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Acclimation of Populus to wind: kinetic of the transcriptomic response to single or repeated stem bending

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HAL Id: hal-02739238

https://hal.inrae.fr/hal-02739238

Submitted on 2 Jun 2020

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Acclimation of Populus to wind: kinetic of the transcriptomic response to single or repeated stem

bending

Lise Pomies, Mélanie Decourteix, Jérôme Franchel, Bruno Moulia, Nathalie Leblanc-Fournier

To cite this version:

Lise Pomies, Mélanie Decourteix, Jérôme Franchel, Bruno Moulia, Nathalie Leblanc-Fournier. Accli-mation of Populus to wind: kinetic of the transcriptomic response to single or repeated stem bending. IUFRO Genomics and Forest Tree Genetics Conference, May 2016, Arcachon, France. IUFRO, 1 p., 2016. �hal-02739238�

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Acclimation of Populus to wind:

kinetic of the transcriptomic response

to single or repeated stem bending.

Lise Pomiès1,2, Mélanie Decourteix1,2,

Jérôme Franchel1,2, Bruno Moulia2,1,

Nathalie Leblanc-Fournier1,2

1 Université Blaise Pascal, UMR 547 PIAF,

8 avenue Blaise Pascal, 63 178 Aubière

2 Inra, UMR 547 PIAF, 5 chemin de Beaulieu,

63 039 Clermont-Ferrand

Identification & characterization

of temporal patterns in gene expression Long-term time series expression profiling

Storms are the 1

st

cause of damages to European forests. Trees are sensitive to stem bending due to chronic wind. After 1 bending, they respond by modifying

their growth during several days [1]. However, repeated stem bending induce a reduction in tree responsiveness, a phenomenon called accommodation [2][3].

Due to climate changes, strong wind may be more frequent [4]. How will trees acclimate or not to such new wind regimes?

Gene expression modifications were

assessed at 0.5 h, 2 h, 24 h and 72 h after a transitory controlled bending (with Affymetrix microarray).

 2,633 differentially expressed genes (DEG)

 75.6% of DEG are detected at 0.5 h and 2 h after the bending

 Many DEG are detected at several

time points.

k-means clustering

40 different temporal patterns

Gene Ontology (GO) enrichment

in each cluster

Temporal patterns are assigned

Example: Cluster 4

31 genes up-regulated 0,5h after 1 bending with a transcription factor activity GO affiliation.

Gene Ontology enrichment

First global and kinetic picture of molecular responses to stem bending

Toward a better understanding of the accommodation process

Refinement of the early time course analysis for the biological processes involved

Refined time course analysis using Q-PCR  6 extra time points between 0,5 h and 24 h for representative genes of each cluster

PtaJAZ2, PtaJAM2 JA-induced transcription factors, negative regulator of JA responses

PtaAOS4, allene oxide synthase, JA biosynthetic pathway

PtaWRKY18, PtaWRKY53, PtaZFP2 (C2H2): transcription factors

[1] C. Coutand, L. Martin, N. Leblanc-Fournier, M. Decourteix, J.-L. Julien, and B. Moulia. 2009. “Strain mechanosensing quantitatively controls diameter growth and PtaZFP2 gene expression in poplar”. Plant Physiol. 151(1): 223–32

[2] L. Martin, N. Leblanc-Fournier, J.-L. Julien, B. Moulia, and C. Coutand. 2010. “Acclimation kinetics of physiological and molecular responses of plants to multiple mechanical loadings.” J. Exp. Bot. 61(9): 2403–12

[3] N. Leblanc-Fournier, L. Martin, C. Lenne, and M. Decourteix. 2014. “To respond or not to respond, the recurring question in plant mechanosensitivity.” Front. Plant Sci., 5: 401

[4] R. J. Haarsma, W. Hazeleger, C. Severijns, H. de Vries, A. Sterl, R. Bintanja, G. J. van Oldenborgh, and H. W. van den Brink. 2013. “More hurricanes to hit western Europe due to global warming”. Geophys. Res. Lett., 40(9): 1783–1788

Accommodated

Less regulated after the 2nd

bending, than after the 1st one. 1,098 genes

Example : PtaWRKY18

(Potri.006G63600)

Non Accommodated

Equally regulated after the 2nd

bending, than after the 1st one. 44 genes

Example : PtaHRD

(Potri.006G021000)

Newly Regulated

Regulated after the 2nd

bending only.

18 genes Example : PtaPEROX

(Potri.007G096200)

Perspectives : We are currently working on new methods of gene network inference to understand the fine regulation of this mechanical signaling pathway.

3 types of genes:

A -

B - •Early regulated genes are

related to “stress response”:

- Transcription factors families (e.g. fig. A);

-Jasmonic acid and ethylene signaling (e.g. fig. B).

Gene expression 0.5 h after 2 bending

(24 h interval) Gene expression

0.5 h after 1 bending

vs.

96% of the early regulated genes after a 1st bending are

less regulated after a 2nd bending

This mechanism may allow the plant to avoid over-reaction to successive bending.

Protein phosphorylation

Regulation of jasmonic acid mediated pathway Jasmonic acid mediated pathway

Response to hormone Response to chitine

Regulation of nucleic acid templated transcription

Defense response

Time after bending

(in hours)

Carbohydrate derivative metabolic process Cell wall organization or biogenesis

0.5 2 5 9 13 17 21 24 72

Photosynthesis

Response to light stimulus

Regulation of nucleic acid templated transcription

Regulation of defense response

Defense response Response to chitine Response to hormone

Chemical homestasis

Regulation of jasmonic acid mediated signaling pathway

Jasmonic acid mediated signaling pathway

BP annotation of clusters of up-regulated genes

BP annotation of clusters of down-regulated genes

Regulation of defense response Regulation of cellular process

Chosen genes represent the

temporal patterns and the GO annotations of the cluster.

(JA)

Objectives: to investigate the extent of the molecular

accommodation and to identify potential molecular actors.

•Some early up-regulated genes are down-regulated in later stages (see PtaJAZ2 fig. B)

negative feedback mechanism?

•Late up-regulated genes (21 h -

72 h), seem to be linked to a

remodeling of cell wall-related processes. (clusters) a biological function Fold induction (log2 (r atio) ) Fold induction (log2 (r atio) ) Fold induction (log2 (r atio) ) Fo ld in d u ct io n (l o g 2(ra ti o ))

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