Ontology highlight
ABSTRACT:
PROVIDER: PRJNA496337 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8056720_1.fastq.gz | Fastqsanger.gz | |||
| SRR8056720_2.fastq.gz | Fastqsanger.gz | |||
| SRR8056730_1.fastq.gz | Fastqsanger.gz | |||
| SRR8056730_2.fastq.gz | Fastqsanger.gz | |||
| SRR8056711_1.fastq.gz | Fastqsanger.gz |
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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.
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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.
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2025-01-01 | E-MTAB-13719 | biostudies-arrayexpress
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:Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2 and H2. C. bescii, C. kronotskyensis and C. saccharolyticus solubilized 38%, 36% and 29% (by weight) of unpretreated switchgrass (5 g/l), repectively, which was about half of the concentration of crystalline cellulose (Avicel, 5 g/l) that was solubilized under the same conditions. The lower yields with C. saccharolyticus were unexpected, given that its genome encodes the same GH9-GH48 multi-domain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing Cellulose to switchgrass showed that many carbohydrate ABC transporters and multi-domain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagella biosynthesis were up-regulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation. A dye swap was completed with each of three Caldicellulosiruptor species: C. bescii, C. kronotskyensis and C. saccharolyticus growing on cellulose and switchgrass. Half of the RNA sample for one condition was labeled with Cy3 and the other half Cy5. The two differentially labeled samples were run on two different slides and analyzed to investigate differences in transcription during growth on cellulose and switchgrass.
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