Gene Expression and Physiological Differences in Neo-Octoploid Switchgrass Subjected to Drought Stress
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ABSTRACT:
PROVIDER: PRJNA548949 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9304920_1.fastq.gz | Fastqsanger.gz | |||
| SRR9304920_2.fastq.gz | Fastqsanger.gz | |||
| SRR9304930_1.fastq.gz | Fastqsanger.gz | |||
| SRR9304930_2.fastq.gz | Fastqsanger.gz | |||
| SRR9304940_1.fastq.gz | Fastqsanger.gz |
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Project description:Switchgrass (Panicum virgatum L.) has been subject to breeding to improve its yield and composition for bioenergy, but improving its tolerance to environmental variability is just beginning. Different ploidy populations act as somewhat distinct gene pools which can only be bridged through whole genome reduction or duplication events. In order to document potential wide-ranging effects of whole genome duplication, we examined the effects of water stress on growth, physiology, and gene expression in individual tetraploid clones of the switchgrass cultivar ‘Liberty’ as well as neo-octoploid lines derived from it. The neo-octoploids behaved similarly to Liberty under water-stress and recovery conditions. Growth rates, photosynthesis, gas exchange, node numbers, and height were reduced in plants under water stress while proline levels were increased. A total of 6134 differentially expressed genes (8% of the annotated genes with detectable expression in crown tissue) were detected under water deficit stress, while 3310 differentially expressed genes were detected in crown tissue after 1 week of recovery from water deficit stress relative to well-watered treatments. Only a small number of genes were identified as being differentially expressed between 4x Liberty and its 8x derivatives.
2020-02-06 | GSE132772 | 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: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.
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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.
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Project description:Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.
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