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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
AT1G43270
#N/A
28.1.1.2
DNA.synthesis/chromatin structure.retrotransposon/transposase.non-LTR retrotransposon
0
#NAME?
0.00531
0.02976
transposable element gene; non-LTR retrotransposon family (LINE), has a 9.0e-37 P-value blast match to GB:NP_038603 L1 repeat, Tf subfamily, member 23 (LINE-element) (Mus musculus)
AT2G22460
Q9SJY8
35.2
not assigned.unknown
0
#NAME?
0.01506
0.06829
Protein of unknown function, DUF617; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF617, plant (InterPro:IPR006460); BEST Arabidopsis thaliana protein match is: Protein of unknown function, DUF617 (TAIR:AT5G65340.1); 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).
AT3G50120
Q9SN06
35.2
not assigned.unknown
0
#NAME?
0.00348
0.0212
Plant protein of unknown function (DUF247); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: leaf apex, petal, leaf whorl, sepal, flower; EXPRESSED DURING: 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF247, plant (InterPro:IPR004158); BEST Arabidopsis thaliana protein match is: Plant protein of unknown function (DUF247) (TAIR:AT3G50170.1); Has 1189 Blast hits to 1046 proteins in 18 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 1189; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT5G65340
Q9FKQ4
35.2
not assigned.unknown
0
#NAME?
0.00484
0.0276
Protein of unknown function, DUF617; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF617, plant (InterPro:IPR006460); BEST Arabidopsis thaliana protein match is: Protein of unknown function, DUF617 (TAIR:AT2G22460.1); 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).
AT4G37370
Q9SZT7
26.1
misc.cytochrome P450
47.84629
5.58034
0
0.00002
Peroxidase superfamily protein; FUNCTIONS IN: protein binding, peroxidase activity; INVOLVED IN: oxidation reduction, response to oxidative stress; LOCATED IN: cytoplasm; 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); BEST Arabidopsis thaliana protein match is: Peroxidase superfamily protein (TAIR:AT4G37530.1); Has 4636 Blast hits to 4606 proteins in 315 species: Archae - 0; Bacteria - 0; Metazoa - 9; Fungi - 258; Plants - 4294; Viruses - 0; Other Eukaryotes - 75 (source: NCBI BLink).
AT2G30750
O49340
26.1
misc.cytochrome P450
47.90111
5.58199
0.00012
0.00142
putative cytochrome P450
AT1G60750
F4HPY8
17.2.3
hormone metabolism.auxin.induced-regulated-responsive-activated
48.13968
5.58915
0.00002
0.0003
HAPLESS 13 (HAP13); INVOLVED IN: intracellular protein transport, transport, vesicle-mediated transport; LOCATED IN: clathrin vesicle coat, clathrin adaptor complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Clathrin adaptor, mu subunit, conserved site (InterPro:IPR018240), Clathrin adaptor, mu subunit, C-terminal (InterPro:IPR008968), Clathrin adaptor, mu subunit (InterPro:IPR001392), Longin-like (InterPro:IPR011012); BEST Arabidopsis thaliana protein match is: Clathrin adaptor complexes medium subunit family protein (TAIR:AT1G10730.1); Has 2206 Blast hits to 2139 proteins in 330 species: Archae - 0; Bacteria - 0; Metazoa - 1107; Fungi - 506; Plants - 213; Viruses - 0; Other Eukaryotes - 380 (source: NCBI BLink).
AT1G06137
F4IBZ9
35.2
not assigned.unknown
49.93439
5.64196
0
0.00001
unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G06135.1); 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).
AT3G21520
Q9LVF4
35.2
not assigned.unknown
51.64069
5.69044
0.00002
0.0003
Encodes protein phosphatase 2A (PP2A) B'zeta subunit. Targeted to mitochondria.
AT1G71520
Q9C9I8
27.3.3
RNA.regulation of transcription.AP2/EREBP, APETALA2/Ethylene-responsive element binding protein family
52.65759
5.71857
0
0.0001
Encodes choline kinase. mRNA levels are increased in response to wounding.
AT5G42380
Q9FIH9
30.3
signalling.calcium
54.17919
5.75967
0
0.00001
B-cell receptor-associated 31-like; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: intracellular protein transport; LOCATED IN: endoplasmic reticulum, plasma membrane; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: B-cell receptor-associated 31-like (InterPro:IPR008417); BEST Arabidopsis thaliana protein match is: B-cell receptor-associated protein 31-like (TAIR:AT1G11905.1); 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).
AT4G11370
Q9SUS4
29.5.11.4.2
protein.degradation.ubiquitin.E3.RING
54.47221
5.76745
0
0
Encodes a cysteine-rich receptor-like protein kinase.

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT3G22510
Q6AWV8
35.2
not assigned.unknown
Inf
Inf
0.0004
0.0016
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein; FUNCTIONS IN: lipid binding; INVOLVED IN: lipid transport; LOCATED IN: chloroplast envelope; EXPRESSED IN: 9 plant structures; EXPRESSED DURING: 4 anthesis, C globular stage, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Bifunctional inhibitor/plant lipid transfer protein/seed storage (InterPro:IPR016140), Plant lipid transfer protein/seed storage/trypsin-alpha amylase inhibitor (InterPro:IPR003612); BEST Arabidopsis thaliana protein match is: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein (TAIR:AT1G05450.2); Has 884 Blast hits to 840 proteins in 101 species: Archae - 0; Bacteria - 84; Metazoa - 49; Fungi - 31; Plants - 622; Viruses - 18; Other Eukaryotes - 80 (source: NCBI BLink).
AT5G43610
Q6A329
34.2.1
transport.sugars.sucrose
Inf
Inf
0
0
BHLH92; FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription; LOCATED IN: nucleus; CONTAINS InterPro DOMAIN/s: Helix-loop-helix DNA-binding domain (InterPro:IPR001092), Helix-loop-helix DNA-binding (InterPro:IPR011598); BEST Arabidopsis thaliana protein match is: basic helix-loop-helix (bHLH) DNA-binding superfamily protein (TAIR:AT4G09820.1); 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).
AT4G37710
Q9SZG3
35.1
not assigned.no ontology
Inf
Inf
0
0
basic leucine-zipper 7 (bZIP7); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription, DNA-dependent; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 7 growth stages; CONTAINS InterPro DOMAIN/s: Basic-leucine zipper (bZIP) transcription factor (InterPro:IPR004827), bZIP transcription factor, bZIP-1 (InterPro:IPR011616); BEST Arabidopsis thaliana protein match is: basic leucine-zipper 6 (TAIR:AT2G22850.2); Has 1802 Blast hits to 1800 proteins in 126 species: Archae - 0; Bacteria - 2; Metazoa - 56; Fungi - 25; Plants - 1671; Viruses - 0; Other Eukaryotes - 48 (source: NCBI BLink).
AT5G49420
Q7X9H5
27.3.24
RNA.regulation of transcription.MADS box transcription factor family
Inf
Inf
0.0022
0.0072
AtCP1 encodes a novel Ca2+-binding protein, which shares sequence similarities with calmodulins. The expression of AtCP1 is induced by NaCl.
AT3G02810
Q9M8S2
29.4.1.57
protein.postranslational modification.kinase.receptor like cytoplasmatic kinase VII
Inf
Inf
0.0079
0.0225
ARM repeat superfamily protein; FUNCTIONS IN: binding; INVOLVED IN: response to other organism, response to ozone; EXPRESSED IN: 16 plant structures; EXPRESSED DURING: 8 growth stages; CONTAINS InterPro DOMAIN/s: Armadillo-like helical (InterPro:IPR011989), Armadillo-type fold (InterPro:IPR016024); BEST Arabidopsis thaliana protein match is: ARM repeat superfamily protein (TAIR:AT5G37490.1); Has 423 Blast hits to 423 proteins in 24 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 422; Viruses - 0; Other Eukaryotes - 1 (source: NCBI BLink).
AT2G05180
Q9SJ39
26.1
misc.cytochrome P450
Inf
Inf
0.0055
0.0165
alpha/beta-Hydrolases superfamily protein; FUNCTIONS IN: triglyceride lipase activity; INVOLVED IN: lipid metabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 15 plant structures; EXPRESSED DURING: 8 growth stages; CONTAINS InterPro DOMAIN/s: Lipase, class 3 (InterPro:IPR002921); BEST Arabidopsis thaliana protein match is: alpha/beta-Hydrolases superfamily protein (TAIR:AT4G10955.2); Has 216 Blast hits to 215 proteins in 14 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 216; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G68450
Q9CA36
35.1
not assigned.no ontology
Inf
Inf
0.0155
0.0409
alpha/beta-Hydrolases superfamily protein; FUNCTIONS IN: hydrolase activity; INVOLVED IN: metabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 11 plant structures; EXPRESSED DURING: LP.06 six leaves visible, LP.04 four leaves visible, 4 anthesis, C globular stage, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Lipase, GDXG, active site (InterPro:IPR002168), Alpha/beta hydrolase fold-3 (InterPro:IPR013094); BEST Arabidopsis thaliana protein match is: carboxyesterase 17 (TAIR:AT5G16080.1); Has 11100 Blast hits to 11083 proteins in 1670 species: Archae - 110; Bacteria - 6437; Metazoa - 919; Fungi - 1098; Plants - 1346; Viruses - 3; Other Eukaryotes - 1187 (source: NCBI BLink).
AT3G29615
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0.0023
0.0075
alpha/beta-Hydrolases superfamily protein; CONTAINS InterPro DOMAIN/s: Alpha/beta hydrolase fold-1 (InterPro:IPR000073); BEST Arabidopsis thaliana protein match is: alpha/beta-Hydrolases superfamily protein (TAIR:AT3G01690.1); Has 4135 Blast hits to 4125 proteins in 834 species: Archae - 12; Bacteria - 1370; Metazoa - 720; Fungi - 213; Plants - 304; Viruses - 6; Other Eukaryotes - 1510 (source: NCBI BLink).
AT3G55790
Q9M045
35.2
not assigned.unknown
Inf
Inf
0.0003
0.0012
A member of the Glycosyltransferase Family 64, homologous to Poplar cambium-expressed GT64 gene. The EPC1 protein plays a critical role during plant development in maintaining the integrity of organs via cell-cell adhesion, thereby providing mechanical strength and facilitating the movement of metabolites throughout the plant.
AT5G52090
Q9FJ83
28.1
DNA.synthesis/chromatin structure
Inf
Inf
0.0034
0.0108
A member of ARF-like GTPase family. A thaliana has 21 members, in two subfamilies, ARF and ARF-like (ARL) GTPases.
AT3G16900
Q9LSQ1
35.2
not assigned.unknown
0
#NAME?
0.0153
0.0403
AT1G45063
Q1G3Z5
35.1
not assigned.no ontology
0
#NAME?
0.0134
0.036
CCCH-type zinc fingerfamily protein with RNA-binding domain; FUNCTIONS IN: RNA binding, nucleotide binding, zinc ion binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 6 plant structures; EXPRESSED DURING: 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Zinc finger, CCCH-type (InterPro:IPR000571), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: Zinc finger (CCCH-type) family protein / RNA recognition motif (RRM)-containing protein (TAIR:AT3G52980.1); Has 286 Blast hits to 218 proteins in 21 species: Archae - 0; Bacteria - 0; Metazoa - 6; Fungi - 0; Plants - 277; Viruses - 0; Other Eukaryotes - 3 (source: NCBI BLink).

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT4G09100
Q9M0R7
29.5.11.4.2
protein.degradation.ubiquitin.E3.RING
0.009743642
0.024800819
AT4G10960
Q9SN58
10.1.2
cell wall.precursor synthesis.UGE
3.72E-06
1.73E-05
AT4G12210
Q9STJ0
29.5.11.4.2
protein.degradation.ubiquitin.E3.RING
0.022171789
0.051520825
AT4G13310
Q9T0K2
26.1
misc.cytochrome P450
3.79E-21
6.85E-20
AT4G19360
Q8L7G2
35.2
not assigned.unknown
0.00020583
0.000733574
AT4G19925
F4JU10
20.1.7
stress.biotic.PR-proteins
0.000255726
0.000895742
AT4G22030
O65451
29.5.11.4.3.2
protein.degradation.ubiquitin.E3.SCF.FBOX
1.02E-06
5.13E-06
AT4G22070
Q93WT0
27.3.32
RNA.regulation of transcription.WRKY domain transcription factor family
0.000393068
0.001330537
AT4G23271
B3H7C0
35.2
not assigned.unknown
2.49E-09
1.68E-08
AT4G25200
Q96331
20.2.1
stress.abiotic.heat
1.60E-09
1.10E-08
AT4G31760
O81772
26.12
misc.peroxidases
0.020574637
0.048205815
AT4G31940
Q9SZ46
26.1
misc.cytochrome P450
0.000412421
0.001390748
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