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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
AT5G64790
Q9LV98
26.4
misc.beta 1,3 glucan hydrolases
137.53851
7.10369
0
0.00005
member of WRKY Transcription Factor; Group II-c. Involved in jasmonic acid inducible defense responses.
AT3G43250
Q9LXK9
31.3
cell.cycle
141.28567
7.14247
0
0.00002
RING/U-box superfamily protein; FUNCTIONS IN: zinc ion binding; EXPRESSED IN: 11 plant structures; EXPRESSED DURING: 4 anthesis, petal differentiation and expansion stage; 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:AT5G20885.1); Has 6030 Blast hits to 6013 proteins in 252 species: Archae - 0; Bacteria - 0; Metazoa - 1395; Fungi - 381; Plants - 3597; Viruses - 16; Other Eukaryotes - 641 (source: NCBI BLink).
AT5G64905
Q8LAX3
20.1.3
stress.biotic.signalling
148.79659
7.2172
0
0.00001
RAB GTPase homolog H1A (RABH1a); FUNCTIONS IN: GTP binding, GTPase activity; INVOLVED IN: intracellular protein transport, signal transduction, nucleocytoplasmic transport, protein transport, small GTPase mediated signal transduction; LOCATED IN: mitochondrion; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Ran GTPase (InterPro:IPR002041), Ras (InterPro:IPR013753), Rab6-related (InterPro:IPR015600), Ras small GTPase, Ras type (InterPro:IPR003577), Small GTPase, Rho type (InterPro:IPR003578), Small GTP-binding protein (InterPro:IPR005225), Ras GTPase (InterPro:IPR001806), Small GTPase (InterPro:IPR020851), Ras small GTPase, Rab type (InterPro:IPR003579); BEST Arabidopsis thaliana protein match is: RAB GTPase homolog H1E (TAIR:AT5G10260.1).
AT2G02320
Q9ZVQ9
31.1
cell.organisation
194.20308
7.60142
0
0.00001
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).
AT5G52400
F4KG63
26.1
misc.cytochrome P450
198.19242
7.63076
0.00145
0.01048
Encodes a cytosolic heat shock protein AtHSP90.1. AtHSP90.1 interacts with disease resistance signaling components SGT1b and RAR1 and is required for RPS2-mediated resistance.
AT4G22030
O65451
29.5.11.4.3.2
protein.degradation.ubiquitin.E3.SCF.FBOX
232.12201
7.85874
0.00004
0.00062
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein; FUNCTIONS IN: methyltransferase activity; INVOLVED IN: metabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: Methyltransferase type 11 (InterPro:IPR013216); BEST Arabidopsis thaliana protein match is: S-adenosyl-L-methionine-dependent methyltransferases superfamily protein (TAIR:AT5G10830.1); Has 1214 Blast hits to 1209 proteins in 451 species: Archae - 2; Bacteria - 749; Metazoa - 75; Fungi - 155; Plants - 166; Viruses - 0; Other Eukaryotes - 67 (source: NCBI BLink).
AT4G04480
Q9XEC5
35.2
not assigned.unknown
267.76887
8.06484
0.0018
0.01246
Encodes a cysteine-rich receptor-like protein kinase.
AT4G18540
A0A1P8B8W3
35.2
not assigned.unknown
349.16977
8.44778
0
0.00009
ATSK (shaggy-like kinase) family member that encodes an AtSK protein involved in the cross-talk between auxin and brassinosteroid signaling pathways. BR-INSENSITIVE 2 mutant indicated that the BR-insensitive dwarf phenotype was due to a semidominant mutation in the BIN2. BIN2 is not allelic to BRI1. BIN2-mediated phosphorylation appears to promote BZR1 export from the nucleus.
AT1G35600
#N/A
28.1.1.5
DNA.synthesis/chromatin structure.retrotransposon/transposase.CACTA-like transposase
Inf
Inf
0.00253
0.01641
unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: plasma membrane; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 11 growth stages; Has 309 Blast hits to 256 proteins in 99 species: Archae - 0; Bacteria - 11; Metazoa - 192; Fungi - 12; Plants - 36; Viruses - 0; Other Eukaryotes - 58 (source: NCBI BLink).
AT1G51915
Q8L9S8
35.1
not assigned.no ontology
Inf
Inf
0.00112
0.00847
unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: stem, stamen; EXPRESSED DURING: 4 anthesis; Has 22 Blast hits to 22 proteins in 5 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 22; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G28180
Q9FZ92
27.1
RNA.processing
Inf
Inf
0.00606
0.03319
unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G12340.1); Has 166 Blast hits to 162 proteins in 36 species: Archae - 0; Bacteria - 2; Metazoa - 15; Fungi - 5; Plants - 124; Viruses - 0; Other Eukaryotes - 20 (source: NCBI BLink).
AT1G44941
B3H6B3
35.2
not assigned.unknown
Inf
Inf
0.00028
0.00274
transposable element gene; similar to unknown protein [Arabidopsis thaliana] (TAIR:AT5G28480.1); similar to Ulp1 protease family protein [Arabidopsis thaliana] (TAIR:AT3G42580.1); similar to Ulp1 protease family protein [Arabidopsis thaliana] (TAIR:AT2G12100.1); similar to Ulp1 protease family protein [Brassica oleracea] (GB:ABD64941.1); contains InterPro domain Peptidase C48, SUMO/Sentrin/Ubl1; (InterPro:IPR003653); contains InterPro domain Collagen triple helix repeat; (InterPro:IPR008160)

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT2G18010
Q9SL45
17.2.3
hormone metabolism.auxin.induced-regulated-responsive-activated
0
#NAME?
0
0.0002
Haloacid dehalogenase-like hydrolase (HAD) superfamily protein; FUNCTIONS IN: hydrolase activity; EXPRESSED IN: 13 plant structures; EXPRESSED DURING: LP.04 four leaves visible, 4 anthesis, petal differentiation and expansion stage; CONTAINS InterPro DOMAIN/s: Pyrimidine 5-nucleotidase (InterPro:IPR010237), HAD-superfamily hydrolase, subfamily IA, variant 3 (InterPro:IPR006402); BEST Arabidopsis thaliana protein match is: Haloacid dehalogenase-like hydrolase (HAD) superfamily protein (TAIR:AT5G59480.1); Has 2327 Blast hits to 2327 proteins in 521 species: Archae - 22; Bacteria - 785; Metazoa - 0; Fungi - 147; Plants - 198; Viruses - 0; Other Eukaryotes - 1175 (source: NCBI BLink).
AT5G17740
Q9FN77
29.5.9
protein.degradation.AAA type
Inf
Inf
0.0312
0.0751
Encodes NADH:cytochrome (Cyt) b5 reductase that displayed strict specificity to NADH for the reduction of a recombinant Cyt b5 (AtB5-A), whereas no Cyt b5 reduction was observed when NADPH was used as the electron donor.
AT5G01490
Q945S5
34.21
transport.calcium
Inf
Inf
0
0
Encodes LecRKA4.2, a member of the lectin receptor kinase subfamily A4 (LecRKA4.1 At5g01540; LecRKA4.2 At5g01550; LecRKA4.3 At5g01560). Together with other members of the subfamily, functions redundantly in the negative regulation of ABA response in seed germination.
AT4G09590
Q9SST3
35.1
not assigned.no ontology
Inf
Inf
0
0
Encodes cytochrome c. Promoter directs preferential expression in vascular tissues of cotyledons, leaves, roots, and hypocotyls, and in anthers.
AT1G22810
O80542
27.3.3
RNA.regulation of transcription.AP2/EREBP, APETALA2/Ethylene-responsive element binding protein family
Inf
Inf
0.0202
0.0514
Encodes cytochrome c. Contains two site II (TGGGCC/T) elements, which interact with a TCP-domain transcription factor, and a downstream internal telomeric repeat, and are required for expression of the Cytc-1 gene. Promoter directs preferential expression in root and shoot meristems and in anthers.
AT1G31270
F4I9B6
35.2
not assigned.unknown
Inf
Inf
0.0022
0.0073
Encodes Argonaute gene that binds viral siRNAs and is involved in antiviral defense response. Regulates innate immunity.
AT1G68250
Q9C9G0
35.2
not assigned.unknown
Inf
Inf
0.0394
0.0916
Encodes an endonuclease ENDO2. ENDO2 purified from transgenic Arabidopsis digests RNA, ssDNA, and dsDNA, with a substrate preference for ssDNA and RNA. ENDO2 produced and purified from Nicotiana benthamiana expression showed no demonstrable endonuclease activity, either towards single stranded DNA or mismatches, in vitro.
AT3G18450
Q9LS45
35.1
not assigned.no ontology
Inf
Inf
0
0.0001
Encodes a TCP transcription factor, closely related to teosinte branched1, arrests axillary bud development and prevents axillary bud outgrowth.
AT5G06839
E3VNM4
27.3.35
RNA.regulation of transcription.bZIP transcription factor family
Inf
Inf
0
0.0001
Encodes a sulfotransferase that acts specifically on 11- and 12-hydroxyjasmonic acid. Transcript levels for this enzyme are increased by treatments with jasmonic acid (JA), 12-hydroxyJA, JA-isoleucine, and 12-oxyphytodienoic acid (a JA precursor).
AT1G55240
Q6NM31
35.2
not assigned.unknown
Inf
Inf
0
0
Encodes a SR spliceosome protein that is localized to nuclear specks, interacts with SR45 and the U1-70K protein of the U1 snRNP, has sequence similar to human SC35 protein. Barta et al (2010) have proposed a nomenclature for Serine/Arginine-Rich Protein Splicing Factors (SR proteins): Plant Cell. 2010, 22:2926.
AT4G19925
F4JU10
20.1.7
stress.biotic.PR-proteins
Inf
Inf
0.0011
0.004
Encodes a potassium ion transmembrane transporter. Also mediates cesium uptake when expressed in E. coli.
AT5G39580
Q9FKA4
26.12
misc.peroxidases
Inf
Inf
0
0.0001
Encodes a NAC-domain transcription factor. Positively regulates aging-induced cell death and senescence in leaves. This gene is upregulated in response to salt stress in wildtype as well as NTHK1 transgenic lines although in the latter case the induction was drastically reduced. It was also upregulated by ABA, ACC and NAA treatment, although in the latter two cases, the induction occurred relatively late when compared with NaCl or ABA treatments. Note: this protein (AtNAC6) on occasion has also been referred to as AtNAC2, not to be confused with the AtNAC2 found at locus AT3G15510.

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT5G27370
Q3E912
35.2
not assigned.unknown
0.011915214
0.029713968
AT5G29075
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
0.014004813
0.034322762
AT5G37140
F4K5W4
28.1
DNA.synthesis/chromatin structure
3.39E-13
3.26E-12
AT5G37750
F4K8L8
20.2.1
stress.abiotic.heat
3.04E-08
1.83E-07
AT5G39390
F4KEF0
30.2.12
signalling.receptor kinases.leucine rich repeat XII
0.003712113
0.010387734
AT5G41780
Q9FJ36
31.1
cell.organisation
0.0359629
0.078873575
AT5G52400
F4KG63
26.1
misc.cytochrome P450
8.48E-15
9.47E-14
AT5G52670
Q9LTF0
35.1
not assigned.no ontology
0.034926848
0.076899663
AT5G52700
Q9LTE7
35.1
not assigned.no ontology
0.000361885
0.001232868
AT5G59510
Q8LE84
33.99
development.unspecified
0.002075018
0.006125318
AT5G60350
Q5XUY1
35.2
not assigned.unknown
8.26E-10
5.83E-09
AT5G64890
Q9LV88
20.1.3
stress.biotic.signalling
0.000311856
0.001077032
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