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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
AT4G06708
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0.01776
0.07748
transposable element gene; pseudogene, hypothetical protein, contains Pfam profile PF03078: ATHILA ORF-1 family
AT2G09900
#N/A
35.2
not assigned.unknown
Inf
Inf
0.00165
0.01162
transposable element gene; gypsy-like retrotransposon family (Athila), has a 2.3e-75 P-value blast match to GB:CAA57397 Athila ORF 1 (Arabidopsis thaliana)
AT5G28923
#N/A
28.1.1.5
DNA.synthesis/chromatin structure.retrotransposon/transposase.CACTA-like transposase
Inf
Inf
0.01829
0.07923
transposable element gene; CACTA-like transposase family (Ptta/En/Spm), has a 1.1e-19 P-value blast match to At1g15560.1/58-302 CACTA-like transposase family (Ptta/En/Spm) (CACTA-element) (Arabidopsis thaliana)
AT1G16230
F4I2U8
31.4
cell.vesicle transport
Inf
Inf
0.00808
0.04187
Target SNARE coiled-coil domain protein; CONTAINS InterPro DOMAIN/s: Target SNARE coiled-coil domain (InterPro:IPR000727); BEST Arabidopsis thaliana protein match is: syntaxin of plants 51 (TAIR:AT1G16240.2); Has 184 Blast hits to 184 proteins in 71 species: Archae - 0; Bacteria - 4; Metazoa - 11; Fungi - 66; Plants - 93; Viruses - 0; Other Eukaryotes - 10 (source: NCBI BLink).
AT1G21850
Q9SFF2
26.7
misc.oxidases - copper, flavone etc
Inf
Inf
0
0.0001
SKU5 similar 8 (sks8); FUNCTIONS IN: oxidoreductase activity, copper ion binding; INVOLVED IN: oxidation reduction; LOCATED IN: endomembrane system; EXPRESSED IN: embryo; EXPRESSED DURING: C globular stage; CONTAINS InterPro DOMAIN/s: Multicopper oxidase, type 3 (InterPro:IPR011707), Cupredoxin (InterPro:IPR008972), Multicopper oxidase, type 2 (InterPro:IPR011706), Multicopper oxidase, type 1 (InterPro:IPR001117); BEST Arabidopsis thaliana protein match is: SKU5 similar 7 (TAIR:AT1G21860.1); Has 5145 Blast hits to 5091 proteins in 951 species: Archae - 16; Bacteria - 1604; Metazoa - 263; Fungi - 1857; Plants - 1262; Viruses - 0; Other Eukaryotes - 143 (source: NCBI BLink).
AT5G64540
Q5BPE9
35.2
not assigned.unknown
Inf
Inf
0.0078
0.04071
Similar to Inflorescence deficient in abscission (IDA). Involved in floral organ abscission.
AT1G66870
Q9C9N9
26.4
misc.beta 1,3 glucan hydrolases
Inf
Inf
0.00328
0.02024
Protein kinase superfamily protein; FUNCTIONS IN: protein serine/threonine kinase activity, protein kinase activity, ATP binding; INVOLVED IN: protein amino acid phosphorylation; LOCATED IN: plasma membrane; EXPRESSED IN: 21 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), Serine/threonine-protein kinase-like domain (InterPro:IPR017442), Protein kinase-like domain (InterPro:IPR011009), Serine/threonine-protein kinase, active site (InterPro:IPR008271), Protein kinase, catalytic domain (InterPro:IPR000719), Tyrosine-protein kinase, catalytic domain (InterPro:IPR020635); BEST Arabidopsis thaliana protein match is: Protein kinase family protein (TAIR:AT5G38210.1); Has 129213 Blast hits to 127053 proteins in 4833 species: Archae - 128; Bacteria - 14675; Metazoa - 47420; Fungi - 11551; Plants - 35229; Viruses - 624; Other Eukaryotes - 19586 (source: NCBI BLink).
AT1G07128
#N/A
32
micro RNA, natural antisense etc
Inf
Inf
0.02295
0.09405
Potential natural antisense gene, locus overlaps with AT1G07130
AT5G15480
Q9LF34
27.3.11
RNA.regulation of transcription.C2H2 zinc finger family
Inf
Inf
0.00039
0.00357
Mitochondrial substrate carrier family protein; FUNCTIONS IN: binding; INVOLVED IN: transport, mitochondrial transport, transmembrane transport; LOCATED IN: mitochondrion, mitochondrial inner membrane; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Mitochondrial carrier protein (InterPro:IPR002067), Mitochondrial substrate carrier (InterPro:IPR001993), Mitochondrial substrate/solute carrier (InterPro:IPR018108); BEST Arabidopsis thaliana protein match is: Mitochondrial substrate carrier family protein (TAIR:AT1G72820.1); 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).
AT1G53990
Q9SYF5
26.28
misc.GDSL-motif lipase
Inf
Inf
0.02247
0.09259
GDSL-like Lipase/Acylhydrolase superfamily protein; FUNCTIONS IN: lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity; INVOLVED IN: lipid metabolic process; LOCATED IN: vacuolar membrane, plasma membrane, vacuole, plant-type cell wall, plant-type vacuole; EXPRESSED IN: stem, cultured cell, callus; EXPRESSED DURING: seedling growth; CONTAINS InterPro DOMAIN/s: Lipase, GDSL (InterPro:IPR001087); BEST Arabidopsis thaliana protein match is: GDSL-like Lipase/Acylhydrolase superfamily protein (TAIR:AT1G54010.1); Has 3190 Blast hits to 3160 proteins in 155 species: Archae - 0; Bacteria - 224; Metazoa - 0; Fungi - 4; Plants - 2945; Viruses - 0; Other Eukaryotes - 17 (source: NCBI BLink).
AT1G35330
Q9C7I1
29.5.11.4.2
protein.degradation.ubiquitin.E3.RING
Inf
Inf
0.00002
0.00028
EXS (ERD1/XPR1/SYG1) family protein; LOCATED IN: integral to membrane; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: EXS, C-terminal (InterPro:IPR004342), SPX, N-terminal (InterPro:IPR004331); BEST Arabidopsis thaliana protein match is: EXS (ERD1/XPR1/SYG1) family protein (TAIR:AT1G26730.1); Has 1149 Blast hits to 1073 proteins in 218 species: Archae - 1; Bacteria - 33; Metazoa - 257; Fungi - 379; Plants - 329; Viruses - 0; Other Eukaryotes - 150 (source: NCBI BLink).
AT4G26930
Q9S773
27.3.25
RNA.regulation of transcription.MYB domain transcription factor family
Inf
Inf
0.01807
0.07847
Encodes an aconitase that can catalyze the conversion of citrate to isocitrate through a cis-aconitate intermediate, indicating that it may participate in the TCA cycle and other primary metabolic pathways. The protein is believed to accumulate in the mitochondria and the cytosol. It affects CSD2 (At2g28190 - a superoxide dismutase) transcript levels and may play a role in the response to oxidative stress. One member of the family (ACO1 - At35830) was shown to specifically bind to the 5' UTR of CSD2 in vitro.

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT3G46613
Q6IM86
33.99
development.unspecified
Inf
Inf
0.0011
0.0039
Encodes a myb family transcription factor with a single Myb DNA-binding domain (type SHAQKYF) that is unique to plants and is essential for circadian rhythms, specifically for transcriptional regulation within the circadian clock. LUX is required for normal rhythmic expression of multiple clock outputs in both constant light and darkness. It is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter.
AT5G37140
F4K5W4
28.1
DNA.synthesis/chromatin structure
Inf
Inf
0
0
Encodes a MYB family transcription factor Circadian 1 (CIR1). Involved in circadian regulation in Arabidopsis.
AT2G31345
Q8L9Z1
35.2
not assigned.unknown
Inf
Inf
0
0
Encodes a mitochondrial glyoxalase 2 that can accommodate a number of different metal centers and with the predominant metal center being Fe(III)Zn(II).
AT3G23220
Q9LTC6
17.5.2
hormone metabolism.ethylene.signal transduction
Inf
Inf
0
0
encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ERF1). The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5. EREBP like protein that binds GCC box of ethylene regulated promoters such as basic chitinases. Constitutive expression of ERF1 phenocopies ethylene over production. Involved in ethylene signaling cascade,downstream of EIN2 and EIN3.
AT3G42996
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0.0091
0.0257
Encodes a kinesin TETRASPORE. Required for cytokinesis in pollen. In mutants, all four microspore nuclei remain within the same cytoplasm after meiosis.
AT2G06470
Q9SKI8
28.1
DNA.synthesis/chromatin structure
Inf
Inf
0.0147
0.039
Encodes a homolog of Replication Protein A that is involved in meiosis I in pollen mother cells. rpa1a mutants have a reduced number of class I crossovers. The protein is located in chromatin-associated foci in early leptotene and can be detected in these foci until late pachytene of meiosis I.
AT5G53980
Q9FN29
27.3.22
RNA.regulation of transcription.HB,Homeobox transcription factor family
Inf
Inf
0.0001
0.0005
Encodes a highly polar protein with more than 60% hydrophilic amino acid residues that is associated with the plasma membrane. It has limited secondary structure similarity to VAP-33 from Aplysia, which may be involved in membrane trafficking.
AT3G51680
Q9SCU0
26.22
misc.short chain dehydrogenase/reductase (SDR)
Inf
Inf
0.0186
0.048
Encodes a heme-binding protein located in the mitochondrial inner membrane that is involved in cytochrome c maturation.
AT1G61320
O64788
27.3.67
RNA.regulation of transcription.putative transcription regulator
Inf
Inf
0.0182
0.0472
Encodes a F-box protein induced by various biotic or abiotic stress.
AT4G11430
Q9M3G8
10.5.4
cell wall.cell wall proteins.HRGP
Inf
Inf
0.0287
0.0699
Encodes a cysteine-rich receptor-like protein kinase.
AT1G76480
Q9S712
35.2
not assigned.unknown
Inf
Inf
0
0.0001
Encodes a 3-hydroxy-3-methylglutaryl coenzyme A reductase, which is involved in melavonate biosynthesis and performs the first committed step in isoprenoid biosynthesis. Expression is activated in dark in leaf tissue but not controlled by light in the root (confine
AT3G09280
Q9SR35
35.2
not assigned.unknown
Inf
Inf
0
0
DHHC-type zinc finger family protein; FUNCTIONS IN: zinc ion binding; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, DHHC-type (InterPro:IPR001594); BEST Arabidopsis thaliana protein match is: DHHC-type zinc finger family protein (TAIR:AT5G04270.1); Has 5137 Blast hits to 5129 proteins in 251 species: Archae - 0; Bacteria - 0; Metazoa - 2212; Fungi - 755; Plants - 839; Viruses - 0; Other Eukaryotes - 1331 (source: NCBI BLink).

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT5G66390
Q9FJZ9
26.12
misc.peroxidases
4.31E-08
2.55E-07
AT2G22810
Q43309
17.5.1.1
hormone metabolism.ethylene.synthesis-degradation.1-aminocyclopropane-1-carboxylate synthase
4.49E-06
2.07E-05
key regulatory enzyme in the biosynthesis of the plant hormone ethylene. ACS4 is specifically induced by indoleacetic acid (IAA).
AT3G28060
F4IXT6
33.99
development.unspecified
0.013846443
0.033984861
nodulin MtN21-like transporter family protein
AT5G63350
Q9FGW7
35.2
not assigned.unknown
0.025967845
0.059251281
embryo defective 2746 (emb2746); FUNCTIONS IN: hydrolase activity, DNA binding, catalytic activity; INVOLVED IN: metabolic process, embryo development ending in seed dormancy; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), RNA-metabolising metallo-beta-lactamase (InterPro:IPR011108), Beta-lactamase-like (InterPro:IPR001279), MYB-like (InterPro:IPR017877); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT2G38250.1); 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).
AT1G05330
O23036
35.2
not assigned.unknown
0.035139805
0.077306949
Ankyrin repeat family protein; CONTAINS InterPro DOMAIN/s: Ankyrin repeat-containing domain (InterPro:IPR020683), Ankyrin repeat (InterPro:IPR002110); BEST Arabidopsis thaliana protein match is: Ankyrin repeat family protein (TAIR:AT2G24600.4); Has 23228 Blast hits to 12811 proteins in 577 species: Archae - 31; Bacteria - 1612; Metazoa - 12827; Fungi - 1604; Plants - 2793; Viruses - 138; Other Eukaryotes - 4223 (source: NCBI BLink).
AT2G22320
Q9SID6
35.2
not assigned.unknown
1.46E-06
7.18E-06
AMP-dependent synthetase and ligase family protein; FUNCTIONS IN: catalytic activity; INVOLVED IN: fatty acid biosynthetic process; EXPRESSED IN: 7 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: AMP-binding, conserved site (InterPro:IPR020845), AMP-dependent synthetase/ligase (InterPro:IPR000873); BEST Arabidopsis thaliana protein match is: AMP-dependent synthetase and ligase family protein (TAIR:AT4G23850.1); 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).
AT1G09550
F4I107
10.8.2
cell wall.pectin*esterases.acetyl esterase
0.001515622
0.004584467
AT3G25655
Q29PV4
33.99
development.unspecified
0.002239995
0.006577194
AT3G29615
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
0.011813449
0.02947801
AT3G44830
Q9FYC7
11.8.10
lipid metabolism.'exotics' (steroids, squalene etc).phosphatidylcholinesterol O-acyltransferase
3.04E-96
1.06E-93
AT3G44840
Q9FYC6
29.4
protein.postranslational modification
0.009189897
0.023547987
AT3G46140
Q9LX81
29.4
protein.postranslational modification
0.036189375
0.079286384
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