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Whole transcriptome analysis of smoke-water treated maize seeds. Endre Sebestyén Agricultural Research Institute of the Hungarian Academy of Sciences H-2462, Martonvásár, Brunszvik út 2. Introduction. Smoke released from burning vegetation contains a chemical signal, which : - PowerPoint PPT Presentation
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Whole transcriptome Whole transcriptome analysis of smoke-water analysis of smoke-water treated maize seedstreated maize seedsEndre Sebestyén
Agricultural Research Institute of the Hungarian Academy of SciencesH-2462, Martonvásár, Brunszvik út 2.
IntroductionIntroductionSmoke released from burning
vegetation contains a chemical signal, which :◦ is a germination cue◦breaks dormancy and promotes seed
germination◦also improves seedling vigour
Effect on plants varies◦Fire-prone species (Australia, South A.)◦Non fire-prone species◦Crops
3-methyl-2H-furo[2,3-c]pyran-2-one
OOO
Experimental layoutExperimental layout Maize microarray with 46k features from
maizearray.org◦ Chip annotation is incomplete◦ Funding for the project ended
Samples◦ Germinating maize embryos
3, 6, 9, 12, 24, 27h control vs smoke
1.5, 3, 6, 9, 12, 24, 27h control vs butenolide butenolide vs smoke
◦ Early postgermination phase 24, 48h smoke vs control
The molecular background of smoke action is largely unknown
Postgermination phasePostgermination phase24h results (1121/711
up/downregulated)◦Sulfiredoxin-like protein, LRR-receptor like
kinase 2, ubiquitin activating enzyme, etc◦Lots of genes without annotation
48h results (765/887 up/downregulated)◦Auxin regulated protein, zinc finger protein,
etc◦Also lots of genes without function
Validated by rtPCRWhat about the overall process?
Gene Ontology analysisGene Ontology analysisGene Ontology
◦Biological process◦Molecular function◦Cellular component
GeneMerge software◦Modified version to speed up analysis◦1,5h -> 1-2min◦Search for significantly
overrepresented GO terms in the up- and downregulated gene lists
Gene Ontology analysisGene Ontology analysis
Promoter analysisPromoter analysisBLAST search with available cDNA
sequences against available maize genome sequence
Extract promoters up to 1500 bp upstream
Search for known transcription factor binding sites (TFBS)◦TRANSFAC 12.1◦834 experimentally verified plant
TFBS
Germinating phaseGerminating phaseSimilar results as in the 24, 48h
experiments, based on GO an promoter analysis
A large number of genes are upregulated at the 1.5, 3h time points only.
Only a few constantly upregulated genes◦control vs smoke: ubiquitin system, LRR
receptor◦control vs butenolide: ubiquitin system,
aquaporine-like protein
Clustering of germinating Clustering of germinating phase dataphase data
ConclusionsConclusionsSmoke induces stress related
changesSupported by Gene Ontology and
promoter analysisRapid decay of mRNAs present in
embryosSmoke/butenolide effect is
different◦Synergistic effect?◦More active compounds?
ParticipantsParticipantsVilmos SoósAngéla JuhászJános PintérMarnie E. LightJohannes van StadenErvin Balázs