whole transcriptome analysis of smoke-water treated maize seeds
DESCRIPTION
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 PresentationTRANSCRIPT
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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.
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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
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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
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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?
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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
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Gene Ontology analysisGene Ontology analysis
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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
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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
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Clustering of germinating Clustering of germinating phase dataphase data
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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?
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ParticipantsParticipantsVilmos SoósAngéla JuhászJános PintérMarnie E. LightJohannes van StadenErvin Balázs