Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Arabidopsis plants exposed to combined heat and drought stress

ABSTRACT: One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits. Indeed much progress has been made in this area, particularly in biomedicine where functional genomic information can be used to determine the physiological state (e.g., diagnosis) and predict phenotypic outcome (e.g., patient survival). Until now, ecology has lacked an analogous approach where genomic information can be used to diagnose the presence of a given physiological state (e.g., stress response) and then predict likely phenotypic outcomes (e.g., stress tolerance, fitness). We demonstrate that a compendium of genomic signatures can be used to classify the plant abiotic stress phenotype in Arabidopsis according to the architecture of the transcriptome, and then be linked with gene coexpression network analysis to determine the underlying signaling pathways and ultimately the genes governing the phenotypic response. Here, we release microarray data from an expression profiling study where plants were exposed to heat and drought alone, and in combination with each other. A direct loop design with 6 biological replicates for control, heat, drought, and combined heat and drought was performed. A schematic describing the design is provide as supplementary information.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Stan Wullschleger

PROVIDER: E-GEOD-9415 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants.

Weston David J DJ Gunter Lee E LE Rogers Alistair A Wullschleger Stan D SD

BMC systems biology 20080204

<h4>Background</h4>One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits. Indeed much progress has been made in this area, particularly in biomedicine where functional genomic information can be used to determine the physiological state (e.g., diagnosis) and predict phenotypic outcome ( ...[more]

PMID: 18248680

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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.

Project description:In this study expression levels of 732 genes were analyzed for European maize (Zea mays L.) inbred lines (4 Flint and 5 Dent) and nine corresponding hybrids by microarray analysis. The selection of the 732 genes was based on a previous study (Thiemann et al., Theor Appl Genet 2010, 120:401-413), which sequences were derived from the 46k microarray (platform GPL6438) (University of Arizona, USA). 558 of the 732 genes represented on the microarray were differentially expressed between the original 21 parental inbred lines and were correlated with at least one of the three characteristics MPH (mid-parent heterosis) and/or HP (hybrid performance) of the trait GY (grain yield) and/or HP of the trait grain dry matter content. Some of those correlated genes show overlapping correlations. The residual 174 non-correlated genes belong to the top 6 biological processes that were found to be enriched among the HP for GY-correlated genes (Thiemann et al., Theor Appl Genet 2010, 120:401M-bM-^@M-^S413). The aim of this study was the identification of the hybrid expression pattern of the subset of genes, which mid-parental expression levels were shown to be correlated with MPH for GY or showed no correlation. For the analysis total RNA of 7-day old seedlings was extracted and amino-allyl-labeled RNA was synthesized. The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). Hybridizations were conducted between each pair of parental inbred lines and its corresponding hybrids. In total 4 biological replicates per genotype were analyzed. As a result 119 (22.9 %) of the 519 MPH for GY or non-correlated genes showed differential expression in at least one of the nine inbred-hybrid comparisons. These differentially expressed genes were further analyzed for hybrid expression, resulting in a mainly additive expression. Of all differential expression, additive expression of 86.21 % (with 13.79 % non-additive) of the MPH-correlated genes, and a slightly smaller contingent of 79.66 % (with 20.34 % non-additive) of the non-correlated genes was measured. Four biological replicates of each of the nine parental inbred lines (4 Flint: F012, F039, F047, L024; 5 Dent: S028, S036, P024, P033, P048) and of the nine corresponding hybrids (P033xF047, P048xF047, P024xF039, S036xL024, S028xL024, S028xF012, S028xF039, P024xF012, F012xF039) were grown under controlled conditions (25 M-BM-0C 16 h day, 21 M-BM-0C 8 h night, 70 % air humidity) for seven days in a climate chamber. Whole seedlings were frozen in liquid nitrogen and were finely pounded. Total RNA was extracted and then precipitated (4 M LiCl). Residual genomic DNA was hydrolyzed with DNaseI (Fermentas, St. Leon-Rot, Germany) and purified with the M-bM-^@M-^\NucleoSpin RNA Clean-up KitM-bM-^@M-^] (Macherey-Nagel, DM-CM-<ren, Germany). For first strand cDNA synthesis, 5 M-BM-5g of total RNA and the Superscript II from Invitrogen (Life Technologies, Carlsbad, USA) were used. Second strand synthesis was performed using DNA Polymerase I and RNase H followed by a 5 min incubation step of T4 DNA Polymerase (Fermentas, St. Leon-Rot). Residual RNA was hydrolyzed with RNase A. In-vitro transcription was performed with the T7 RNA Polymerase (Fermentas, St. Leon-Rot, Germany) for 4 h to incorporate aminoallyl-labeled UTPs (Fermentas, St. Leon-Rot, Germany). Finally, residual DNA was degraded with DNase I (Fermentas). Synthesized aaRNA was coupled with fluorescence dyes Cy3 or Cy5 (GE Healthcare, Chalfont St. Giles, UK). The RNeasy MinElute Kit (Qiagen, Hilden, Germany) was used for purification and removal of unbound dye. In total 105 hybridizations were realized. The dye used for each biological replicate of each genotype was alternated to reduce systematic bias.

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Dataset Information

Arabidopsis plants exposed to combined heat and drought stress

Publications

Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants.

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