top of page
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
AT2G37980
Q9SH89
17.2.3
hormone metabolism.auxin.induced-regulated-responsive-activated
38.89438
5.28149
0
0.00005
chaperone protein dnaJ-related; Has 1004 Blast hits to 976 proteins in 392 species: Archae - 24; Bacteria - 688; Metazoa - 92; Fungi - 4; Plants - 51; Viruses - 0; Other Eukaryotes - 145 (source: NCBI BLink).
AT1G17180
Q9SHH7
26.9
misc.glutathione S transferases
39.05675
5.2875
0.00111
0.00844
Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).
AT3G46340
Q9SNA3
30.2.99
signalling.receptor kinases.misc
39.40005
5.30013
0.00002
0.00035
GRAS family transcription factor; CONTAINS InterPro DOMAIN/s: Transcription factor GRAS (InterPro:IPR005202); BEST Arabidopsis thaliana protein match is: GRAS family transcription factor (TAIR:AT5G59450.1); Has 2508 Blast hits to 2402 proteins in 303 species: Archae - 0; Bacteria - 7; Metazoa - 2; Fungi - 0; Plants - 2499; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT2G41230
Q8RWS1
35.2
not assigned.unknown
40.4914
5.33954
0
0
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein; FUNCTIONS IN: methyltransferase activity; INVOLVED IN: response to cadmium ion; LOCATED IN: mitochondrion; EXPRESSED IN: 12 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Methyltransferase type 11 (InterPro:IPR013216); BEST Arabidopsis thaliana protein match is: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein (TAIR:AT3G61210.1); Has 1429 Blast hits to 1424 proteins in 497 species: Archae - 6; Bacteria - 922; Metazoa - 80; Fungi - 179; Plants - 160; Viruses - 0; Other Eukaryotes - 82 (source: NCBI BLink).
AT5G35735
Q9FKH6
17.2.3
hormone metabolism.auxin.induced-regulated-responsive-activated
40.80361
5.35062
0
0.00001
Uncharacterized protein family (UPF0016); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Uncharacterised protein family UPF0016 (InterPro:IPR001727); BEST Arabidopsis thaliana protein match is: Uncharacterized protein family (UPF0016) (TAIR:AT1G25520.1); Has 1755 Blast hits to 1667 proteins in 691 species: Archae - 14; Bacteria - 1095; Metazoa - 159; Fungi - 139; Plants - 208; Viruses - 0; Other Eukaryotes - 140 (source: NCBI BLink).
AT1G79680
Q8VYA3
30.2.25
signalling.receptor kinases.wall associated kinase
41.03791
5.35889
0
0.00004
nudix hydrolase homolog 3 (NUDT3); FUNCTIONS IN: dipeptidyl-peptidase activity, hydrolase activity; INVOLVED IN: proteolysis; LOCATED IN: cytosol, vacuole; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: NUDIX hydrolase domain-like (InterPro:IPR015797), Peptidase M49, dipeptidyl-peptidase III (InterPro:IPR005317), NUDIX hydrolase domain (InterPro:IPR000086); 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).
AT1G51920
F4IB79
35.2
not assigned.unknown
41.07274
5.36011
0
0.00006
IQ-domain 27 (IQD27); CONTAINS InterPro DOMAIN/s: IQ calmodulin-binding region (InterPro:IPR000048); BEST Arabidopsis thaliana protein match is: IQ-domain 26 (TAIR:AT3G16490.1); Has 770 Blast hits to 761 proteins in 32 species: Archae - 0; Bacteria - 0; Metazoa - 5; Fungi - 5; Plants - 754; Viruses - 0; Other Eukaryotes - 6 (source: NCBI BLink).
AT1G68390
Q9M9C4
35.2
not assigned.unknown
41.50009
5.37504
0.00001
0.00013
Protein phosphatase 2C family protein; FUNCTIONS IN: protein serine/threonine phosphatase activity, catalytic activity; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: 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:AT1G09160.1); Has 5348 Blast hits to 5347 proteins in 441 species: Archae - 2; Bacteria - 344; Metazoa - 1196; Fungi - 481; Plants - 2242; Viruses - 4; Other Eukaryotes - 1079 (source: NCBI BLink).
AT3G14225
Q9LJP1
26.28
misc.GDSL-motif lipase
41.54907
5.37674
0.00491
0.02788
unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to oxidative stress; LOCATED IN: mitochondrion; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; Has 16 Blast hits to 16 proteins in 7 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 16; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT4G37710
Q9SZG3
35.1
not assigned.no ontology
41.5988
5.37847
0.00252
0.01637
Protein of unknown function (duplicated DUF1399); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1399 (InterPro:IPR009836); BEST Arabidopsis thaliana protein match is: Protein of unknown function (duplicated DUF1399) (TAIR:AT2G22660.2); Has 24258 Blast hits to 6156 proteins in 640 species: Archae - 4; Bacteria - 13513; Metazoa - 5207; Fungi - 694; Plants - 2964; Viruses - 274; Other Eukaryotes - 1602 (source: NCBI BLink).
AT4G01870
Q9SYI5
35.1
not assigned.no ontology
41.59904
5.37848
0.00004
0.00055
Cysteine/Histidine-rich C1 domain family protein; CONTAINS InterPro DOMAIN/s: DC1 (InterPro:IPR004146), C1-like (InterPro:IPR011424); BEST Arabidopsis thaliana protein match is: Cysteine/Histidine-rich C1 domain family protein (TAIR:AT4G01910.1); 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).
AT3G25250
Q9LSF1
29.4
protein.postranslational modification
41.86979
5.38784
0.00002
0.00033
unknown protein; LOCATED IN: endomembrane system; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G26140.1); 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).

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT3G49540
Q9SCK5
35.2
not assigned.unknown
556.0197
9.119
0
0
FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: mRNA splicing factor, Cwf21 (InterPro:IPR013170); 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).
AT5G42380
Q9FIH9
30.3
signalling.calcium
578.0761
9.1751
0
0
Abscisic acid-responsive (TB2/DP1, HVA22) family protein; CONTAINS InterPro DOMAIN/s: TB2/DP1/HVA22 related protein (InterPro:IPR004345); BEST Arabidopsis thaliana protein match is: HVA22-like protein H (ATHVA22H) (TAIR:AT1G19950.1); 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).
AT3G49620
Q8H113
33.99
development.unspecified
658.5908
9.3632
0
0
Phytosulfokine 3 precursor, coding for a unique plant peptide growth factor. Plants overexpressing this gene (under a 35S promoter), develop normal cotyledons and hypocotyls but their growth, in particular that of their roots, was faster than that of wildtype.
AT1G14540
Q9LE15
26.9
misc.glutathione S transferases
661.8696
9.3704
0
0
Peroxidase superfamily protein; FUNCTIONS IN: peroxidase activity, heme binding; INVOLVED IN: response to oxidative stress, oxidation reduction; LOCATED IN: endomembrane system; EXPRESSED IN: leaf apex, sepal, root, stamen; EXPRESSED DURING: 4 anthesis; CONTAINS InterPro DOMAIN/s: Haem peroxidase (InterPro:IPR010255), Plant peroxidase (InterPro:IPR000823), Peroxidases heam-ligand binding site (InterPro:IPR019793), Haem peroxidase, plant/fungal/bacterial (InterPro:IPR002016), Peroxidase, active site (InterPro:IPR019794); BEST Arabidopsis thaliana protein match is: Peroxidase superfamily protein (TAIR:AT1G14550.1); Has 4581 Blast hits to 4555 proteins in 302 species: Archae - 0; Bacteria - 6; Metazoa - 19; Fungi - 179; Plants - 4302; Viruses - 0; Other Eukaryotes - 75 (source: NCBI BLink).
AT5G64890
Q9LV88
20.1.3
stress.biotic.signalling
767.212
9.5835
0
0
elicitor peptide 3 precursor (PROPEP3); 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).
AT4G16820
O23522
11.9.2.1
lipid metabolism.lipid degradation.lipases.triacylglycerol lipase
784.8362
9.6162
0
0
unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G31130.1); 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).
AT2G21910
Q9SJ08
26.1
misc.cytochrome P450
812.4302
9.6661
0
0
A paternally expressed imprinted gene.
AT5G61160
Q9FNP9
16.8.1.21
secondary metabolism.flavonoids.anthocyanins.anthocyanin 5-aromatic acyltransferase
850.0555
9.7314
0
0
Leucine-rich repeat (LRR) family protein; CONTAINS InterPro DOMAIN/s: Leucine-rich repeat, typical subtype (InterPro:IPR003591), Leucine-rich repeat-containing N-terminal domain, type 2 (InterPro:IPR013210), Leucine-rich repeat (InterPro:IPR001611); BEST Arabidopsis thaliana protein match is: Leucine-rich repeat (LRR) family protein (TAIR:AT1G13910.1).
AT1G56240
Q9C7J9
31.1
cell.organisation
967.4304
9.918
0
0.0001
Encodes an F-box protein that can functionally replace VirF, regulating levels of the VirE2 and VIP1 proteins via a VBF-containing SCF complex. It is thought to be involved in DNA integration and T-DNA degradation.
AT2G02310
Q9ZVR0
31.1
cell.organisation
1042.6785
10.0261
0
0
phloem protein 2-B7 (PP2-B7); CONTAINS InterPro DOMAIN/s: F-box domain, cyclin-like (InterPro:IPR001810), F-box domain, Skp2-like (InterPro:IPR022364); BEST Arabidopsis thaliana protein match is: phloem protein 2-B8 (TAIR:AT2G02340.1); Has 490 Blast hits to 475 proteins in 28 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 490; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G56060
A0A178WF56
35.2
not assigned.unknown
1050.275
10.0366
0
0
Leucine-rich repeat transmembrane protein kinase; FUNCTIONS IN: protein serine/threonine kinase activity, protein kinase activity, ATP binding; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasma membrane, membrane; EXPRESSED IN: cultured cell; CONTAINS InterPro DOMAIN/s: Serine/threonine-protein kinase domain (InterPro:IPR002290), Leucine-rich repeat (InterPro:IPR001611), Serine-threonine/tyrosine-protein kinase (InterPro:IPR001245), Serine/threonine-protein kinase, active site (InterPro:IPR008271), Protein kinase-like domain (InterPro:IPR011009), Protein kinase, catalytic domain (InterPro:IPR000719), Malectin/receptor-like protein kinase (InterPro:IPR021720), Tyrosine-protein kinase, catalytic domain (InterPro:IPR020635); BEST Arabidopsis thaliana protein match is: Leucine-rich repeat transmembrane protein kinase (TAIR:AT1G56140.1); Has 183160 Blast hits to 131873 proteins in 4617 species: Archae - 129; Bacteria - 16542; Metazoa - 50297; Fungi - 10850; Plants - 82984; Viruses - 436; Other Eukaryotes - 21922 (source: NCBI BLink).
AT1G71520
Q9C9I8
27.3.3
RNA.regulation of transcription.AP2/EREBP, APETALA2/Ethylene-responsive element binding protein family
1237.3881
10.2731
0
0
Encodes choline kinase. mRNA levels are increased in response to wounding.

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT5G67080
Q9FHA5
29.4
protein.postranslational modification
3.03E-31
9.84E-30
AT1G57650
A0A1P8ARZ1
20.1.7
stress.biotic.PR-proteins
3.52E-78
7.68E-76
tRNAHis guanylyltransferase; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: cultured cell; CONTAINS InterPro DOMAIN/s: tRNAHis guanylyltransferase (InterPro:IPR007537); BEST Arabidopsis thaliana protein match is: tRNAHis guanylyltransferase (TAIR:AT2G32320.1); 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).
AT5G66890
Q9FKZ2
20.1.7
stress.biotic.PR-proteins
7.26E-18
1.04E-16
AT1G05675
P0C7P7
26.2
misc.UDP glucosyl and glucoronyl transferases
8.47E-36
3.45E-34
alpha/beta-Hydrolases superfamily protein; INVOLVED IN: glycerol biosynthetic process; LOCATED IN: endomembrane system; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; BEST Arabidopsis thaliana protein match is: alpha/beta-Hydrolases superfamily protein (TAIR:AT1G23330.1); Has 782 Blast hits to 782 proteins in 229 species: Archae - 0; Bacteria - 631; Metazoa - 3; Fungi - 4; Plants - 47; Viruses - 0; Other Eukaryotes - 97 (source: NCBI BLink).
AT1G32350
Q8LEE7
9.4
mitochondrial electron transport / ATP synthesis.alternative oxidase
3.51E-82
8.33E-80
RNA-binding (RRM/RBD/RNP motifs) family protein; FUNCTIONS IN: nucleotide binding, nucleic acid binding; INVOLVED IN: biological_process unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: nucleotide binding;nucleic acid binding (TAIR:AT1G21320.2); Has 631 Blast hits to 628 proteins in 151 species: Archae - 0; Bacteria - 4; Metazoa - 278; Fungi - 177; Plants - 131; Viruses - 0; Other Eukaryotes - 41 (source: NCBI BLink).
AT1G59950
Q1PFI5
16.8.2
secondary metabolism.flavonoids.chalcones
4.94E-159
1.36E-155
Major facilitator superfamily protein; INVOLVED IN: transmembrane transport; LOCATED IN: endomembrane system; CONTAINS InterPro DOMAIN/s: Major facilitator superfamily (InterPro:IPR020846), Nodulin-like (InterPro:IPR010658), Major facilitator superfamily MFS-1 (InterPro:IPR011701), Major facilitator superfamily, general substrate transporter (InterPro:IPR016196); BEST Arabidopsis thaliana protein match is: Nodulin-like / Major Facilitator Superfamily protein (TAIR:AT2G34350.1); 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).
AT5G65600
Q9LSL5
29.4
protein.postranslational modification
2.44E-38
1.13E-36
AT1G08860
Q5XQC7
30.3
signalling.calcium
7.18E-32
2.45E-30
Family of unknown function (DUF572) ; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF572 (InterPro:IPR007590); BEST Arabidopsis thaliana protein match is: Family of unknown function (DUF572) (TAIR:AT2G32050.1); Has 1391 Blast hits to 1324 proteins in 252 species: Archae - 3; Bacteria - 52; Metazoa - 454; Fungi - 341; Plants - 148; Viruses - 5; Other Eukaryotes - 388 (source: NCBI BLink).
AT1G69930
Q9CAS6
26.9
misc.glutathione S transferases
1.32E-12
1.22E-11
Protein of unknown function (DUF3755); INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF3755 (InterPro:IPR022228); BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF3755) (TAIR:AT1G10820.2).
AT5G61160
Q9FNP9
16.8.1.21
secondary metabolism.flavonoids.anthocyanins.anthocyanin 5-aromatic acyltransferase
5.72E-32
1.97E-30
AT1G05880
Q84RQ9
29.5.11.4.2
protein.degradation.ubiquitin.E3.RING
2.28E-40
1.16E-38
unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G61170.1).
AT2G22760
Q1PF16
27.3.6
RNA.regulation of transcription.bHLH,Basic Helix-Loop-Helix family
1.17E-05
5.06E-05
Zinc finger, C3HC4 type (RING finger) family protein; FUNCTIONS IN: zinc ion binding; LOCATED IN: plasma membrane; EXPRESSED IN: cultured cell; CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, C3HC4 RING-type (InterPro:IPR018957); BEST Arabidopsis thaliana protein match is: Zinc finger, C3HC4 type (RING finger) family protein (TAIR:AT1G12760.1); 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).
bottom of page