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

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
AT2G32210	Q9SKX9	35.2	not assigned.unknown	33.67628	5.07366	0	0.00001	FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to cadmium ion; LOCATED IN: plasma membrane; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Prefoldin (InterPro:IPR009053); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G05320.3); Has 470429 Blast hits to 168274 proteins in 4282 species: Archae - 6896; Bacteria - 131956; Metazoa - 175525; Fungi - 33166; Plants - 25441; Viruses - 2243; Other Eukaryotes - 95202 (source: NCBI BLink).
AT2G18690	Q9ZV49	35.2	not assigned.unknown	33.98228	5.08671	0	0	Encodes an enzyme putatively involved in trehalose biosynthesis. The protein has a trehalose synthase (TPS)-like domain that may or may not be active as well as a trehalose phosphatase (TPP)-like domain.
AT1G14540	Q9LE15	26.9	misc.glutathione S transferases	34.14641	5.09366	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).
AT4G39670	Q8L7U7	35.2	not assigned.unknown	34.23376	5.09735	0	0.00001	Cupredoxin superfamily protein; FUNCTIONS IN: oxidoreductase activity, L-ascorbate oxidase activity, copper ion binding; INVOLVED IN: oxidation reduction; LOCATED IN: endomembrane system, extracellular region; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Multicopper oxidase, type 3 (InterPro:IPR011707), Multicopper oxidase, type 2 (InterPro:IPR011706), Cupredoxin (InterPro:IPR008972), Multicopper oxidase, copper-binding site (InterPro:IPR002355), Multicopper oxidase, type 1 (InterPro:IPR001117), L-ascorbate oxidase, plants (InterPro:IPR017760); BEST Arabidopsis thaliana protein match is: Plant L-ascorbate oxidase (TAIR:AT5G21100.1); Has 10346 Blast hits to 8779 proteins in 1558 species: Archae - 67; Bacteria - 4905; Metazoa - 456; Fungi - 3230; Plants - 1293; Viruses - 0; Other Eukaryotes - 395 (source: NCBI BLink).
AT1G61810	O80689	26.3	misc.gluco-, galacto- and mannosidases	34.23796	5.09752	0.00002	0.0003	Encodes a non-specific lipase that hydrolyzes phospholipids as well as galactolipids, at both sn-1 and sn-2 positions. Involved in basal jasmonic acid biosynthesis by releasing the precursor fatty acid from membrane lipids. Mutant plants were impacted in resistance to fungus B. cinerea.
AT2G02340	Q9ZVQ8	31.1	cell.organisation	34.23968	5.0976	0	0.00005	encodes a protein containing an F-box domain and physically interacts with SCF subunit SKP1/ASK1. The protein also exhibits similarity in sequence to phloem protein 2 (PP2) from cucumber.
AT5G65600	Q9LSL5	29.4	protein.postranslational modification	34.26079	5.09849	0	0.00005	ARM repeat superfamily protein; FUNCTIONS IN: ubiquitin-protein ligase activity, binding; INVOLVED IN: protein ubiquitination; LOCATED IN: ubiquitin ligase complex; CONTAINS InterPro DOMAIN/s: U box domain (InterPro:IPR003613), Armadillo-like helical (InterPro:IPR011989), Armadillo-type fold (InterPro:IPR016024); BEST Arabidopsis thaliana protein match is: ARM repeat superfamily protein (TAIR:AT3G49810.1); 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).
AT5G56960	Q9LTS4	27.3.6	RNA.regulation of transcription.bHLH,Basic Helix-Loop-Helix family	34.33565	5.10164	0	0.00003	unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 12 growth stages; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT4G26130.1); 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).
AT4G28460	Q1PE40	35.2	not assigned.unknown	34.39156	5.10398	0.00103	0.00795	member of Receptor kinase-like protein family
AT1G74080	Q9C9C8	27.3.25	RNA.regulation of transcription.MYB domain transcription factor family	34.43353	5.10574	0	0.00001	encodes a desulfoglucosinolate sulfotransferase, involved in the final step of glucosinolate core structure biosynthesis. Has a broad-substrate specificity with different desulfoglucosinolates, the best substrate is indole-3-methyl-dsGS, followed by benzyl-dsGS. Expression was induced by wounding, jasmonate and ethylene stimulates.
AT2G14290	Q9ZQ60	29.5.11.4.3.2	protein.degradation.ubiquitin.E3.SCF.FBOX	34.60829	5.11305	0.00001	0.00016	encodes a vacuolar sorting receptor
AT1G78410	Q8VYI5	35.1	not assigned.no ontology	34.74249	5.11863	0	0.00001	RING/U-box superfamily protein; FUNCTIONS IN: zinc ion binding; INVOLVED IN: N-terminal protein myristoylation; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type (InterPro:IPR001841); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT1G17145.1); Has 267 Blast hits to 267 proteins in 123 species: Archae - 0; Bacteria - 0; Metazoa - 19; Fungi - 154; Plants - 74; Viruses - 0; Other Eukaryotes - 20 (source: NCBI BLink).

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CT101:

AGI Gene code	Uniprot ID	Bin Code	Bin Name	FoldChange	log2FC	p-value	FDR adjusted p-value	Functional annotation
AT2G27270	Q9XIN4	35.2	not assigned.unknown	Inf	Inf	0	0.0001	F-box family protein; BEST Arabidopsis thaliana protein match is: F-box family protein (TAIR:AT2G36090.1); Has 105 Blast hits to 105 proteins in 13 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 105; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT5G67430	Q9FN10	17.5.1	hormone metabolism.ethylene.synthesis-degradation	Inf	Inf	0.0003	0.0011	Encodes zinc-finger protein. mRNA levels are elevated in response to low temperature, cold temperatures and high salt. The protein is localized to the nucleus and acts as a transcriptional repressor.
AT5G43410	Q9LSX0	17.5.2	hormone metabolism.ethylene.signal transduction	Inf	Inf	0.0184	0.0474	Encodes the electron transfer flavoprotein ETF beta, a putative subunit of the mitochondrial electron transfer flavoprotein complex (ETF alpha is At1g50940) in Arabidopsis. Mutations of the ETF beta gene result in accelerated senescence and early death compared to wild-type during extended darkness. Also involved in the catabolism of leucine and chlorophyll degradation pathway activated during darkness-induced carbohydrate deprivation.
AT2G39530	Q8GWD5	35.1	not assigned.no ontology	Inf	Inf	0	0	encodes the beta subunit of geranylgeranyl transferase (GGT-IB), involved in both ABA-mediated and auxin signaling pathways.
AT3G15960	F4J1D9	28.2	DNA.repair	Inf	Inf	0.0002	0.0007	Encodes sulfate transporter Sultr3;4.
AT2G30750	O49340	26.1	misc.cytochrome P450	392.8837	8.618	0	0	putative cytochrome P450
AT1G59950	Q1PFI5	16.8.2	secondary metabolism.flavonoids.chalcones	397.4473	8.6346	0	0	Matrixin family protein; FUNCTIONS IN: metallopeptidase activity, metalloendopeptidase activity, zinc ion binding; INVOLVED IN: proteolysis, metabolic process; LOCATED IN: plasma membrane, anchored to membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase M10, metallopeptidase (InterPro:IPR001818), Peptidoglycan binding-like (InterPro:IPR002477), Peptidase M10A, cysteine switch, zinc binding site (InterPro:IPR021158), Peptidase M10A, matrix metallopeptidase (InterPro:IPR021190), Peptidase, metallopeptidase (InterPro:IPR006026); BEST Arabidopsis thaliana protein match is: Matrixin family protein (TAIR:AT1G24140.1); Has 2665 Blast hits to 2469 proteins in 210 species: Archae - 2; Bacteria - 119; Metazoa - 2216; Fungi - 6; Plants - 186; Viruses - 42; Other Eukaryotes - 94 (source: NCBI BLink).
AT3G54150	A0A1I9LLF7	33.99	development.unspecified	400.5927	8.646	0	0	SAC3/GANP/Nin1/mts3/eIF-3 p25 family; CONTAINS InterPro DOMAIN/s: SAC3/GANP/Nin1/mts3/eIF-3 p25 (InterPro:IPR005062); BEST Arabidopsis thaliana protein match is: SAC3/GANP/Nin1/mts3/eIF-3 p25 family (TAIR:AT3G06290.1); Has 539 Blast hits to 535 proteins in 177 species: Archae - 0; Bacteria - 0; Metazoa - 197; Fungi - 200; Plants - 96; Viruses - 0; Other Eukaryotes - 46 (source: NCBI BLink).
AT1G69920	Q6NMS0	26.9	misc.glutathione S transferases	423.0326	8.7246	0	0	Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).
AT3G23550	Q9LUH3	34.99	transport.misc	430.177	8.7488	0	0	Ubiquitin-like superfamily protein; CONTAINS InterPro DOMAIN/s: UBX (InterPro:IPR001012); BEST Arabidopsis thaliana protein match is: structural constituent of ribosome (TAIR:AT4G14250.1); Has 105 Blast hits to 100 proteins in 22 species: Archae - 0; Bacteria - 0; Metazoa - 4; Fungi - 0; Plants - 91; Viruses - 0; Other Eukaryotes - 10 (source: NCBI BLink).
AT1G11610	Q9SAB6	26.1	misc.cytochrome P450	433.8138	8.7609	0	0	putative cytochrome P450
AT1G53625	Q9LPH9	35.2	not assigned.unknown	436.5637	8.77	0	0	hydroxyproline-rich glycoprotein family protein; Has 15375 Blast hits to 12179 proteins in 920 species: Archae - 8; Bacteria - 1425; Metazoa - 5915; Fungi - 2848; Plants - 1527; Viruses - 230; Other Eukaryotes - 3422 (source: NCBI BLink).

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Te:

AGI Gene code	Uniprot ID	Bin Code	Bin Name	p-value	FDR adjusted p-value	Functional annotation
AT1G54955	Q9C7L9	35.2	not assigned.unknown	0.042200522	0.090847636	Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family; CONTAINS InterPro DOMAIN/s: Late embryogenesis abundant protein, group 2 (InterPro:IPR004864); BEST Arabidopsis thaliana protein match is: Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family (TAIR:AT5G21130.1); Has 1062 Blast hits to 1061 proteins in 28 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 1062; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT2G40113	Q58FY6	35.2	not assigned.unknown	0.000166194	0.000600313	Heavy metal transport/detoxification superfamily protein ; FUNCTIONS IN: metal ion binding; INVOLVED IN: metal ion transport; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Heavy metal transport/detoxification protein (InterPro:IPR006121); BEST Arabidopsis thaliana protein match is: Heavy metal transport/detoxification superfamily protein (TAIR:AT2G36950.1); Has 4632 Blast hits to 3385 proteins in 434 species: Archae - 9; Bacteria - 451; Metazoa - 988; Fungi - 256; Plants - 2406; Viruses - 0; Other Eukaryotes - 522 (source: NCBI BLink).
AT1G06137	F4IBZ9	35.2	not assigned.unknown	0.037606087	0.082036151	heat shock protein 70 (Hsp 70) family protein; FUNCTIONS IN: ATP binding; INVOLVED IN: protein folding; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: 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:AT1G79920.1); Has 25020 Blast hits to 24886 proteins in 4391 species: Archae - 151; Bacteria - 11311; Metazoa - 3542; Fungi - 1480; Plants - 1013; Viruses - 97; Other Eukaryotes - 7426 (source: NCBI BLink).
AT2G02310	Q9ZVR0	31.1	cell.organisation	1.28E-09	8.87E-09	GRAS family transcription factor; CONTAINS InterPro DOMAIN/s: Transcription factor GRAS (InterPro:IPR005202); BEST Arabidopsis thaliana protein match is: GRAS family transcription factor (TAIR:AT5G66770.1); Has 2907 Blast hits to 2857 proteins in 413 species: Archae - 0; Bacteria - 24; Metazoa - 184; Fungi - 97; Plants - 2517; Viruses - 13; Other Eukaryotes - 72 (source: NCBI BLink).
AT1G36605	#N/A	28.1.1.3	DNA.synthesis/chromatin structure.retrotransposon/transposase.copia-like retrotransposon	0.000939643	0.00296558	Galactose oxidase/kelch repeat superfamily protein; CONTAINS InterPro DOMAIN/s: Galactose oxidase/kelch, beta-propeller (InterPro:IPR011043), Kelch repeat type 1 (InterPro:IPR006652), Kelch related (InterPro:IPR013089), Kelch-type beta propeller (InterPro:IPR015915); BEST Arabidopsis thaliana protein match is: Galactose oxidase/kelch repeat superfamily protein (TAIR:AT1G14330.1); Has 7278 Blast hits to 4161 proteins in 259 species: Archae - 4; Bacteria - 397; Metazoa - 5328; Fungi - 9; Plants - 1063; Viruses - 147; Other Eukaryotes - 330 (source: NCBI BLink).
AT3G02270	Q9SRU3	29.2.3	protein.synthesis.initiation	6.99E-06	3.13E-05	FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Lipopolysaccharide-modifying protein (InterPro:IPR006598), Protein of unknown function DUF821, CAP10-like (InterPro:IPR008539); BEST Arabidopsis thaliana protein match is: Arabidopsis thaliana protein of unknown function (DUF821) (TAIR:AT3G48980.1); 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).
AT1G26400	Q9FZC6	26.8	misc.nitrilases, *nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases	1.05E-15	1.28E-14	Family of unknown function (DUF577); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF577 (InterPro:IPR007598); BEST Arabidopsis thaliana protein match is: Family of unknown function (DUF577) (TAIR:AT5G37410.1); Has 76 Blast hits to 50 proteins in 3 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 76; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).
AT1G30814	B6EUC0	35.2	not assigned.unknown	1.57E-21	2.91E-20	Exostosin family protein; FUNCTIONS IN: catalytic activity; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system, membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Exostosin-like (InterPro:IPR004263); BEST Arabidopsis thaliana protein match is: exostosin family protein (TAIR:AT3G45400.1); Has 1193 Blast hits to 1185 proteins in 64 species: Archae - 0; Bacteria - 4; Metazoa - 45; Fungi - 4; Plants - 1081; Viruses - 0; Other Eukaryotes - 59 (source: NCBI BLink).
AT1G14420	Q9M9S2	10.6.3	cell wall.degradation.pectate lyases and polygalacturonases	0.002370732	0.006924286	double-stranded DNA-binding family protein; FUNCTIONS IN: double-stranded DNA binding, DNA binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: DNA-binding TFAR19-related protein (InterPro:IPR002836); Has 679 Blast hits to 679 proteins in 318 species: Archae - 256; Bacteria - 0; Metazoa - 134; Fungi - 121; Plants - 56; Viruses - 0; Other Eukaryotes - 112 (source: NCBI BLink).
AT1G31270	F4I9B6	35.2	not assigned.unknown	0.001468517	0.00445821	DNA-directed RNA polymerases; FUNCTIONS IN: DNA-directed RNA polymerase activity; INVOLVED IN: transcription; LOCATED IN: cellular_component unknown; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA polymerase Rpb7, N-terminal (InterPro:IPR005576); Has 67 Blast hits to 67 proteins in 26 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 6; Plants - 48; Viruses - 0; Other Eukaryotes - 13 (source: NCBI BLink).
AT1G20740	F4HUN7	35.2	not assigned.unknown	0.006153005	0.01638759	DNA/RNA-binding protein Kin17, conserved region; FUNCTIONS IN: zinc ion binding; INVOLVED IN: biological_process unknown; LOCATED IN: intracellular; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, C2H2-like (InterPro:IPR015880), DNA/RNA-binding protein Kin17, conserved region (InterPro:IPR019447), KOW (InterPro:IPR005824); BEST Arabidopsis thaliana protein match is: DNA/RNA-binding protein Kin17, conserved region (TAIR:AT5G51795.1); Has 1885 Blast hits to 1561 proteins in 251 species: Archae - 4; Bacteria - 25; Metazoa - 715; Fungi - 242; Plants - 160; Viruses - 13; Other Eukaryotes - 726 (source: NCBI BLink).
AT2G02340	Q9ZVQ8	31.1	cell.organisation	2.10E-07	1.15E-06	DNA glycosylase superfamily protein; FUNCTIONS IN: catalytic activity; INVOLVED IN: DNA repair, base-excision repair; LOCATED IN: chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA glycosylase (InterPro:IPR011257), HhH-GPD domain (InterPro:IPR003265); BEST Arabidopsis thaliana protein match is: DNA glycosylase superfamily protein (TAIR:AT1G19480.2); Has 4313 Blast hits to 4311 proteins in 953 species: Archae - 62; Bacteria - 2052; Metazoa - 1; Fungi - 144; Plants - 80; Viruses - 0; Other Eukaryotes - 1974 (source: NCBI BLink).

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