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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
AT3G28210
Q67YE6
27.3.11
RNA.regulation of transcription.C2H2 zinc finger family
29.04456
4.8602
0.00002
0.00038
Leucine-rich repeat protein kinase family protein; FUNCTIONS IN: protein serine/threonine kinase activity, kinase activity, ATP binding; INVOLVED IN: transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation; LOCATED IN: chloroplast, plasma membrane, membrane; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Protein kinase, catalytic domain (InterPro:IPR000719), Leucine-rich repeat-containing N-terminal domain, type 2 (InterPro:IPR013210), Leucine-rich repeat (InterPro:IPR001611), Serine-threonine/tyrosine-protein kinase (InterPro:IPR001245), Protein kinase-like domain (InterPro:IPR011009); BEST Arabidopsis thaliana protein match is: Leucine-rich repeat protein kinase family protein (TAIR:AT1G27190.1); Has 101664 Blast hits to 59951 proteins in 2302 species: Archae - 40; Bacteria - 6408; Metazoa - 16028; Fungi - 2446; Plants - 69126; Viruses - 161; Other Eukaryotes - 7455 (source: NCBI BLink).
AT5G44990
Q9FL98
35.2
not assigned.unknown
29.12763
4.86432
0.00015
0.00172
Encodes a member of WRKY Transcription Factor (Group II-e) that confers resistance to tobacco ringspot nepovirus.
AT2G15490
Q7Y232
26.2
misc.UDP glucosyl and glucoronyl transferases
29.12915
4.86439
0.0001
0.00125
chloroplast protein similar to prokaryotic thioredoxin.
AT1G22400
Q9SK82
17.4.1
hormone metabolism.cytokinin.synthesis-degradation
29.34802
4.87519
0
0.00011
other RNA
AT3G02800
Q681Z2
35.2
not assigned.unknown
29.47862
4.8816
0
0.00007
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).
AT4G17500
O80337
17.5.2
hormone metabolism.ethylene.signal transduction
29.54027
4.88461
0
0.00004
Bax inhibitor-1 family protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: negative regulation of apoptosis, apoptosis, regulation of apoptosis; LOCATED IN: integral to membrane; CONTAINS InterPro DOMAIN/s: Inhibitor of apoptosis-promoting Bax1 related (InterPro:IPR006214), Bax inhibitor 1, conserved site (InterPro:IPR006213); BEST Arabidopsis thaliana protein match is: BAX inhibitor 1 (TAIR:AT5G47120.1); Has 1499 Blast hits to 1499 proteins in 627 species: Archae - 0; Bacteria - 825; Metazoa - 347; Fungi - 90; Plants - 93; Viruses - 11; Other Eukaryotes - 133 (source: NCBI BLink).
AT1G69930
Q9CAS6
26.9
misc.glutathione S transferases
29.73092
4.89389
0.00048
0.00427
type 2A serine/threonine protein phosphatase (PP2A) mRNA,
AT1G26420
Q9FZC8
26.8
misc.nitrilases, *nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases
29.77813
4.89618
0
0
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; BEST Arabidopsis thaliana protein match is: ELM2 domain-containing protein (TAIR:AT2G03470.1); Has 161 Blast hits to 161 proteins in 17 species: Archae - 0; Bacteria - 0; Metazoa - 1; Fungi - 4; Plants - 156; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT3G15518
Q8GYA5
35.2
not assigned.unknown
29.93854
4.90393
0
0
unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G52720.1); Has 61 Blast hits to 61 proteins in 13 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 61; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G02400
Q9FZ21
17.6.1.13
hormone metabolism.gibberelin.synthesis-degradation.GA2 oxidase
30.23558
4.91818
0
0.00007
Encodes a gibberellin 2-oxidase that acts on C19 gibberellins but not C20 gibberellins.
AT4G04510
Q9XEC8
30.2.17
signalling.receptor kinases.DUF 26
30.3632
4.92425
0
0
transposable element gene; non-LTR retrotransposon family (LINE), has a 1.0e-19 P-value blast match to GB:NP_038602 L1 repeat, Tf subfamily, member 18 (LINE-element) (Mus musculus)
AT1G09080
Q8H1B3
20.2.1
stress.abiotic.heat
30.37344
4.92474
0.00001
0.00012
BIP3; FUNCTIONS IN: ATP binding; INVOLVED IN: protein folding, response to heat, pollen tube growth; LOCATED IN: endoplasmic reticulum lumen; EXPRESSED IN: 10 plant structures; EXPRESSED DURING: 10 growth stages; CONTAINS InterPro DOMAIN/s: Heat shock protein 70, conserved site (InterPro:IPR018181), Heat shock protein Hsp70 (InterPro:IPR001023), Heat shock protein 70 (InterPro:IPR013126); BEST Arabidopsis thaliana protein match is: heat shock protein 70 (Hsp 70) family protein (TAIR:AT5G28540.1); Has 36561 Blast hits to 35981 proteins in 4871 species: Archae - 169; Bacteria - 17528; Metazoa - 4151; Fungi - 1824; Plants - 1283; Viruses - 337; Other Eukaryotes - 11269 (source: NCBI BLink).

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT3G19615
A8MR54
35.1
not assigned.no ontology
228.6361
7.8369
0
0
Guanine nucleotide exchange factor VPS9a. Can ctivate all Rab5 members to GTP-bound forms in vitro. Required for embryogenesis. Regulates the localization of ARA7 and ARA6. Involved in postembryonic root development.
AT4G08770
Q9LDN9
26.12
misc.peroxidases
230.1897
7.8467
0
0
Calcium binding protein involved in cryptochrome and phytochrome coaction
AT5G59490
Q7XJ55
35.1
not assigned.no ontology
231.0713
7.8522
0
0
2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein; CONTAINS InterPro DOMAIN/s: Oxoglutarate/iron-dependent oxygenase (InterPro:IPR005123); BEST Arabidopsis thaliana protein match is: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein (TAIR:AT5G59540.1); 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).
AT1G15520
Q9M9E1
34.16
transport.ABC transporters and multidrug resistance systems
234.395
7.8728
0
0
ABC transporter family involved in ABA transport and resistance to lead. Localizes to plasma membrane. Upregulated by lead. Expressed in leaves, flowers, stomata and roots.
AT1G19020
Q8VYY6
35.2
not assigned.unknown
235.4859
7.8795
0
0
unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT3G48180.1); Has 88 Blast hits to 88 proteins in 15 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 88; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT2G15490
Q7Y232
26.2
misc.UDP glucosyl and glucoronyl transferases
236.8497
7.8878
0
0
chloroplast protein similar to prokaryotic thioredoxin.
AT1G05880
Q84RQ9
29.5.11.4.2
protein.degradation.ubiquitin.E3.RING
243.976
7.9306
0
0
Encodes ARI12 (ARIADNE 12). ARI12 belongs to a family of ?RING between RING fingers' (RBR) domain proteins with E3 ligase activity. Expression of ARI12 is induced by UV-B exposure.
AT2G37430
Q9SLD4
27.3.11
RNA.regulation of transcription.C2H2 zinc finger family
245.8068
7.9414
0
0
Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger domain; FUNCTIONS IN: DNA binding, zinc ion binding; INVOLVED IN: regulation of transcription, DNA-dependent; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Acyl-CoA N-acyltransferase (InterPro:IPR016181), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger domain (TAIR:AT3G53680.1); 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).
AT5G41730
Q9FGG5
35.2
not assigned.unknown
250.4292
7.9683
0
0
Disease resistance protein (TIR-NBS-LRR class) family; FUNCTIONS IN: transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding; INVOLVED IN: signal transduction, defense response, apoptosis, innate immune response; LOCATED IN: intrinsic to membrane; CONTAINS InterPro DOMAIN/s: ATPase, AAA+ type, core (InterPro:IPR003593), NB-ARC (InterPro:IPR002182), Toll-Interleukin receptor (InterPro:IPR000157), Disease resistance protein (InterPro:IPR000767); BEST Arabidopsis thaliana protein match is: Disease resistance protein (TIR-NBS-LRR class) family (TAIR:AT5G41740.1); 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).
AT2G02320
Q9ZVQ9
31.1
cell.organisation
256.3502
8.002
0
0
phloem protein 2-B8 (PP2-B8); 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-B7 (TAIR:AT2G02320.1); Has 560 Blast hits to 546 proteins in 38 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 560; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT2G34500
O64697
26.1
misc.cytochrome P450
257.7518
8.0098
0
0
CONTAINS InterPro DOMAIN/s: Herpesvirus UL139, cytomegalovirus (InterPro:IPR021042); 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).
AT1G52200
Q9M815
35.1
not assigned.no ontology
261.7195
8.0319
0
0
Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. Unlike several other PDI family members, transcript levels for this gene are not up-regulated in response to three different chemical inducers of ER stress (dithiothreitol, beta-mercaptoethanol, and tunicamycin).

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT5G64750
Q9FGF8
27.3.3
RNA.regulation of transcription.AP2/EREBP, APETALA2/Ethylene-responsive element binding protein family
1.67E-89
4.89E-87
AT3G25250
Q9LSF1
29.4
protein.postranslational modification
9.40E-35
3.64E-33
AT1G44130
Q9C6Y5
29.5
protein.degradation
3.94E-25
9.16E-24
Cation efflux family protein; FUNCTIONS IN: cation transmembrane transporter activity, efflux transmembrane transporter activity; INVOLVED IN: cation transport, transmembrane transport; LOCATED IN: membrane; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Cation efflux protein (InterPro:IPR002524); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G38380.1); 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).
AT5G19880
P59120
26.12
misc.peroxidases
6.47E-12
5.60E-11
AT4G11655
Q3EA54
35.1
not assigned.no ontology
8.21E-20
1.35E-18
AT3G53075
B3H6K7
26.3
misc.gluco-, galacto- and mannosidases
1.34E-68
2.22E-66
AT2G35980
Q9SJ52
33.99
development.unspecified
6.83E-31
2.19E-29
SBP (S-ribonuclease binding protein) family protein; CONTAINS InterPro DOMAIN/s: S-ribonuclease binding protein, SBP1, pollen (InterPro:IPR017066); BEST Arabidopsis thaliana protein match is: S-ribonuclease binding protein 1 (TAIR:AT1G45976.1); Has 975 Blast hits to 929 proteins in 127 species: Archae - 2; Bacteria - 21; Metazoa - 288; Fungi - 13; Plants - 377; Viruses - 18; Other Eukaryotes - 256 (source: NCBI BLink).
AT4G18540
A0A1P8B8W3
35.2
not assigned.unknown
1.14E-25
2.74E-24
AT1G51890
C0LGG6
30.2.99
signalling.receptor kinases.misc
2.85E-53
2.75E-51
transposable element gene; copia-like retrotransposon family, has a 0. P-value blast match to GB:CAA72989 open reading frame 1 (Ty1_Copia-element) (Brassica oleracea)
AT5G05300
Q9FLC4
35.2
not assigned.unknown
1.87E-105
8.62E-103
AT4G21390
O81906
30.2.24
signalling.receptor kinases.S-locus glycoprotein like
5.22E-25
1.21E-23
AT2G37430
Q9SLD4
27.3.11
RNA.regulation of transcription.C2H2 zinc finger family
6.84E-11
5.40E-10
unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to karrikin; LOCATED IN: endomembrane system; EXPRESSED IN: cotyledon, hypocotyl, leaf; EXPRESSED DURING: LP.04 four leaves visible; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT2G23270.1); 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).
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