Signal integration between ethylene- and shade-induced Arabidopsis hypocotyl elongation DEBATOSH DAS, PhD, Utrecht University
Signal integration between ethylene- and shade-induced Arabidopsis hypocotyl elongationDEBATOSH DAS, PhD, Utrecht University
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
Mickelbart et al., 2015
Flood adapting strategies
Tolerance vs.
Escape
Ethylene accumulation
Differential responsebased on genetics
LIGHT & Plant Development
SHADE As a Stress
YIELD Decreased photosynthesis & low biomass.
STRESS-RESISTANCEReduced resistance & competitive ability.
Yvon Jaillais & Joanne Chory (2010).
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)
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
SHADE
CONTROL
Treatment & tissue-specific gene expression
Differentially expressed
genes
Factors underlyingtranscriptome
variation
Biological Enrichment
Mapman Bin Enrichment
Cluster Number
B) Temporal Clustering
Gene Ontology Enrichment
Cluster Number
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
1) KIDARI (PRE6), a non-DNA binding bHLH protein
KIDARI overexpression
Transcriptional regulators
Hormone-related&
Signalling
HORMONE PHYSIOLOGY
AUXIN
GA
BR
PerceptionBiosynthesis
Transport
SignallingBiosynthesis
PerceptionBiosynthesis
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
Shared transcriptional network
Project-2Natural variation and hypocotyl transcriptomics in Arabidopsis accessions
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
Outcome from natural variation study
Bai et al., 2012
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.
Lilley et al., 2012
Kutschera and Niklas, 2013
Physiological importance of cotyledon?
Loss of SUCROSE source: Auxin and turgor pressure.
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