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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 |
|---|---|---|---|---|---|---|---|---|
AT1G61800 | Q94B38 | 34.8 | transport.metabolite transporters at the envelope membrane | 21.08945 | 4.39845 | 0.00006 | 0.00084 | beta-glucosidase 45 (BGLU45); FUNCTIONS IN: cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity; INVOLVED IN: lignin biosynthetic process; LOCATED IN: endomembrane system; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: Glycoside hydrolase, family 1 (InterPro:IPR001360), Glycoside hydrolase, family 1, active site (InterPro:IPR018120), Glycoside hydrolase, catalytic core (InterPro:IPR017853), Glycoside hydrolase, subgroup, catalytic core (InterPro:IPR013781); BEST Arabidopsis thaliana protein match is: beta glucosidase 46 (TAIR:AT1G61820.1). |
AT3G15356 | Q9LJR2 | 26.16 | misc.myrosinases-lectin-jacalin | 21.19126 | 4.4054 | 0 | 0.00001 | Encodes an ATAF-like NAC-domain transcription factor that doesn't contain C-terminal sequences shared by CUC1, CUC2 and NAM. Note: this protein (AtNAC3) is not to be confused with the protein encoded by locus AT3G29035, which, on occasion, has also been referred to as AtNAC3. |
AT1G21110 | Q9LPU6 | 26.6 | misc.O-methyl transferases | 21.24669 | 4.40917 | 0 | 0 | O-methyltransferase family protein; FUNCTIONS IN: methyltransferase activity, O-methyltransferase activity, protein dimerization activity; LOCATED IN: cytosol; CONTAINS InterPro DOMAIN/s: Winged helix-turn-helix transcription repressor DNA-binding (InterPro:IPR011991), Plant methyltransferase dimerisation (InterPro:IPR012967), O-methyltransferase, family 2 (InterPro:IPR001077), O-methyltransferase, COMT, eukaryota (InterPro:IPR016461); BEST Arabidopsis thaliana protein match is: O-methyltransferase family protein (TAIR:AT1G21120.1); Has 3289 Blast hits to 3284 proteins in 565 species: Archae - 1; Bacteria - 890; Metazoa - 104; Fungi - 640; Plants - 1549; Viruses - 0; Other Eukaryotes - 105 (source: NCBI BLink). |
AT5G47850 | Q9FIJ6 | 30.2.26 | signalling.receptor kinases.crinkly like | 21.2989 | 4.41271 | 0 | 0 | NADPH/respiratory burst oxidase protein D (RbohD).Interacts with AtrbohF gene to fine tune the spatial control of ROI production and hypersensitive response to cell in and around infection site. |
AT2G26390 | O48706 | 29.5.5 | protein.degradation.serine protease | 21.3296 | 4.41478 | 0.00002 | 0.00031 | Plant invertase/pectin methylesterase inhibitor superfamily; FUNCTIONS IN: enzyme inhibitor activity, pectinesterase activity; INVOLVED IN: cell wall modification; LOCATED IN: endomembrane system, cell wall, plant-type cell wall; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Pectinesterase, active site (InterPro:IPR018040), Pectin lyase fold/virulence factor (InterPro:IPR011050), Pectinesterase, catalytic (InterPro:IPR000070), Pectinesterase inhibitor (InterPro:IPR006501), Pectin lyase fold (InterPro:IPR012334); BEST Arabidopsis thaliana protein match is: Plant invertase/pectin methylesterase inhibitor superfamily (TAIR:AT4G02330.1); Has 2898 Blast hits to 2847 proteins in 362 species: Archae - 6; Bacteria - 671; Metazoa - 1; Fungi - 192; Plants - 2003; Viruses - 0; Other Eukaryotes - 25 (source: NCBI BLink). |
AT1G14870 | Q9LQU4 | 35.1 | not assigned.no ontology | 21.35287 | 4.41636 | 0 | 0.00005 | PCR2 encodes a membrane protein involved in zinc transport and detoxification. |
AT1G21326 | Q9LMP5 | 35.1 | not assigned.no ontology | 21.40226 | 4.41969 | 0 | 0 | VQ motif-containing protein; CONTAINS InterPro DOMAIN/s: VQ (InterPro:IPR008889); BEST Arabidopsis thaliana protein match is: nucleotide binding;nucleic acid binding (TAIR:AT1G21320.1); Has 294 Blast hits to 294 proteins in 63 species: Archae - 0; Bacteria - 0; Metazoa - 108; Fungi - 21; Plants - 144; Viruses - 0; Other Eukaryotes - 21 (source: NCBI BLink). |
AT5G27420 | Q8LGA5 | 29.5.11.4.2 | protein.degradation.ubiquitin.E3.RING | 21.40864 | 4.42012 | 0 | 0 | encodes a peroxisomal adenine nucleotide transporter, involved in fatty acid beta-oxidation during early stage of postgerminative growth. |
AT3G04220 | A0A1I9LNB0 | 20.1.7 | stress.biotic.PR-proteins | 21.43163 | 4.42167 | 0 | 0 | Ribosomal protein S5 domain 2-like superfamily protein; FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic small ribosomal subunit, cytosolic ribosome, nucleolus, chloroplast, membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein S9 (InterPro:IPR000754), Ribosomal protein S5 domain 2-type fold (InterPro:IPR020568), Ribosomal protein S5 domain 2-type fold, subgroup (InterPro:IPR014721); BEST Arabidopsis thaliana protein match is: Ribosomal protein S5 domain 2-like superfamily protein (TAIR:AT5G18380.1); Has 6825 Blast hits to 6825 proteins in 2403 species: Archae - 233; Bacteria - 4309; Metazoa - 365; Fungi - 183; Plants - 150; Viruses - 0; Other Eukaryotes - 1585 (source: NCBI BLink). |
AT5G25910 | Q7FZR1 | 20.1.7 | stress.biotic.PR-proteins | 21.49341 | 4.42582 | 0 | 0 | Protein kinase family protein with leucine-rich repeat domain; FUNCTIONS IN: kinase activity; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasma membrane, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site (InterPro:IPR017441), Protein kinase, catalytic domain (InterPro:IPR000719), Leucine-rich repeat-containing N-terminal domain, type 2 (InterPro:IPR013210), Leucine-rich repeat (InterPro:IPR001611), Serine/threonine-protein kinase-like domain (InterPro:IPR017442), Protein kinase-like domain (InterPro:IPR011009), Serine/threonine-protein kinase, active site (InterPro:IPR008271); BEST Arabidopsis thaliana protein match is: receptor like protein 52 (TAIR:AT5G25910.1); 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). |
AT1G62300 | Q9C519 | 27.3.32 | RNA.regulation of transcription.WRKY domain transcription factor family | 21.52488 | 4.42793 | 0 | 0.00009 | Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein; CONTAINS InterPro DOMAIN/s: Core-2/I-Branching enzyme (InterPro:IPR021141); BEST Arabidopsis thaliana protein match is: Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein (TAIR:AT1G11940.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink). |
AT4G21840 | O49707 | 29.4 | protein.postranslational modification | 21.59656 | 4.43273 | 0.00001 | 0.00023 | unknown protein; Has 11 Blast hits to 11 proteins in 4 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 11; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
CT101:
AGI Gene code | Uniprot ID | Bin Code | Bin Name | FoldChange | log2FC | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|---|---|
AT3G28210 | Q67YE6 | 27.3.11 | RNA.regulation of transcription.C2H2 zinc finger family | 311.0798 | 8.2811 | 0 | 0 | Protein of unknown function (DUF677); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF677 (InterPro:IPR007749); BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF677) (TAIR:AT3G28290.1); Has 57 Blast hits to 57 proteins in 3 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 57; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
AT1G17170 | Q9SHH6 | 26.9 | misc.glutathione S transferases | 312.5839 | 8.2881 | 0 | 0 | Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002). |
AT2G35980 | Q9SJ52 | 33.99 | development.unspecified | 330.7659 | 8.3697 | 0 | 0 | Encodes a plant-specific B3 DNA-binding domain transcription factor. Has transcription repressor activity. |
AT1G70170 | O04529 | 29.5.7 | protein.degradation.metalloprotease | 330.8343 | 8.37 | 0 | 0 | encodes an adenosine transporter that catalyze a proton-dependent adenosine transport. |
AT3G44830 | Q9FYC7 | 11.8.10 | lipid metabolism.'exotics' (steroids, squalene etc).phosphatidylcholinesterol O-acyltransferase | 341.5532 | 8.416 | 0 | 0 | Encodes a farnesoic acid carboxyl-O-methyltransferase. |
AT5G01380 | Q9SDW0 | 27.3.30 | RNA.regulation of transcription.Trihelix, Triple-Helix transcription factor family | 348.0578 | 8.4432 | 0 | 0 | Got1/Sft2-like vescicle transport protein family; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: vesicle-mediated transport; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: Vesicle transport protein, Got1/SFT2-like (InterPro:IPR007305); BEST Arabidopsis thaliana protein match is: Got1/Sft2-like vescicle transport protein family (TAIR:AT3G49420.1); 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). |
AT1G76470 | F4I2E5 | 16.2 | secondary metabolism.phenylpropanoids | 352.4067 | 8.4611 | 0 | 0 | unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G20890.1). |
AT2G45760 | Q58FX0 | 35.1 | not assigned.no ontology | 364.1134 | 8.5082 | 0 | 0 | U-box domain-containing protein kinase family protein; FUNCTIONS IN: ubiquitin-protein ligase activity, protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding; INVOLVED IN: protein amino acid phosphorylation, response to stress, protein ubiquitination; LOCATED IN: ubiquitin ligase complex; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: UspA (InterPro:IPR006016), Protein kinase, ATP binding site (InterPro:IPR017441), Protein kinase, catalytic domain (InterPro:IPR000719), U box domain (InterPro:IPR003613), Serine/threonine-protein kinase-like domain (InterPro:IPR017442), Protein kinase-like domain (InterPro:IPR011009), Serine/threonine-protein kinase, active site (InterPro:IPR008271); BEST Arabidopsis thaliana protein match is: U-box domain-containing protein kinase family protein (TAIR:AT3G49060.1); Has 126911 Blast hits to 124541 proteins in 4743 species: Archae - 223; Bacteria - 14733; Metazoa - 47002; Fungi - 10910; Plants - 34737; Viruses - 429; Other Eukaryotes - 18877 (source: NCBI BLink). |
AT4G30280 | Q9M0D2 | 10.7 | cell wall.modification | 385.6201 | 8.591 | 0 | 0.0002 | encodes a diacylglycerol kinase. Applying a specific diacylglycerol kinase inhibitor to the growth media resulted in reduced root elongation and plant growth. Gene is expressed throughout the plant but is strongest in flowers and young seedlings. |
AT1G80820 | Q9SAH9 | 16.2.1.7 | secondary metabolism.phenylpropanoids.lignin biosynthesis.CCR1 | 125.6188 | 6.9729 | 0 | 0 | Thought to be involved in iron homeostasis. Induced in leaves in response to iron deficiency. Transgenic plants accumulate toxic levels of iron. Gene complements yeast iron uptake mutants. |
AT4G18430 | O49513 | 30.5 | signalling.G-proteins | 126.619 | 6.9844 | 0 | 0 | unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). |
AT2G29460 | Q9ZW27 | 26.9 | misc.glutathione S transferases | 126.9374 | 6.988 | 0 | 0 | Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002). |
Te:
AGI Gene code | Uniprot ID | Bin Code | Bin Name | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|
AT4G37370 | Q9SZT7 | 26.1 | misc.cytochrome P450 | 1.75E-89 | 5.06E-87 | |
AT1G70170 | O04529 | 29.5.7 | protein.degradation.metalloprotease | 4.67E-41 | 2.49E-39 | Thymidine kinase; FUNCTIONS IN: thymidine kinase activity, ATP binding; INVOLVED IN: pyrimidine deoxyribonucleoside interconversion, anaerobic respiration; LOCATED IN: cellular_component unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Thymidine kinase (InterPro:IPR001267), Thymidine kinase, conserved site (InterPro:IPR020633); BEST Arabidopsis thaliana protein match is: Thymidine kinase (TAIR:AT5G23070.1); Has 4049 Blast hits to 4037 proteins in 1500 species: Archae - 38; Bacteria - 2547; Metazoa - 142; Fungi - 7; Plants - 74; Viruses - 356; Other Eukaryotes - 885 (source: NCBI BLink). |
AT3G23250 | Q9LTC4 | 27.3.25 | RNA.regulation of transcription.MYB domain transcription factor family | 8.58E-15 | 9.57E-14 | |
AT1G13520 | Q6NNH1 | 35.2 | not assigned.unknown | 7.48E-14 | 7.63E-13 | Function unknown. Interacts with eIF3. |
AT5G42380 | Q9FIH9 | 30.3 | signalling.calcium | 2.96E-33 | 1.08E-31 | |
AT1G79680 | Q8VYA3 | 30.2.25 | signalling.receptor kinases.wall associated kinase | 1.92E-25 | 4.57E-24 | FAD/NAD(P)-binding oxidoreductase family protein; FUNCTIONS IN: electron carrier activity, oxidoreductase activity, FAD binding; INVOLVED IN: oxidation reduction; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Pyridine nucleotide-disulphide oxidoreductase, class-II (InterPro:IPR000103), FAD-dependent pyridine nucleotide-disulphide oxidoreductase (InterPro:IPR013027), Pyridine nucleotide-disulphide oxidoreductase, NAD-binding region (InterPro:IPR001327); BEST Arabidopsis thaliana protein match is: FAD/NAD(P)-binding oxidoreductase family protein (TAIR:AT5G22140.1); Has 14374 Blast hits to 14371 proteins in 2395 species: Archae - 444; Bacteria - 11667; Metazoa - 157; Fungi - 716; Plants - 246; Viruses - 0; Other Eukaryotes - 1144 (source: NCBI BLink). |
AT4G11170 | O82500 | 20.1.7 | stress.biotic.PR-proteins | 3.49E-28 | 9.64E-27 | |
AT2G34500 | O64697 | 26.1 | misc.cytochrome P450 | 2.58E-74 | 4.97E-72 | ENTH/ANTH/VHS superfamily protein; FUNCTIONS IN: phospholipid binding, clathrin binding, binding, phosphatidylinositol binding; INVOLVED IN: clathrin coat assembly; LOCATED IN: cytosol, nucleus, plasma membrane; EXPRESSED IN: guard cell, cultured cell; CONTAINS InterPro DOMAIN/s: Epsin-like, N-terminal (InterPro:IPR013809), ANTH (InterPro:IPR011417), ENTH/VHS (InterPro:IPR008942), Clathrin adaptor, phosphoinositide-binding, GAT-like (InterPro:IPR014712); BEST Arabidopsis thaliana protein match is: epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-related (TAIR:AT2G25430.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). |
AT4G39670 | Q8L7U7 | 35.2 | not assigned.unknown | 1.13E-38 | 5.35E-37 | |
AT2G44370 | O64871 | 35.1.26 | not assigned.no ontology.DC1 domain containing protein | 2.24E-16 | 2.85E-15 | unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G28190.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). |
AT1G15520 | Q9M9E1 | 34.16 | transport.ABC transporters and multidrug resistance systems | 4.82E-55 | 4.99E-53 | MATE efflux family protein; FUNCTIONS IN: antiporter activity, drug transmembrane transporter activity, transporter activity; INVOLVED IN: drug transmembrane transport, transmembrane transport; LOCATED IN: membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Multi antimicrobial extrusion protein MatE (InterPro:IPR002528); BEST Arabidopsis thaliana protein match is: MATE efflux family protein (TAIR:AT1G33100.1); Has 9952 Blast hits to 9876 proteins in 1988 species: Archae - 205; Bacteria - 7065; Metazoa - 140; Fungi - 326; Plants - 1371; Viruses - 0; Other Eukaryotes - 845 (source: NCBI BLink). |
AT2G30750 | O49340 | 26.1 | misc.cytochrome P450 | 5.01E-58 | 5.77E-56 | S-adenosyl-L-methionine-dependent methyltransferases superfamily protein; FUNCTIONS IN: methyltransferase activity; INVOLVED IN: metabolic process; LOCATED IN: endomembrane system; CONTAINS InterPro DOMAIN/s: Methyltransferase type 11 (InterPro:IPR013216); BEST Arabidopsis thaliana protein match is: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein (TAIR:AT1G24480.1); Has 388 Blast hits to 388 proteins in 66 species: Archae - 6; Bacteria - 77; Metazoa - 0; Fungi - 2; Plants - 265; Viruses - 0; Other Eukaryotes - 38 (source: NCBI BLink). |
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