Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome profiling of switchgrass leaf grown under heat stress

ABSTRACT: 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.

ORGANISM(S): Panicum virgaturm

SUBMITTER:

PROVIDER: E-MTAB-1897 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.).

Li Yong-Fang YF Wang Yixing Y Tang Yuhong Y Kakani Vijaya Gopal VG Mahalingam Ramamurthy R

BMC plant biology 20131006

<h4>Background</h4>Global warming predictions indicate that temperatures will increase by another 2-6°C by the end of this century. High temperature is a major abiotic stress limiting plant growth and productivity in many areas of the world. Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop, due to its rapid growth rate, reliable biomass yield, minimal requirements of water and nutrients, adaptability to grow on marginal lands and widespread distribution throughout North Ame ...[more]

PMID: 24093800

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Project description:Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering. Root tip (1cm basal fragment, designated as RT1 hereafter) and the elongation/maturation zone (the next upper 1 cm tissue, designated as RT2 hereafter) tissues were collected at the 29th day of drought stress treatment, (named SDT for severe drought treated), one (D1W) and three days (D3W) of re-watering. The tandem mass tags mass spectrometry-based quantitative proteomics analysis was performed to identify the proteomes, and drought-induced differentially expressed proteins (DEPs). From RT1 tissues, 6,156, 7,687 and 7,699 proteins were quantified, and 296, 535 and 384 DEPs were identified in the SDT, D1W and D3W samples, respectively. From RT2 tissues, 7,382, 7,255 and 6,883 proteins were quantified, and 393, 587 and 321 proteins DEPs were identified in the SDT, D1W and D3W samples. Between RT1 and RT2 tissues, very few DEPs overlapped at SDT, but the number of such proteins increased during the recovery phase. A large number of hydrophilic proteins and stress-responsive proteins were induced during SDT and remained at a higher level during the recovery stages. A large number of DEPs in RT1 tissues maintained the same expression pattern throughout drought treatment and the recovery phases. The DEPs in RT1 tissues were classified in cell proliferation, mitotic cell division, and chromatin modification, and those in RT2 were placed in cell wall remodeling and cell expansion processes. This study provided information pertaining to root zone-specific proteome changes during drought and recover phases, which will allow us to choose the proteins (genes) as better defined targets for developing drought tolerant plants.

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.

Dataset Information

Transcriptome profiling of switchgrass leaf grown under heat stress

Publications

Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.).

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