ChIP-Seq analysis of switchgrass transcriptome in response to single drought and combinations of drought and heat stress
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ABSTRACT:
ORGANISM(S): Panicum virgatum
PROVIDER: GSE196295 | GEO | 2023/07/23
REPOSITORIES: GEO
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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.
2022-03-31 | GSE174278 | 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.
2016-08-09 | PXD004675 | Pride
Project description:In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light:dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.
2014-07-01 | GSE57887 | GEO
Project description:In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light:dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses. mRNA profiles of leaf tissue from clonal replicates at various time points during drydown and recovery were generated by deep sequencing 3' mRNA tags using SOLiD.
2014-07-01 | E-GEOD-57887 | biostudies-arrayexpress
Project description:RNA-Seq analysis of switchgrass transcriptome in response to single drought and combinations of drought and heat stress
| PRJNA729063 | ENA
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:Drought-responsive genes were identified in leaf tissues of the cotton Acala 15-1799, a cotton genotype derived in the Southwest USA. Most of the identified genes such as the heat shock proteins have been described as responsive to drought and heat in other plant species. Microarray analysis was used to identify drought-responsive genes that might confer this cotton genotype with an improved tolerance to drought stress. Leaves from cotton plants watered or exposed to drought stress were used for RNA extraction and generarion of cRNA probes for hybridization of Affymetrix microarrays. Microarray technology was used to identify drought-responsive genes in cotton to assist in molecular breeding program. The supplementary file 'GSE18253_differentially_expressed.txt' lists the differentially expressed genes.
2010-05-22 | E-GEOD-18253 | biostudies-arrayexpress
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: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.
2023-07-13 | GSE237285 | GEO
Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment.
2013-06-10 | GSE46759 | GEO