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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 |
|---|---|---|---|---|---|---|---|---|
AT5G46950 | Q9FJR6 | 26.18 | misc.invertase/pectin methylesterase inhibitor family protein | 21.76179 | 4.44373 | 0 | 0.00006 | SBP (S-ribonuclease binding protein) family protein; FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type (InterPro:IPR001841), S-ribonuclease binding protein, SBP1, pollen (InterPro:IPR017066); BEST Arabidopsis thaliana protein match is: SBP (S-ribonuclease binding protein) family protein (TAIR:AT4G17680.1); 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). |
AT4G08780 | Q9LDA4 | 26.12 | misc.peroxidases | 21.81249 | 4.44708 | 0.00004 | 0.00057 | transposable element gene; copia-like retrotransposon family, has a 1.2e-236 P-value blast match to GB:AAA57005 Hopscotch polyprotein (Ty1_Copia-element) (Zea mays) |
AT1G36600 | #N/A | 28.1.1.3 | DNA.synthesis/chromatin structure.retrotransposon/transposase.copia-like retrotransposon | 22.20097 | 4.47255 | 0 | 0 | transposable element gene; copia-like retrotransposon family, has a 2.0e-12 P-value blast match to gb|AAG52949.1| gag/pol polyprotein (Endovir1-1) (Arabidopsis thaliana) (Ty1_Copia-family) |
AT2G47140 | Q94K41 | 26.22 | misc.short chain dehydrogenase/reductase (SDR) | 22.26575 | 4.47675 | 0 | 0.00001 | Gene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins. Members of this family are known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct. |
AT2G29470 | Q9ZW28 | 26.9 | misc.glutathione S transferases | 22.43621 | 4.48776 | 0.00003 | 0.00044 | Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002). |
AT5G25450 | F4JWS8 | 9.5 | mitochondrial electron transport / ATP synthesis.cytochrome c reductase | 22.56399 | 4.49595 | 0 | 0 | CHY-type/CTCHY-type/RING-type Zinc finger protein; FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, CTCHY-type (InterPro:IPR017921), Zinc finger, CHY-type (InterPro:IPR008913), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, C3HC4 RING-type (InterPro:IPR018957); BEST Arabidopsis thaliana protein match is: CHY-type/CTCHY-type/RING-type Zinc finger protein (TAIR:AT5G22920.1); Has 943 Blast hits to 942 proteins in 169 species: Archae - 2; Bacteria - 0; Metazoa - 357; Fungi - 128; Plants - 310; Viruses - 0; Other Eukaryotes - 146 (source: NCBI BLink). |
AT1G42367 | #N/A | 35.2 | not assigned.unknown | 22.57183 | 4.49645 | 0.0013 | 0.00956 | P-loop containing nucleoside triphosphate hydrolases superfamily protein; FUNCTIONS IN: motor activity, ATP binding; INVOLVED IN: biological_process unknown; LOCATED IN: myosin complex; CONTAINS InterPro DOMAIN/s: Myosin head, motor domain (InterPro:IPR001609); BEST Arabidopsis thaliana protein match is: P-loop containing nucleoside triphosphate hydrolases superfamily protein (TAIR:AT1G50360.1); Has 5017 Blast hits to 5013 proteins in 547 species: Archae - 0; Bacteria - 0; Metazoa - 3327; Fungi - 529; Plants - 444; Viruses - 0; Other Eukaryotes - 717 (source: NCBI BLink). |
AT1G18290 | Q9LE02 | 35.2 | not assigned.unknown | 22.63017 | 4.50018 | 0.00721 | 0.03824 | unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: N-terminal protein myristoylation; LOCATED IN: chloroplast; EXPRESSED IN: root; Has 94 Blast hits to 94 proteins in 12 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 94; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
AT1G49000 | Q9M9A2 | 35.2 | not assigned.unknown | 22.76146 | 4.50852 | 0 | 0 | Encodes soluble protein containing N-terminal DENN domain and eight C-terminal WD-40 repeats. Involved in cytokinesis of guard mother cells and leaf epidermal cells. The overall growth and development of mutant plants is severely affected, they are smaller than wt, with defects in seedling development, leaf expansion and flower morphology which renders the mutant conditionally sterile. |
AT1G10040 | Q08A69 | 35.2 | not assigned.unknown | 22.81827 | 4.51212 | 0.00006 | 0.0008 | alpha/beta-Hydrolases superfamily protein; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF676, hydrolase-like (InterPro:IPR007751); BEST Arabidopsis thaliana protein match is: alpha/beta-Hydrolases superfamily protein (TAIR:AT4G25770.1); Has 823 Blast hits to 815 proteins in 221 species: Archae - 0; Bacteria - 56; Metazoa - 168; Fungi - 260; Plants - 184; Viruses - 0; Other Eukaryotes - 155 (source: NCBI BLink). |
AT4G14450 | Q6NN02 | 35.2 | not assigned.unknown | 22.91045 | 4.51793 | 0 | 0.00009 | CONTAINS InterPro DOMAIN/s: EGF-like (InterPro:IPR006210); Has 259 Blast hits to 234 proteins in 55 species: Archae - 0; Bacteria - 0; Metazoa - 184; Fungi - 0; Plants - 69; Viruses - 0; Other Eukaryotes - 6 (source: NCBI BLink). |
AT1G28190 | Q9FZ93 | 35.2 | not assigned.unknown | 23.10878 | 4.53037 | 0 | 0.00001 | DnaJ homolog AtJ1 (atj) |
CT101:
AGI Gene code | Uniprot ID | Bin Code | Bin Name | FoldChange | log2FC | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|---|---|
AT5G54165 | Q570N6 | 35.2 | not assigned.unknown | 127.5006 | 6.9944 | 0 | 0 | Protein of unknown function (DUF1223); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1223 (InterPro:IPR010634); BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF1223) (TAIR:AT4G27350.1); 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). |
AT5G36925 | Q8GWS2 | 35.2 | not assigned.unknown | 129.2733 | 7.0143 | 0 | 0 | P-loop containing nucleoside triphosphate hydrolases superfamily protein; FUNCTIONS IN: helicase activity; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: Helicase domain, viral-like (InterPro:IPR000606); BEST Arabidopsis thaliana protein match is: P-loop containing nucleoside triphosphate hydrolases superfamily protein (TAIR:AT5G37150.1); 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). |
AT1G51890 | C0LGG6 | 30.2.99 | signalling.receptor kinases.misc | 129.479 | 7.0166 | 0 | 0 | Regulator of Vps4 activity in the MVB pathway protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: mitochondrion; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF292, eukaryotic (InterPro:IPR005061); BEST Arabidopsis thaliana protein match is: Regulator of Vps4 activity in the MVB pathway protein (TAIR:AT2G14830.1); Has 11301 Blast hits to 8001 proteins in 660 species: Archae - 97; Bacteria - 956; Metazoa - 3829; Fungi - 697; Plants - 524; Viruses - 57; Other Eukaryotes - 5141 (source: NCBI BLink). |
AT1G30370 | Q9C8G6 | 11.9.2.1 | lipid metabolism.lipid degradation.lipases.triacylglycerol lipase | 131.8474 | 7.0427 | 0.0004 | 0.0015 | member of MRP subfamily |
AT1G66090 | Q9C515 | 20.1.7 | stress.biotic.PR-proteins | 132.0807 | 7.0453 | 0 | 0 | Family of unknown function (DUF577); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF577 (InterPro:IPR007598); BEST Arabidopsis thaliana protein match is: Family of unknown function (DUF577) (TAIR:AT5G37410.1); Has 76 Blast hits to 50 proteins in 3 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 76; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
AT1G01480 | Q06402 | 17.5.1.1 | hormone metabolism.ethylene.synthesis-degradation.1-aminocyclopropane-1-carboxylate synthase | 133.562 | 7.0614 | 0 | 0 | a member of the 1-aminocyclopropane-1-carboxylate (ACC) synthase (S-adenosyl-L-methionine methylthioadenosine-lyase, EC 4.4.1.14) gene family, isolated from a flower-specific cDNA library. |
AT2G39518 | Q56X75 | 35.1 | not assigned.no ontology | 136.304 | 7.0907 | 0 | 0 | Uncharacterised protein family (UPF0497); CONTAINS InterPro DOMAIN/s: Uncharacterised protein family UPF0497, trans-membrane plant (InterPro:IPR006702), Uncharacterised protein family UPF0497, trans-membrane plant subgroup (InterPro:IPR006459); BEST Arabidopsis thaliana protein match is: Uncharacterised protein family (UPF0497) (TAIR:AT2G39518.1); Has 200 Blast hits to 200 proteins in 15 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 200; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink). |
AT1G56250 | Q9C7K0 | 31.1 | cell.organisation | 139.6502 | 7.1257 | 0.0005 | 0.0018 | Encodes one of three Arabidopsis calreticulins. In CRT-deficient mouse fibroblasts, this protein restores ER Ca2+ levels. |
AT4G20490 | Q9SUN0 | 28.1.1.1 | DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon | 139.9341 | 7.1286 | 0 | 0 | Calcium sensor involved in trichome branching. |
AT1G02400 | Q9FZ21 | 17.6.1.13 | hormone metabolism.gibberelin.synthesis-degradation.GA2 oxidase | 140.7059 | 7.1365 | 0 | 0 | Encodes a gibberellin 2-oxidase that acts on C19 gibberellins but not C20 gibberellins. |
AT1G13340 | #N/A | 35.2 | not assigned.unknown | 140.7651 | 7.1371 | 0 | 0 | Regulator of Vps4 activity in the MVB pathway protein; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF292, eukaryotic (InterPro:IPR005061); BEST Arabidopsis thaliana protein match is: Regulator of Vps4 activity in the MVB pathway protein (TAIR:AT1G34220.2); Has 628 Blast hits to 628 proteins in 152 species: Archae - 0; Bacteria - 0; Metazoa - 164; Fungi - 130; Plants - 284; Viruses - 0; Other Eukaryotes - 50 (source: NCBI BLink). |
AT4G08780 | Q9LDA4 | 26.12 | misc.peroxidases | 142.0782 | 7.1505 | 0 | 0 | Leucine-rich repeat receptor-like protein kinase family protein; FUNCTIONS IN: kinase activity; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasma membrane, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site (InterPro:IPR017441), Serine/threonine-protein kinase domain (InterPro:IPR002290), 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), Protein kinase, catalytic domain (InterPro:IPR000719), Leucine-rich repeat, typical subtype (InterPro:IPR003591), Tyrosine-protein kinase, active site (InterPro:IPR008266), Tyrosine-protein kinase, catalytic domain (InterPro:IPR020635); BEST Arabidopsis thaliana protein match is: Protein kinase family protein with leucine-rich repeat domain (TAIR:AT1G35710.1); 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). |
Te:
AGI Gene code | Uniprot ID | Bin Code | Bin Name | p-value | FDR adjusted p-value | Functional annotation |
|---|---|---|---|---|---|---|
AT3G49630 | F4IY03 | 17.5.1 | hormone metabolism.ethylene.synthesis-degradation | 8.71E-09 | 5.56E-08 | |
AT1G26380 | Q9FZC4 | 26.8 | misc.nitrilases, *nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases | 2.38E-89 | 6.79E-87 | unknown protein; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF775 (InterPro:IPR008493); Has 285 Blast hits to 283 proteins in 133 species: Archae - 0; Bacteria - 0; Metazoa - 120; Fungi - 88; Plants - 50; Viruses - 0; Other Eukaryotes - 27 (source: NCBI BLink). |
AT1G33030 | A0A1P8AUE2 | 16.1 | secondary metabolism.simple phenols | 1.97E-146 | 3.50E-143 | VQ motif-containing protein; LOCATED IN: chloroplast; EXPRESSED IN: 17 plant structures; EXPRESSED DURING: 10 growth stages; CONTAINS InterPro DOMAIN/s: VQ (InterPro:IPR008889); BEST Arabidopsis thaliana protein match is: VQ motif-containing protein (TAIR:AT2G35230.1); Has 2188 Blast hits to 1760 proteins in 229 species: Archae - 0; Bacteria - 55; Metazoa - 822; Fungi - 398; Plants - 644; Viruses - 80; Other Eukaryotes - 189 (source: NCBI BLink). |
AT3G23550 | Q9LUH3 | 34.99 | transport.misc | 1.75E-252 | 2.17E-248 | |
AT1G66600 | Q9C6H5 | 27.3.32 | RNA.regulation of transcription.WRKY domain transcription factor family | 1.65E-29 | 4.94E-28 | Transmembrane amino acid transporter family protein; CONTAINS InterPro DOMAIN/s: Amino acid transporter, transmembrane (InterPro:IPR013057); BEST Arabidopsis thaliana protein match is: Transmembrane amino acid transporter family protein (TAIR:AT1G61270.1); Has 4381 Blast hits to 4371 proteins in 390 species: Archae - 5; Bacteria - 296; Metazoa - 1264; Fungi - 731; Plants - 1536; Viruses - 3; Other Eukaryotes - 546 (source: NCBI BLink). |
AT3G49620 | Q8H113 | 33.99 | development.unspecified | 1.24E-16 | 1.61E-15 | |
AT1G53625 | Q9LPH9 | 35.2 | not assigned.unknown | 1.89E-53 | 1.85E-51 | RING/U-box superfamily protein; FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, C3HC4 RING-type (InterPro:IPR018957); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT1G19310.1); Has 3846 Blast hits to 3838 proteins in 274 species: Archae - 0; Bacteria - 0; Metazoa - 2175; Fungi - 493; Plants - 714; Viruses - 21; Other Eukaryotes - 443 (source: NCBI BLink). |
AT3G11340 | Q9C768 | 26.2 | misc.UDP glucosyl and glucoronyl transferases | 3.29E-26 | 8.22E-25 | Leucine-rich repeat protein kinase family protein; FUNCTIONS IN: kinase activity; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasma membrane, vacuole; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 13 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: Leucine-rich repeat protein kinase family protein (TAIR:AT5G49770.1); Has 176974 Blast hits to 136078 proteins in 4850 species: Archae - 147; Bacteria - 18062; Metazoa - 52743; Fungi - 11116; Plants - 72814; Viruses - 462; Other Eukaryotes - 21630 (source: NCBI BLink). |
AT2G14290 | Q9ZQ60 | 29.5.11.4.3.2 | protein.degradation.ubiquitin.E3.SCF.FBOX | 1.71E-18 | 2.56E-17 | DEA(D/H)-box RNA helicase family protein; FUNCTIONS IN: helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding; LOCATED IN: nucleolus, peroxisome, plasma membrane; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: RNA helicase, DEAD-box type, Q motif (InterPro:IPR014014), DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: P-loop containing nucleoside triphosphate hydrolases superfamily protein (TAIR:AT2G42520.1); Has 89639 Blast hits to 57959 proteins in 3433 species: Archae - 859; Bacteria - 32130; Metazoa - 25406; Fungi - 6817; Plants - 10992; Viruses - 755; Other Eukaryotes - 12680 (source: NCBI BLink). |
AT3G54150 | A0A1I9LLF7 | 33.99 | development.unspecified | 2.41E-31 | 7.93E-30 | |
AT3G02840 | #N/A | 20.1 | stress.biotic | 2.46E-26 | 6.22E-25 | Major facilitator superfamily protein; CONTAINS InterPro DOMAIN/s: Major facilitator superfamily, general substrate transporter (InterPro:IPR016196), Biopterin transport-related protein BT1 (InterPro:IPR004324); BEST Arabidopsis thaliana protein match is: Major facilitator superfamily protein (TAIR:AT5G25040.2); 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). |
AT5G56960 | Q9LTS4 | 27.3.6 | RNA.regulation of transcription.bHLH,Basic Helix-Loop-Helix family | 9.35E-31 | 2.97E-29 |
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