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Species & Dataset
Experiment
Foliar ozone injury
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Arabidopsis thaliana
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Common name: Thale cress, Mouse-ear cress
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Family: Brassicaceae
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Cultivar: C24 (Ozone tolerant), Te (Ozone sensitive), CT101, Col-0
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Tissue: Rosettes
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Ozone concentration: 350 nL L-1
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Ozone exposure: 2 hours
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Platform: Microarray
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Year of study: 2014
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Location: Helsinki, Finland
Title: Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana.
Summary: As multifaceted molecules, reactive oxygen species (ROS) are known to accumulate in response to various stresses. Ozone (O3) is an air pollutant with detrimental effect on plants and O3 can also be used as a tool to study the role of ROS in signaling. Genetic variation of O3 sensitivity in different Arabidopsis accessions highlights the complex genetic architecture of plant responses to ROS. To investigate the genetic basis of O3 sensitivity, a recombinant inbred line (RIL) population between two Arabidopsis accessions with distinct O3 sensitivity, C24 (O3 tolerant) and Te (O3 sensitive) was used for quantitative trait loci (QTL) mapping. Through analysis of QTL mapping combined with transcriptome changes in response to O3, we identified three causal QTLs and several potential candidate genes regulating the response to O3. Based on gene expression data, water loss, and stomatal conductance measurement, we found that a combination of relatively low stomatal conductance and constitutive activation of salicylic acid (SA)-mediated defense signaling were responsible for the O3 tolerance in C24. Application of exogenous SA prior to O3 exposure can mimic the constitutive SA signaling in C24 and could attenuate O3-induced leaf damage in the sensitive Arabidopsis accessions Te and Cvi-0.
Data repository: Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) (Accession number GSE61542)
Reference: Xu, E., Vaahtera, L., Hõrak, H., Hincha, D.K., Heyer, A.G. and Brosché, M., 2015. Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in A rabidopsis thaliana. Plant, cell & environment, 38(7), pp.1418-1433.
C24:
AGI Gene code | Uniprot Id | Bin Code | Bin Name | FoldChange | log2 FC | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|---|---|
AT5G13150 | Q9FY95 | 27.3.99 | RNA.regulation of transcription.unclassified | Inf | Inf | 0.00169 | 0.01184 | Encodes a NAC domain transcription factor that interacts with VND7 and negatively regulates xylem vessel formation. |
AT2G47270 | O22901 | 27.3.6 | RNA.regulation of transcription.bHLH,Basic Helix-Loop-Helix family | Inf | Inf | 0.00084 | 0.00671 | Encodes a mitochondrial-localized protein. The FUM1 gene appears to be essential, suggesting that FUM1 may play a crucial role as a fumarase in the tricarboxylic acid cycle. |
AT2G31335 | Q1G3B9 | 35.1 | not assigned.no ontology | Inf | Inf | 0.00024 | 0.00248 | Encodes a mitochondrial glyoxalase 2 that can accommodate a number of different metal centers and with the predominant metal center being Fe(III)Zn(II). |
AT1G68630 | Q9SX26 | 35.1 | not assigned.no ontology | Inf | Inf | 0.02081 | 0.08763 | Encodes a member of the proline-rich extensin-like receptor kinase (PERK) family. This family consists of 15 predicted receptor kinases (PMID: 15653807). |
AT5G19890 | Q39034 | 26.12 | misc.peroxidases | Inf | Inf | 0.00216 | 0.0145 | Encodes a Golgi-localized nucleotide-sugar transporter. |
AT1G61105 | F4HRR1 | 20.1.7 | stress.biotic.PR-proteins | Inf | Inf | 0.00417 | 0.02448 | Encodes a geranyllinalool synthase that produces a precursor to TMTT, a volatile plant defense C16-homoterpene. GES transcript levels rise in response to alamethicin, a fungal peptide mixture that damages membranes. This transcriptional response is blocked in JA biosynthetic and JA signaling mutants, but GES transcript levels still rise in response to alamethicin in mutants with salicylic acid and ethylene biosynthetic and/or signaling defects. GES transcripts also accumulate in response to a larval infestation. This enzyme does not localize to the plastids, and it may be present in the cytosol or endoplasmic reticulum. |
AT5G40590 | Q9FM39 | 35.1.26 | not assigned.no ontology.DC1 domain containing protein | Inf | Inf | 0 | 0 | Encodes a cytosolic glucose-6-phosphate dehydrogenase that is insensitive to reduction by DTT and whose mRNA is expressed ubiquitously. |
AT2G33780 | O23660 | 35.1 | not assigned.no ontology | Inf | Inf | 0.00372 | 0.02233 | Dormancy/auxin associated family protein; CONTAINS InterPro DOMAIN/s: Dormancyauxin associated (InterPro:IPR008406); BEST Arabidopsis thaliana protein match is: dormancy-associated protein-like 1 (TAIR:AT1G28330.1); Has 165 Blast hits to 165 proteins in 47 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 165; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
AT5G05290 | Q38866 | 10.7 | cell wall.modification | Inf | Inf | 0.00803 | 0.04165 | Cytochrome b-c1 complex, subunit 8 protein; CONTAINS InterPro DOMAIN/s: Cytochrome b-c1 complex, subunit 8 (InterPro:IPR020101); BEST Arabidopsis thaliana protein match is: Cytochrome b-c1 complex, subunit 8 protein (TAIR:AT3G10860.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). |
AT5G52700 | Q9LTE7 | 35.1 | not assigned.no ontology | Inf | Inf | 0.00113 | 0.00856 | Copper transport protein family; BEST Arabidopsis thaliana protein match is: Copper transport protein family (TAIR:AT5G52720.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). |
AT1G35537 | Q2V4I8 | 20.1.7.12 | stress.biotic.PR-proteins.plant defensins | Inf | Inf | 0 | 0.00009 | CINV1 / A/N-InvG is an alkaline/neutral invertase that breaks sucrose down into fructose and glucose (GH100). The exact localization of CINV1 remains under investigation but there is evidence that fluorescently-tagged CINV1 localizes to the cytoplasm. atinvg mutants have reduced root growth, reduced invertase activity, and increased expression of antioxidant genes under basal conditions. The levels of CINV1 / A/N-InvG transcripts rise in response to a hydrogen peroxide treatment. The protein has been shown to interact with PIP5K9. |
AT5G37140 | F4K5W4 | 28.1 | DNA.synthesis/chromatin structure | Inf | Inf | 0.0126 | 0.05926 | Chaperone DnaJ-domain superfamily protein; FUNCTIONS IN: unfolded protein binding, heat shock protein binding; INVOLVED IN: protein folding; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: Molecular chaperone, heat shock protein, Hsp40, DnaJ (InterPro:IPR015609), Heat shock protein DnaJ, N-terminal (InterPro:IPR001623), Heat shock protein DnaJ (InterPro:IPR003095); BEST Arabidopsis thaliana protein match is: Chaperone DnaJ-domain superfamily protein (TAIR:AT5G37750.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). |
CT101:
AGI Gene code | Uniprot ID | Bin Code | Bin Name | FoldChange | log2FC | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|---|---|
AT2G20150 | #N/A | 35.2 | not assigned.unknown | Inf | Inf | 0.0002 | 0.0008 | DENN (AEX-3) domain-containing protein; CONTAINS InterPro DOMAIN/s: uDENN (InterPro:IPR005113), dDENN (InterPro:IPR005112), DENN (InterPro:IPR001194); BEST Arabidopsis thaliana protein match is: DENN (AEX-3) domain-containing protein (TAIR:AT5G35560.1); Has 1567 Blast hits to 1546 proteins in 147 species: Archae - 0; Bacteria - 2; Metazoa - 1072; Fungi - 78; Plants - 117; Viruses - 0; Other Eukaryotes - 298 (source: NCBI BLink). |
AT2G07678 | Q27GM2 | 35.2 | not assigned.unknown | Inf | Inf | 0.0282 | 0.0689 | Cytochrome c oxidase, subunit III; FUNCTIONS IN: cytochrome-c oxidase activity; INVOLVED IN: mitochondrial electron transport, cytochrome c to oxygen; LOCATED IN: membrane; CONTAINS InterPro DOMAIN/s: Cytochrome c oxidase, subunit III (InterPro:IPR000298); BEST Arabidopsis thaliana protein match is: cytochrome c oxidase subunit 3 (TAIR:ATMG00730.1); Has 29038 Blast hits to 29025 proteins in 5946 species: Archae - 74; Bacteria - 4466; Metazoa - 19232; Fungi - 401; Plants - 673; Viruses - 0; Other Eukaryotes - 4192 (source: NCBI BLink). |
AT5G64540 | Q5BPE9 | 35.2 | not assigned.unknown | Inf | Inf | 0.0091 | 0.0257 | CYS, MET, PRO, and GLY protein 2 (CMPG2); FUNCTIONS IN: ubiquitin-protein ligase activity, binding; INVOLVED IN: response to chitin; LOCATED IN: ubiquitin ligase complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: U box domain (InterPro:IPR003613), Armadillo-like helical (InterPro:IPR011989), Armadillo-type fold (InterPro:IPR016024); BEST Arabidopsis thaliana protein match is: ARM repeat superfamily protein (TAIR:AT5G09800.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). |
AT5G52700 | Q9LTE7 | 35.1 | not assigned.no ontology | Inf | Inf | 0.0002 | 0.001 | Copper transport protein family; BEST Arabidopsis thaliana protein match is: Copper transport protein family (TAIR:AT5G52720.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink). |
AT5G52670 | Q9LTF0 | 35.1 | not assigned.no ontology | Inf | Inf | 0.0004 | 0.0016 | Copper transport protein family; BEST Arabidopsis thaliana protein match is: Copper transport protein family (TAIR:AT5G52670.1); Has 113 Blast hits to 106 proteins in 12 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 113; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
AT3G46340 | Q9SNA3 | 30.2.99 | signalling.receptor kinases.misc | Inf | Inf | 0 | 0.0002 | Confers resistance to the biotrophic oomycete, Peronospora parasitica. Encodes an NBS-LRR type R protein with a putative amino-terminal leucine zipper. Fungal protein ATR13 induces RPP13 gene expression and disease resistance. |
AT2G43580 | O24598 | 20.1 | stress.biotic | Inf | Inf | 0 | 0 | Chitinase family protein; FUNCTIONS IN: chitin binding, chitinase activity; INVOLVED IN: carbohydrate metabolic process, cell wall macromolecule catabolic process; LOCATED IN: endomembrane system; EXPRESSED IN: 7 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, C globular stage, LP.02 two leaves visible; CONTAINS InterPro DOMAIN/s: Chitin-binding, type 1, conserved site (InterPro:IPR018371), Glycoside hydrolase, family 19 (InterPro:IPR016283), Chitin-binding, type 1 (InterPro:IPR001002), Glycoside hydrolase, family 19, catalytic (InterPro:IPR000726); BEST Arabidopsis thaliana protein match is: Chitinase family protein (TAIR:AT2G43580.1); Has 2744 Blast hits to 2502 proteins in 524 species: Archae - 0; Bacteria - 615; Metazoa - 34; Fungi - 202; Plants - 1760; Viruses - 20; Other Eukaryotes - 113 (source: NCBI BLink). |
AT5G03000 | Q9LYY5 | 29.5.11.4.3.2 | protein.degradation.ubiquitin.E3.SCF.FBOX | Inf | Inf | 0.0012 | 0.0043 | Chaperone DnaJ-domain superfamily protein; FUNCTIONS IN: heat shock protein binding; INVOLVED IN: protein folding; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Heat shock protein DnaJ, N-terminal (InterPro:IPR001623); BEST Arabidopsis thaliana protein match is: Chaperone DnaJ-domain superfamily protein (TAIR:AT2G35795.1); Has 904 Blast hits to 904 proteins in 304 species: Archae - 0; Bacteria - 188; Metazoa - 208; Fungi - 196; Plants - 87; Viruses - 5; Other Eukaryotes - 220 (source: NCBI BLink). |
AT1G76640 | Q9SRE7 | 30.3 | signalling.calcium | Inf | Inf | 0.0002 | 0.0007 | calmodulin-like 38 (CML38); FUNCTIONS IN: calcium ion binding; INVOLVED IN: response to wounding; LOCATED IN: plasma membrane; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: EF-Hand 1, calcium-binding site (InterPro:IPR018247), EF-HAND 2 (InterPro:IPR018249), Calcium-binding EF-hand (InterPro:IPR002048), EF-hand-like domain (InterPro:IPR011992); BEST Arabidopsis thaliana protein match is: Calcium-binding EF-hand family protein (TAIR:AT1G76640.1); Has 14301 Blast hits to 11244 proteins in 1181 species: Archae - 0; Bacteria - 48; Metazoa - 5820; Fungi - 2427; Plants - 3932; Viruses - 0; Other Eukaryotes - 2074 (source: NCBI BLink). |
AT3G51410 | Q6NMZ5 | 35.2 | not assigned.unknown | Inf | Inf | 0.0136 | 0.0363 | Calcium-dependent phosphotriesterase superfamily protein; FUNCTIONS IN: strictosidine synthase activity; INVOLVED IN: alkaloid biosynthetic process, biosynthetic process; LOCATED IN: endoplasmic reticulum; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 10 growth stages; CONTAINS InterPro DOMAIN/s: Strictosidine synthase, conserved region (InterPro:IPR018119), Strictosidine synthase (InterPro:IPR004141), Six-bladed beta-propeller, TolB-like (InterPro:IPR011042); BEST Arabidopsis thaliana protein match is: Calcium-dependent phosphotriesterase superfamily protein (TAIR:AT3G51430.1); Has 1624 Blast hits to 1611 proteins in 398 species: Archae - 36; Bacteria - 672; Metazoa - 222; Fungi - 24; Plants - 455; Viruses - 0; Other Eukaryotes - 215 (source: NCBI BLink). |
AT1G42980 | Q9C7S1 | 35.1.20 | not assigned.no ontology.formin homology 2 domain-containing protein | Inf | Inf | 0 | 0 | bZIP60 consists of a bZIP DNA binding domain followed by a putative transmembrane domain. bZIP60 mRNA is upregulated by the addition of ER stress inducers, tunicamycin (inhibitor of N-linked glycosylation), DTT (inhibitor of disulfide bond formation) and azetin-2-carboxylate (proline analog perturbing protein structure). Upon ER stress, bZIP60 mRNA is spliced by IRE1A and IRE1B to produce bZIP60-S, an active transcription factor without the transmembrane domain. bZIP60-U, a product of unspliced form of bZIP60 mRNA, is localized at the ER membrane and bZIP60-S is localized in the nucleus. |
AT2G10780 | Q9SK57 | 28.1 | DNA.synthesis/chromatin structure | Inf | Inf | 0 | 0 | BSD domain-containing protein; CONTAINS InterPro DOMAIN/s: BSD (InterPro:IPR005607); BEST Arabidopsis thaliana protein match is: BSD domain-containing protein (TAIR:AT3G49800.1); Has 187 Blast hits to 175 proteins in 30 species: Archae - 0; Bacteria - 2; Metazoa - 28; Fungi - 3; Plants - 134; Viruses - 0; Other Eukaryotes - 20 (source: NCBI BLink). |
Te:
AGI Gene code | Uniprot ID | Bin Code | Bin Name | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|
AT3G46340 | Q9SNA3 | 30.2.99 | signalling.receptor kinases.misc | 0.000810427 | 0.002587644 | |
AT3G46613 | Q6IM86 | 33.99 | development.unspecified | 0.022034991 | 0.05124705 | |
AT3G46614 | #N/A | 35.2 | not assigned.unknown | 0.022991698 | 0.053143063 | |
AT3G49540 | Q9SCK5 | 35.2 | not assigned.unknown | 1.90E-50 | 1.58E-48 | |
AT3G49845 | F4IZ80 | 35.1.42 | not assigned.no ontology.proline rich family | 7.93E-09 | 5.09E-08 | |
AT3G54410 | Q9M2U6 | 35.2 | not assigned.unknown | 0.037798986 | 0.082370263 | |
AT3G57270 | Q9M2M0 | 26.4.1 | misc.beta 1,3 glucan hydrolases.glucan endo-1,3-beta-glucosidase | 2.56E-06 | 1.22E-05 | |
AT4G01535 | F4JI37 | 35.2 | not assigned.unknown | 0.000209482 | 0.000744883 | |
AT4G03840 | O81508 | 28.1 | DNA.synthesis/chromatin structure | 0.005605548 | 0.015087847 | |
AT4G03950 | O81514 | 34.8 | transport.metabolite transporters at the envelope membrane | 2.32E-14 | 2.48E-13 | |
AT4G05018 | B3H479 | 35.2 | not assigned.unknown | 1.23E-07 | 6.89E-07 | |
AT4G08095 | #N/A | 28.1.1.1 | DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon | 0.00376188 | 0.010511035 |
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