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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
AT2G21910
Q9SJ08
26.1
misc.cytochrome P450
54.62566
5.77151
0.00063
0.0053
A paternally expressed imprinted gene.
AT1G70170
O04529
29.5.7
protein.degradation.metalloprotease
54.89167
5.77852
0
0.00007
Unknown gene
AT2G35970
Q9SJ53
35.1
not assigned.no ontology
54.95072
5.78007
0.0001
0.00126
Encodes a protein whose sequence is similar to tobacco hairpin-induced gene (HIN1) and Arabidopsis non-race specific disease resistance gene (NDR1). Expression of this gene is induced by cucumber mosaic virus, spermine and during senescence. The gene product is localized to the chloroplast.
AT1G19020
Q8VYY6
35.2
not assigned.unknown
55.46616
5.79354
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).
AT4G31950
O49396
26.1
misc.cytochrome P450
55.52762
5.79513
0.00791
0.04117
member of CYP82C
AT5G43650
Q9FIX5
27.3.6
RNA.regulation of transcription.bHLH,Basic Helix-Loop-Helix family
55.78859
5.8019
0.00216
0.01449
pfkB-like carbohydrate kinase family protein; FUNCTIONS IN: kinase activity, ribokinase activity; INVOLVED IN: D-ribose metabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Carbohydrate/purine kinase (InterPro:IPR011611), Ribokinase (InterPro:IPR002139), Carbohydrate/puine kinase, PfkB, conserved site (InterPro:IPR002173); BEST Arabidopsis thaliana protein match is: pfkB-like carbohydrate kinase family protein (TAIR:AT4G28706.3); 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).
AT2G34500
O64697
26.1
misc.cytochrome P450
56.28085
5.81457
0
0.00007
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).
AT5G37490
Q5PNY6
17.6.2
hormone metabolism.gibberelin.signal transduction
56.95015
5.83163
0.00015
0.0017
ALWAYS EARLY 4 (ALY4); FUNCTIONS IN: nucleotide binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: nucleolus; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: RNA-binding (RRM/RBD/RNP motifs) family protein (TAIR:AT1G66260.2); Has 8810 Blast hits to 7454 proteins in 559 species: Archae - 0; Bacteria - 678; Metazoa - 4105; Fungi - 1555; Plants - 1582; Viruses - 59; Other Eukaryotes - 831 (source: NCBI BLink).
AT1G17147
Q1G3U8
35.2
not assigned.unknown
57.11598
5.83582
0.00005
0.0007
VQ motif-containing protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: VQ (InterPro:IPR008889); BEST Arabidopsis thaliana protein match is: VQ motif-containing protein (TAIR:AT1G78410.1); 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).
AT1G69920
Q6NMS0
26.9
misc.glutathione S transferases
57.39298
5.8428
0.00002
0.00038
Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).
AT3G54150
A0A1I9LLF7
33.99
development.unspecified
61.53704
5.94338
0
0.00002
Encodes a member of Synaptobrevin -like protein family. VAMP727 is a R-SNARE and interacts with SYP22/VTI11/SYP51. It is required for trafficking of storage proteins to the protein storage vacuoles (PSV) and also for PSV organization and biogenesis. Loss of function mutations have no phenotype but double mutants with SYP22 are embryo lethal.
AT1G13480
Q56Y29
35.2
not assigned.unknown
61.64544
5.94592
0
0.00001
Protein of unknown function (DUF1262); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1262 (InterPro:IPR010683); BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF1262) (TAIR:AT1G13520.1); Has 111 Blast hits to 104 proteins in 9 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 111; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).

CT101:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
FoldChange
log2FC
p-value
FDR adjusted p-value
Functional annotation
AT5G65340
Q9FKQ4
35.2
not assigned.unknown
0
#NAME?
0.0094
0.0265
AT5G07200
Q39112
17.6.1.11
hormone metabolism.gibberelin.synthesis-degradation.GA20 oxidase
0
#NAME?
0.0041
0.0126
AT1G78520
F4IA92
26.4
misc.beta 1,3 glucan hydrolases
0
#NAME?
0.0011
0.004
unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G40600.1); Has 43 Blast hits to 43 proteins in 15 species: Archae - 0; Bacteria - 0; Metazoa - 3; Fungi - 0; Plants - 39; Viruses - 0; Other Eukaryotes - 1 (source: NCBI BLink).
AT2G01026
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0
0
transposable element gene; gypsy-like retrotransposon family, has a 3.0e-150 P-value blast match to GB:AAD27547 polyprotein (Gypsy_Ty3-element) (Oryza sativa subsp. indica)
AT2G01028
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0.0001
0.0003
transposable element gene; gypsy-like retrotransposon family, has a 1.7e-215 P-value blast match to GB:AAD11615 prpol (gypsy_Ty3-element) (Zea mays)
AT2G09910
Q0WMF0
35.2
not assigned.unknown
Inf
Inf
0.0037
0.0116
transposable element gene; gypsy-like retrotransposon family, has a 1.5e-132 P-value blast match to GB:AAD19359 polyprotein (gypsy_Ty3-element) (Sorghum bicolor)
AT2G01024
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0.0188
0.0484
transposable element gene; gypsy-like retrotransposon family, has a 0. P-value blast match to GB:AAD27547 polyprotein (Gypsy_Ty3-element) (Oryza sativa subsp. indica)
AT2G09920
#N/A
28.1.1.1
DNA.synthesis/chromatin structure.retrotransposon/transposase.gypsy-like retrotransposon
Inf
Inf
0.0293
0.071
transposable element gene; gypsy-like retrotransposon family, has a 0. P-value blast match to GB:AAD27547 polyprotein (Gypsy_Ty3-element) (Oryza sativa subsp. indica)
AT1G36600
#N/A
28.1.1.3
DNA.synthesis/chromatin structure.retrotransposon/transposase.copia-like retrotransposon
Inf
Inf
0
0
transposable element gene; copia-like retrotransposon family, has a 2.0e-12 P-value blast match to gb|AAG52949.1| gag/pol polyprotein (Endovir1-1) (Arabidopsis thaliana) (Ty1_Copia-family)
AT5G05290
Q38866
10.7
cell wall.modification
Inf
Inf
0.0199
0.0508
TLC ATP/ADP transporter; Has 647 Blast hits to 643 proteins in 131 species: Archae - 0; Bacteria - 265; Metazoa - 0; Fungi - 0; Plants - 52; Viruses - 0; Other Eukaryotes - 330 (source: NCBI BLink).
AT1G28375
Q9SGN5
35.2
not assigned.unknown
Inf
Inf
0.0185
0.0476
This gene is predicted to encode a protein involved in negatively regulating salicylic acid-related defense responses and cell death programs. nsl1 mutants develop necrotic lesions spontaneously and show other features of a defense response, such as higher levels of SA and disease resistance-related transcripts, in the absence of a biotic stimulus. The NSL1 protein is predicted to have a MACPF domain, found in proteins that form a transmembrane pore in mammalian immune responses. NSL1 transcript levels do not appear to change in response to biotic stresses, but are elevated by cycloheximide in seedlings, and by sodium chloride in roots.
AT4G39675
Q8LEP7
35.2
not assigned.unknown
Inf
Inf
0.0186
0.0479
Tetratricopeptide repeat (TPR)-like superfamily protein; FUNCTIONS IN: 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: Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026); Has 285 Blast hits to 281 proteins in 117 species: Archae - 4; Bacteria - 22; Metazoa - 124; Fungi - 26; Plants - 36; Viruses - 0; Other Eukaryotes - 73 (source: NCBI BLink).

Te:

AGI Gene code
Uniprot ID
Bin Code
Bin Name
p-value
FDR adjusted p-value
Functional annotation
AT4G31960
O49395
35.2
not assigned.unknown
7.39E-11
5.81E-10
AT4G34210
O49484
29.5.11.4.3.1
protein.degradation.ubiquitin.E3.SCF.SKP
1.39E-08
8.66E-08
AT4G34470
O65674
29.5.11.4.3.1
protein.degradation.ubiquitin.E3.SCF.SKP
3.95E-08
2.35E-07
AT4G37780
F4JSU0
27.3.25
RNA.regulation of transcription.MYB domain transcription factor family
0.031469861
0.070208078
AT4G39020
Q9SVJ1
35.1
not assigned.no ontology
0.001378725
0.004210318
AT4G39610
#N/A
35.2
not assigned.unknown
3.90E-28
1.07E-26
AT5G01210
Q9LFB5
16.2
secondary metabolism.phenylpropanoids
0.023291076
0.053760108
AT5G01540
Q9M021
30.2.99
signalling.receptor kinases.misc
6.68E-07
3.44E-06
AT5G03590
Q9LZS9
26.28
misc.GDSL-motif lipase
0.022097713
0.051365149
AT5G06839
E3VNM4
27.3.35
RNA.regulation of transcription.bZIP transcription factor family
1.41E-09
9.71E-09
AT5G12340
Q94CK8
35.2
not assigned.unknown
7.14E-09
4.60E-08
AT5G13150
Q9FY95
27.3.99
RNA.regulation of transcription.unclassified
1.65E-05
7.01E-05
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