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Species & Dataset
Experiment
Foliar ozone injury

  • Arabidopsis thaliana

  • Common name: Thale cress, Mouse-ear cress

  • Family: Brassicaceae

  • Cultivar: C24 (Ozone tolerant), Te (Ozone sensitive), CT101, Col-0

  • Tissue: Rosettes

  • Ozone concentration: 350 nL L-1

  • Ozone exposure: 2 hours

  • Platform: Microarray

  • Year of study: 2014

  • Location: Helsinki, Finland

Arabidopsis_injury.png

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
AT4G23030
O82752
34.16
transport.ABC transporters and multidrug resistance systems
23.15406
4.53319
0
0.00001
Arabidopsis thaliana receptor-like protein kinase. Naming convention from Chen et al 2003 (PMID 14756307)
AT4G37290
F4JRC5
35.2
not assigned.unknown
23.20349
4.53627
0.00013
0.00152
member of CYP81F
AT1G32350
Q8LEE7
9.4
mitochondrial electron transport / ATP synthesis.alternative oxidase
23.46927
4.5527
0.00003
0.00046
unknown protein; Has 19 Blast hits to 19 proteins in 8 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 19; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G17170
Q9SHH6
26.9
misc.glutathione S transferases
23.58991
4.5601
0.00134
0.00985
Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).
AT3G13433
F4JDB5
35.2
not assigned.unknown
23.72351
4.56825
0.00005
0.00073
Physically interacts with CIPK1.
AT1G51890
C0LGG6
30.2.99
signalling.receptor kinases.misc
23.76948
4.57104
0
0.00001
cryptdin protein-related; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: petal, male gametophyte, flower; EXPRESSED DURING: L mature pollen stage, 4 anthesis, petal differentiation and expansion stage; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT3G21352.1); Has 27 Blast hits to 27 proteins in 5 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 27; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G22420
Q9SK85
35.1.41
not assigned.no ontology.hydroxyproline rich proteins
23.80935
4.57346
0.00129
0.00953
RING/U-box protein with domain of unknown function (DUF 1232); FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1232 (InterPro:IPR010652); BEST Arabidopsis thaliana protein match is: RING/U-box protein with domain of unknown function (DUF 1232) (TAIR:AT1G72175.1).
AT1G26410
Q9FZC7
26.8
misc.nitrilases, *nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases
23.88708
4.57816
0
0.00001
FAD-binding Berberine family protein; FUNCTIONS IN: electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity; LOCATED IN: endomembrane system; EXPRESSED IN: stem, stamen; EXPRESSED DURING: 4 anthesis; CONTAINS InterPro DOMAIN/s: FAD-binding, type 2 (InterPro:IPR016166), Berberine/berberine-like (InterPro:IPR012951), FAD linked oxidase, N-terminal (InterPro:IPR006094); BEST Arabidopsis thaliana protein match is: FAD-binding Berberine family protein (TAIR:AT1G26380.1); Has 4265 Blast hits to 4053 proteins in 603 species: Archae - 34; Bacteria - 1861; Metazoa - 0; Fungi - 1585; Plants - 662; Viruses - 0; Other Eukaryotes - 123 (source: NCBI BLink).
AT1G02920
Q9SRY5
26.9
misc.glutathione S transferases
23.88928
4.57829
0
0
Encodes glutathione transferase belonging to the phi class of GSTs. Naming convention according to Wagner et al. (2002).
AT5G09800
Q9LXE3
27.3.64
RNA.regulation of transcription.PHOR1
23.90318
4.57913
0
0
Major facilitator superfamily protein; FUNCTIONS IN: carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity; INVOLVED IN: transmembrane transport; LOCATED IN: membrane; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Major facilitator superfamily (InterPro:IPR020846), Major facilitator superfamily MFS-1 (InterPro:IPR011701), Major facilitator superfamily, general substrate transporter (InterPro:IPR016196); BEST Arabidopsis thaliana protein match is: Major facilitator superfamily protein (TAIR:AT1G78130.1); 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).
AT3G01760
Q9SS86
34.3
transport.amino acids
23.90459
4.57922
0.00359
0.02173
Encodes TPLATE, a cytokinesis protein targeted to the cell plate. Functions in vesicle-trafficking events required for site-specific cell wall modifications during pollen germination and for anchoring of the cell plate to the mother wall at the correct cortical position.
AT1G47890
Q9C699
20.1.7
stress.biotic.PR-proteins
24.02763
4.58662
0
0.00007
Protein phosphatase 2C family protein; FUNCTIONS IN: protein serine/threonine phosphatase activity, catalytic activity; INVOLVED IN: protein amino acid dephosphorylation; LOCATED IN: protein serine/threonine phosphatase complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Protein phosphatase 2C, manganese/magnesium aspartate binding site (InterPro:IPR000222), Protein phosphatase 2C-related (InterPro:IPR001932), Protein phosphatase 2C (InterPro:IPR015655), Protein phosphatase 2C, N-terminal (InterPro:IPR014045); BEST Arabidopsis thaliana protein match is: Protein phosphatase 2C family protein (TAIR:AT3G17250.1); Has 6585 Blast hits to 6541 proteins in 378 species: Archae - 8; Bacteria - 146; Metazoa - 1665; Fungi - 743; Plants - 2687; Viruses - 9; Other Eukaryotes - 1327 (source: NCBI BLink).

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT1G02920
Q9SRY5
26.9
misc.glutathione S transferases
143.0855
7.1607
0
0
Encodes glutathione transferase belonging to the phi class of GSTs. Naming convention according to Wagner et al. (2002).
AT3G01830
Q9SGI8
30.3
signalling.calcium
148.1349
7.2108
0
0
Encodes a LysM-containing receptor-like kinase. Induction of chitin-responsive genes by chitin treatment is not blocked in the mutant.
AT5G02490
P22954
29.6
protein.folding
148.3951
7.2133
0
0
Oligosaccaryltransferase; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; CONTAINS InterPro DOMAIN/s: Oligosaccaryltransferase (InterPro:IPR018943); BEST Arabidopsis thaliana protein match is: Oligosaccaryltransferase (TAIR:AT3G12587.1); 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).
AT1G69930
Q9CAS6
26.9
misc.glutathione S transferases
149.4424
7.2234
0
0
type 2A serine/threonine protein phosphatase (PP2A) mRNA,
AT2G32190
Q9SKY1
35.2
not assigned.unknown
150.0008
7.2288
0
0
unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT2G32210.1); Has 131 Blast hits to 131 proteins in 14 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 1; Plants - 130; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT2G02340
Q9ZVQ8
31.1
cell.organisation
150.1708
7.2305
0
0
encodes a protein containing an F-box domain and physically interacts with SCF subunit SKP1/ASK1. The protein also exhibits similarity in sequence to phloem protein 2 (PP2) from cucumber.
AT1G30814
B6EUC0
35.2
not assigned.unknown
150.1844
7.2306
0
0
Involved in trichome maturation. mutant displays enlarged trichomes
AT5G52640
P27323
20.2.1
stress.abiotic.heat
150.4608
7.2332
0
0
Copper transport protein family; BEST Arabidopsis thaliana protein match is: Copper transport protein family (TAIR:AT5G52680.1); 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).
AT3G53600
Q9LFG0
27.3.11
RNA.regulation of transcription.C2H2 zinc finger family
151.2596
7.2409
0
0.0002
member of Putative Na+/H+ antiporter family. Involved in the osmoregulation through K(+) fluxes and possibly pH modulation of an active endomembrane system in guard cells.
AT5G64750
Q9FGF8
27.3.3
RNA.regulation of transcription.AP2/EREBP, APETALA2/Ethylene-responsive element binding protein family
151.5503
7.2437
0
0
Member of a large family of putative ligands homologous to the Clavata3 gene. Consists of a single exon.
AT3G21520
Q9LVF4
35.2
not assigned.unknown
153.0972
7.2583
0
0
Acid phosphatase/vanadium-dependent haloperoxidase-related protein; CONTAINS InterPro DOMAIN/s: Acid phosphatase/vanadium-dependent haloperoxidase related (InterPro:IPR003832); BEST Arabidopsis thaliana protein match is: Acid phosphatase/vanadium-dependent haloperoxidase-related protein (TAIR:AT1G67600.1); Has 1115 Blast hits to 1115 proteins in 408 species: Archae - 0; Bacteria - 729; Metazoa - 0; Fungi - 0; Plants - 228; Viruses - 0; Other Eukaryotes - 158 (source: NCBI BLink).
AT5G67310
#N/A
26.1
misc.cytochrome P450
154.2659
7.2693
0
0
ARM repeat superfamily protein; FUNCTIONS IN: ubiquitin-protein ligase activity, binding; INVOLVED IN: protein ubiquitination; LOCATED IN: endomembrane system, ubiquitin ligase complex; EXPRESSED IN: 11 plant structures; EXPRESSED DURING: 7 growth stages; CONTAINS InterPro DOMAIN/s: U box domain (InterPro:IPR003613), Armadillo-like helical (InterPro:IPR011989), Armadillo (InterPro:IPR000225), Armadillo-type fold (InterPro:IPR016024); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein with ARM repeat domain (TAIR:AT2G23140.2); 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).

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT5G37490
Q5PNY6
17.6.2
hormone metabolism.gibberelin.signal transduction
1.87E-09
1.27E-08
AT5G38900
Q9FMB1
35.1
not assigned.no ontology
5.61E-107
2.74E-104
AT5G43650
Q9FIX5
27.3.6
RNA.regulation of transcription.bHLH,Basic Helix-Loop-Helix family
9.06E-05
0.000342902
AT1G11610
Q9SAB6
26.1
misc.cytochrome P450
8.34E-36
3.40E-34
NAD(P)-binding Rossmann-fold superfamily protein; FUNCTIONS IN: 3-oxoacyl-[acyl-carrier-protein] reductase activity, copper ion binding; INVOLVED IN: oxidation reduction, metabolic process, fatty acid biosynthetic process; LOCATED IN: chloroplast stroma, chloroplast, chloroplast envelope; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: 3-oxoacyl-(acyl-carrier-protein) reductase (InterPro:IPR011284), Short-chain dehydrogenase/reductase, conserved site (InterPro:IPR020904), NAD(P)-binding domain (InterPro:IPR016040), Glucose/ribitol dehydrogenase (InterPro:IPR002347), Short-chain dehydrogenase/reductase SDR (InterPro:IPR002198); BEST Arabidopsis thaliana protein match is: NAD(P)-binding Rossmann-fold superfamily protein (TAIR:AT2G29370.1); Has 133396 Blast hits to 132816 proteins in 3924 species: Archae - 1008; Bacteria - 83642; Metazoa - 7884; Fungi - 7548; Plants - 3127; Viruses - 5; Other Eukaryotes - 30182 (source: NCBI BLink).
AT2G22880
O81005
35.1
not assigned.no ontology
2.04E-61
2.71E-59
INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast; BEST Arabidopsis thaliana protein match is: non-yellowing 1 (TAIR:AT4G22920.1); Has 206 Blast hits to 202 proteins in 67 species: Archae - 0; Bacteria - 86; Metazoa - 0; Fungi - 0; Plants - 118; Viruses - 0; Other Eukaryotes - 2 (source: NCBI BLink).
AT1G51870
F4IB71
30.2.1
signalling.receptor kinases.leucine rich repeat I
1.81E-19
2.89E-18
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).
AT3G15500
Q9LDY8
27.3.27
RNA.regulation of transcription.NAC domain transcription factor family
3.32E-25
7.77E-24
Leucine-rich repeat protein kinase family protein; FUNCTIONS IN: kinase activity; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: endomembrane system; EXPRESSED IN: 7 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: Protein kinase, ATP binding site (InterPro:IPR017441), Protein kinase, catalytic domain (InterPro:IPR000719), 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:AT5G59650.1); 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).
AT3G01830
Q9SGI8
30.3
signalling.calcium
3.12E-42
1.75E-40
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).
AT1G16420
Q9SA41
29.5
protein.degradation
2.63E-29
7.75E-28
VQ motif-containing protein; CONTAINS InterPro DOMAIN/s: VQ (InterPro:IPR008889); BEST Arabidopsis thaliana protein match is: VQ motif-containing protein (TAIR:AT5G65170.1); Has 1167 Blast hits to 1059 proteins in 155 species: Archae - 0; Bacteria - 36; Metazoa - 369; Fungi - 192; Plants - 292; Viruses - 57; Other Eukaryotes - 221 (source: NCBI BLink).
AT1G36622
Q1G3E7
35.1
not assigned.no ontology
2.18E-62
3.07E-60
emp24/gp25L/p24 family/GOLD family protein; INVOLVED IN: transport; LOCATED IN: integral to membrane; EXPRESSED IN: pollen tube; CONTAINS InterPro DOMAIN/s: GOLD (InterPro:IPR009038), emp24/gp25L/p24 (InterPro:IPR000348); BEST Arabidopsis thaliana protein match is: emp24/gp25L/p24 family/GOLD family protein (TAIR:AT2G03290.1); Has 637 Blast hits to 637 proteins in 130 species: Archae - 0; Bacteria - 0; Metazoa - 362; Fungi - 29; Plants - 206; Viruses - 0; Other Eukaryotes - 40 (source: NCBI BLink).
AT2G32200
Q1PEX8
35.2
not assigned.unknown
6.18E-43
3.67E-41
RING/U-box superfamily protein; FUNCTIONS IN: zinc ion binding; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: 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:AT2G20650.2); Has 309 Blast hits to 308 proteins in 35 species: Archae - 0; Bacteria - 0; Metazoa - 74; Fungi - 25; Plants - 165; Viruses - 0; Other Eukaryotes - 45 (source: NCBI BLink).
AT5G36925
Q8GWS2
35.2
not assigned.unknown
1.46E-21
2.73E-20
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