Whole transcriptome analysis of smoke-water treated maize seeds

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