Whole transcriptome analysis of germinating smoke water treated maize seeds
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Whole transcriptome analysis of germinating smoke water treated maize seedsEndre Sebestyén
ARI-HAS
Department of Applied Genomics
H-2462 Martonvásár, Brunszvik street 2.
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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
OOO
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Experimental layout & problems
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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?
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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
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Gene Ontology analysis (24h, )
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Gene Ontology analysis (48h, )
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Gene Ontology analysis (24h, )
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Gene Ontology analysis (48h, )
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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
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Promoter analysis (24h, )TRANSFAC ID Numbe
rDescription
NT$PR1A 68 (21%)
Pathogensis rel. prot. 1a, GT box
PEA$IAA45_06 52 (16%)
Auxin regulated gene 4/5, footprint-F element
AT$WCOR413_01, etc
52 (16%)
Cold regulated genes,DRE element
MAIZE$DHN1_09, etc
45 (14%)
DHN1 gene, ABRE element
RICE$CRL1_01 42 (13%)
CRL1 gene, AUXRE2 element 317 promoters available from the 24h upregulated list Other promoter elements (TATA-box, etc)
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Experimental validation
B/1: control B/2: ABA B/3: smoke B/4 ABA+smoke
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Germination phase results
3-12h – germination phase 24-27h – postgermination phase
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Germination phase results3h 6h 9h 12h
Ubiquitin act. enzyme +40
Ubiquitin act. enzyme +27
Hypothetical prot. -16 Put. hASNA-I +12
Expressed prot. -30 Put. senesc. assoc. prot. -11 No description -13 Expressed prot. +10
Putat. cyt. P450 +12
Put. endonuclease -10 Put. splicing factor -13 Expressed prot. +10
Auxin reg. prot. -10 Put. xylose isomerase +9 Put. NLI intercting fact. +13 Unk. prot. +9
Calcineurin B-like pr. 9 -8 Putat. cyt. P450 -9 TaWIN1 -13 Unk. prot. +8
NADPH cyt. P450 -13 Put. DHHC type prot. +9 Lipid-transf. prot. like +12 TF MADS32 +8
No description -15 Put. glucanase +9 Put. DHHC type prot. -6 Put. chitinase +7
Hypothetical prot. -11 Put. cyt. P450 +7 Calcineurin B-like pr. 9 -7 Ubiquitin act. enzyme +6
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Germination phase results24h 27h
Adenylate translocator +18
Photosystem II OE17 +37
No description +12
Glycosyltransferase +27
No description +12
Hypothetical prot. +23
Put. cyt. P450 -9 Unknown prot. +22
Ubiquitin act. enzyme +6 ZmGR1b +20
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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
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K-means clustering
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K-means clustering
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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
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Participants
Vilmos Soós Angéla Juhász János Pintér Marnie E. Light Johannes van Staden Ervin Balázs