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.

THANKYOU