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Whole transcriptome analysis of germinating smoke water treated maize seeds

Whole transcriptome analysis of germinating smoke water treated maize seeds. Endre Sebestyén ARI-HAS Department of Applied Genomics H-2462 Martonvásár, Brunszvik street 2. Introduction. Smoke released from burning vegetation contains a chemical signal, which : is a germination cue

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Whole transcriptome analysis of germinating smoke water treated maize seeds

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  1. Whole transcriptome analysis of germinating smoke water treated maize seeds Endre Sebestyén ARI-HAS Department of Applied Genomics H-2462 Martonvásár, Brunszvik street 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 & problems • Maize microarray with 46k features from www.maizearray.org • Chip annotation is incomplete • Funding for the project ended • Samples • Germinating maize embryos (3, 6, 9, 12, 18, 24, 27h) • Early postgermination phase (24, 48h) • Smoke treated vs control samples • The molecular background of smoke action is unknown

  4. Postgermination phase results • 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 • Some of the significantly up- or downregulated genes might be good candidates for further analysis, but what about the overall process?

  5. Gene Ontology analysis • Gene Ontology www.geneontology.org • 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 (24h, )

  7. Gene Ontology analysis (48h, )

  8. Gene Ontology analysis (24h, )

  9. Gene Ontology analysis (48h, )

  10. 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 (www.gene-regulation.com) • 834 experimentally verified plant TFBS

  11. Promoter analysis (24h, ) • 317 promoters available from the 24h upregulated list • Other promoter elements (TATA-box, etc)

  12. Experimental validation B/1: control B/2: ABA B/3: smoke B/4 ABA+smoke

  13. Germination phase results • 3-12h – germination phase • 24-27h – postgermination phase

  14. Germination phase results

  15. Germination phase results

  16. Gene Ontology analysis • Significantly enriched GO terms • 3h : response to heat, salt stress, trancription • 6h : response to cold, salt stress, water depr., transcription • 9h : no significantly enriched terms • 12h : translation, biosynth. processes, response to cold, etc • 24h : response to bacterium, growth, development • 27h : growth, morphogenesis, response to bacterium

  17. K-means clustering

  18. K-means clustering

  19. Conclusions • Smoke induces stress related changes • Supported by Gene Ontology and promoter analysis • Rapid decay of mRNAs present in embryos • The hardening effect of smoke is similar to that of caused by ABA • Vigour test also shows possible interaction between smoke and ABA

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

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