doctoral research presentation_debatosh das
TRANSCRIPT
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Signal integration between ethylene- and shade-induced Arabidopsis hypocotyl elongationDEBATOSH DAS, PhD, Utrecht University
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Geographic floodcenters
Impact: Pakistan (>4 billion $ worth crop loss in 2010)
Flood Observatory, Colorado, 1985-2010
Second only to drought
Bailey-Serres et al., 2012
FLOODING As a Stress
Crop damage
B
C
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Mickelbart et al., 2015
Flood adapting strategies
Tolerance vs.
Escape
Ethylene accumulation
Differential responsebased on genetics
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LIGHT & Plant Development
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SHADE As a Stress
YIELD Decreased photosynthesis & low biomass.
STRESS-RESISTANCEReduced resistance & competitive ability.
Yvon Jaillais & Joanne Chory (2010).
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Ethylene Shaded
Project-1 Stress Escape from Flooding & Shade by Shoot
Elongation
Approach-1 Arabidopsis Col-0 hypocotyl transcriptomics(Accepted to Plant Physiology focus edition “Ecophysiology”) Approach-2 Natural variation and hypocotyl transcriptomics in Arabidopsis accessions (Manuscript in preparation)
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Mimic : Ethylene (1 ppm) as flooding and Green Filter as Shade. Epidermal cell elongation (no change in cell number, 20 cells):
Cell wall modification.
Approach -1 Arabidopsis Col-0 hypocotyl transcriptomics
(Hypocotyl = Embryonic stem)
Model for Shoot Elongation
1mm
1.2 mm 1.6 mm 3.6 mmControl
Ethylene
Shade
1 m
m
At 33 hrs.
Control Ethylene Shade
Epidermalcell
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SHADE
CONTROL
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Treatment & tissue-specific gene expression
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Differentially expressed
genes
Factors underlyingtranscriptome
variation
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Biological Enrichment
Mapman Bin Enrichment
Cluster Number
B) Temporal Clustering
Gene Ontology Enrichment
Cluster Number
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Functional characterization(SALK mutants, overexpression lines etc.)
Classification into TranscriptionRegulators, Hormone-related, Signalling and Cell wall genes
(SAURs, Cell wall genes,AGPs, Kinases, Lipases etc.)
Log2FC filter
Transcriptional regulators
IBL1KIDARI
ATHB28
Hormone BR6OX1
BAS1GA20OX1
SignallingTHE1
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1) KIDARI (PRE6), a non-DNA binding bHLH protein
KIDARI overexpression
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Transcriptional regulators
Hormone-related&
Signalling
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HORMONE PHYSIOLOGY
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AUXIN
GA
BR
PerceptionBiosynthesis
Transport
SignallingBiosynthesis
PerceptionBiosynthesis
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CACATGBHLH transcription factorsPhytochrome Interacting Factors(light mediated growth promotion)MYC transcription factors(abiotic and biotic stress)MYCs have growth controlling roles.
TTATAAHomeobox transcription factorsHD-ZIP(light regulated growth control)ZF-HD e.g. ATHB28 in this study.(growth control)
GENE
1000 bp upstream sequence5’ UTR
MOTIF ANALYSIS
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Shared transcriptional network
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Project-2Natural variation and hypocotyl transcriptomics in Arabidopsis accessions
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Strong responder Weak responder
0
5
10
0 50 100 150
Treatment time (h)
ControlEthyleneGreen Shade
0
5
10
0 50 100 150
Hyp
oco
tyl l
engt
h (
mm
)
Treatment time (h)
Natural variation349 accessions.
1) GWAS study
3) GWAS + transcriptomics : BHLH TFs
LOD
val
ue
Ethylene correlation plots
Shade correlation plots
2) Comparative transcriptomics
(TANOVA: Accession dependent differences)
ETHYLENE SHADE
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Outcome from natural variation study
Bai et al., 2012
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Significance Control plant height: Semi-
dwarf stature due to GA20ox1mutation (ortholog to high-yield green-revolution ricelocus) improved lodgingresistance and harvest index incrop production.
Optimize growth: resourcestowards stress-resistance.
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Lilley et al., 2012
Kutschera and Niklas, 2013
Physiological importance of cotyledon?
Loss of SUCROSE source: Auxin and turgor pressure.
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THANKYOU