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Whole transcriptome analysis of smoke-water treated maize seeds

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 :

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Whole transcriptome analysis of smoke-water treated maize seeds

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  1. 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.

  2. Introduction • Smoke 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

  3. Experimental 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

  4. Postgermination phase • 24h 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 rtPCR • What about the overall process?

  5. Gene Ontology analysis • Gene 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

  6. Gene Ontology analysis

  7. Promoter analysis • BLAST 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

  8. Germinating phase • Similar 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

  9. Clustering of germinating phase data

  10. Conclusions • Smoke induces stress related changes • Supported by Gene Ontology and promoter analysis • Rapid decay of mRNAs present in embryos • Smoke/butenolide effect is different • Synergistic effect? • More active compounds?

  11. Participants • Vilmos Soós • Angéla Juhász • János Pintér • Marnie E. Light • Johannes van Staden • Ervin Balázs

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