgrass cultivar that is widely grown in the south-western USA and where 38C day temperatures have been reported for more than 100 days in the recent years. Switchgrass Alamo plants were subjected to chronic heat stress for 50 days (38 C/30C; day/night) or maintained under optimal conditions (28C/20C). Leaves were collected at the end of the heat regime for transcriptome analysis.
2014-01-14 | E-MTAB-1897 | biostudies-arrayexpress
Project description:Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production to produce bioethanol directly from cellulosic biomass. However, few transcriptomic studies have been reported so far for C. thermocellum using biomass as carbon source. In this study, samples were taken from exponential and stationary phases of C. thermocellum cells growing in MTC media with pretreated switchgrass as carbon source, and transcriptomic profiling change of C. thermocellum during different growth phase was investigated using both expression array and tiling array. This study will help the understanding of gene expression of C. thermocellum using cellulosic biomass as carbon source and the knowledge will facilitate future metabolic engineering effort for strain improvement. [HX12 expression array]: A eleven array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different growth phase of T2 and T3 with switchgrass as carbon source. Two biological replicates used for each phase. [3Plex tiling array]: A six array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different growth phase of T2 and T3 with switchgrass as carbon source. Two biological replicates used for each phase.
2014-05-08 | E-GEOD-26926 | biostudies-arrayexpress
Project description:Microarray analysis was performed to determine downstream gene expression effects of miR156 overexpression. Three tillers were collected from each plot, resulting in four biological replicates for each of the four transgenic and ‘Alamo’ nontransgenic control lines.
2017-10-25 | E-MTAB-5948 | biostudies-arrayexpress
Project description:The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. High quality RNA was extracted using a method we report for C. thermocellum grown on solid substrates. Transcriptome profiles were obtained at two time points during actively growing fermentations (12 h and 37 h post inoculation). A comparison of two transcriptomic analytical techniques, microarray and RNAseq, was performed and the data analyzed for statistical significance. When thresholds for genes passing significance of FDR>0.05 were applied, microarray (2351 genes) had a greater number of significant genes relative to RNA-seq (280 genes when normalized by KDMM). When a 2-fold difference in expression threshold was applied, seventy-three genes were significantly differentially expressed in common between the two techniques. We identified genes differentially expressed when C. thermocellum ATC 27405 was grown on the two biomass substrates, with two putative efflux/transport systems highly differentially regulated (>5-fold). This study has revealed consistency between these two transcriptomics analytical platforms that gives confidence in our switch from the DNA microarray platform to an RNAseq based platform for routine transcriptomics analyses. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. High quality RNA was extracted using a method we report for C. thermocellum grown on solid substrates. Transcriptome profiles were obtained at two time points during actively growing fermentations (12 h and 37 h post inoculation). A comparison of two transcriptomic analytical techniques, microarray and RNAseq, was performed and the data analyzed for statistical significance.
2013-05-16 | E-GEOD-47010 | biostudies-arrayexpress
Project description:Switchgrass (Panicum virgatum) is a perennial crop producing deep roots thus highly tolerant to soil water deficit conditions. However, seedling establishment in field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7,006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (P < 0.05, fold change < 0.6 or > 1.7) from the non-treated control to drought-treated conditions. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under soil drought condition.
2016-08-09 | PXD004675 | Pride
Project description:Small RNA libraries were constructed, sequenced, and analyzed with our Sequence Homology Pipeline for miRNA discovery (Jeong et al. 2013) to identify 59 unique conserved miRNA sequences from 199 precursors in switchgrass.
2019-01-01 | GSE112228 | GEO
Project description:Sustainable production of switchgrass (Panicum virgatum) as a bioenergy crop hinges in part on efficient use of soil macronutrients, especially nitrogen (N). This study investigated the physiological, metabolic and transcriptomic responses of switchgrass to N limitation. Moderate N limitation marked a tipping point for large changes in plant growth, root-to-shoot ratio, root system architecture and total nitrogen content. Integration of transcriptomic and metabolic data revealed that N limitation reduced switchgrass photosynthetic capacity and carbon(C)-fixation activities. Switchgrass balanced C-fixation with N-assimilation, transport and recycling of N compounds by rerouting C-flux from glycolysis, the oxidative branch of the pentose phosphate pathway (OPPP) and from the tricarboxylic acid (TCA) cycle in an organ specific manner. The energy and reduction power so generated, and C-skeletons appear to be directed towards N uptake, biosynthesis of energy storage compounds with high C/N ratio such as sucrose, non-N-containing lipids, and various branches of secondary metabolism.
2023-12-31 | GSE237286 | GEO
Project description:Purpose: Increasing biomass yield and quality of feedstock have been a recent interest in switchgrass research. Despite the economic importance of switchgrass, increasing temperature and water deficit are limiting factors to the cultivation of bioenergy crops in the semi-arid areas. The effect of individual drought or heat stress has been studied separately in switchgrass. However, there is relatively limited or no report on the molecular basis of combined abiotic stress tolerance in switchgrass particularly the combination of drought and heat stress. We used RNA-Seq approaches to elucidate the transcriptome changes of switchgrass in response to drought and high temperatures simultaneously. Method: We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Results:Out of total 32,190 genes, we identified 3,912, as DT responsive genes, 2,339 and 4,635 as , heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively Conclusion: Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.
2022-03-31 | GSE174278 | GEO
Project description:The combined heat and drought stress influence the plant growth and development. Switchgrass is an economically important crop due to the availability of high biomass with little water and nutrient requirements. Earlier reports suggested that switchgrass growth and yield highly influenced by heat and drought. The mechanism behind heat and drought stress is not fully understood in switchgrass. This study has undertaken to analyze the epigenetic modification using ChIP-Seq analysis with the activation histone mark H3K4me3. Conclusion: Our study provides the first epigenomic analysis of heat and drought response in switchgrass. This comprehensive resource will provide other epigenomic regulated information in non-model plant species.
2023-07-23 | GSE196295 | GEO