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Bridging Physiological and EvolutionaryTime Scales in a Gene Regulatory Network

Case study of the Drought Gene Regulatory Network

in Sunflower

Nicolas LangladeINRA Toulouse

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Gene Regulatory Network

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Complex molecular and physiological functionsare the product of many genes that

are coordinated spacially and temporally = GRN

Are molecular and physiological functions related in the GRN?

Is genetic diversification constrained by the GRN?Speciation?

Domestication?Breeding?

Drought Gene Regulatory Networkin Sunflower

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Drought Gene Regulatory NetworkGene selection

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51

1657

316 247

Growth chamberABA 10µM

Plantlet

367

+ key genes in hormonalsignaling pathways = 182 genes selected

FieldFTSW 0.2 vs 0.6Post-flowering

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Glasshouse FTSW 0.1 vs 1Pre-flowering

Rengel et al., 2012 PLoS ONE

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Time (h)ΔΔ

Ct

Drought Gene Regulatory NetworkGene selection

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51

1657

316 247

Growth chamberABA 10µM

Plantlet

367

+ key genes in hormonalsignaling pathways = 182 genes selected x

FieldFTSW 0.2 vs 0.6Post-flowering

7 Times9 Hormones3 Repeats

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ABF2

Glasshouse FTSW 0.1 vs 1Pre-flowering

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• Goals of the modeling:• Obtain a meta-network• Identify hormone-specific edges/pathways

• Nature of the prediction• Oriented edges

• Statistical methodsperformed by M. Vignes (INRA Toulouse) and P. Geurts and V.-A. Huynh-Thu (U. Liège)

• Gaussian Graphical ModelSIMoNe (J. Chiquet, Evry)

• Random ForestGENIE3 (P. Geurts, Liège)

META-ANALYSIS

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Gene iTime = t

Gene jTime = t+1

Drought Gene Regulatory NetworkInference Methodology

described in Marchand et al. 2014 Supp. Mat.

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Sunflower drought GRN69 genes

2/3 from sunflower transcriptomic studies1/3 from model species data

79 edges

Several hormonesABAEthyleneMe-Jasmonate…

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GRN topological parameters

Average ShortestPath Length

Degree of connectivity

What is the relation between molecular functions are position in the GRN?

What is the link between genetic diversity and position in the GRN?

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Low degree of connectivity: Enzyme activity Metabolic process Redox activity ATP binding Protein phosphorylation

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Intermediate degree of connectivity: Transcription Factor Chromatin interaction DNA binding to specific sequence

ABF2

MYC2

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High degree of connectivity: Transporter Ion Channel Cl- and NO3

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CLC-A

NRT1.1

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SULTR1 ABF2

NRT1.1

PMEAMT

APX1

CCT2

CLC-a

PLD α2

HaT13l028104

MYC 2

HAB1

ARIA

ABA1

GUN5

HaT13l074901

CPK5

Emb1075

Anion transporter

Cell protection

Signal transduction

Transcription factor

Genes involved in ABA pathways

Links from literature

Links inferred in the GRN :ABA dependent pathway

Links inferred in the GRN : ABA independent pathway

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ABA

JA

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How GRN can allow or constrain evolution?

Domestication Local adaptation

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Genetic diversity in the drought GRN

14Map from Renault et al., 2013, Nat Comm

Collaboration N. Kane & L. Rieseberg (UC Boulder & UBC Vancouver)

H. annuus

H. petiolaris H. argophyllus

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Genetic diversity in the drought GRN

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GRN levelNo significant correlation between

topological parameters and FST

Gene levelNRT1.1 (hub)

Significant loss of diversityin H. argophyllus

H. annuus

H. petiolaris H. argophyllus

? Evolution of the topology of the GRN during speciation

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Genetic diversity in the drought GRN

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GRN topology parameters , FST

rho = 0.976, p=10-4

WildH. annuus Elite

H. annuus

Landrace H. annuus

GRN topology parameters , FST

rho = 0.946, p=0.002

ASPL, FST

R = 0.74, p=0.003

Average ShortestPath Length

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Who constrains who?

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Many thanks to our collaborators

Publication: Marchand et al. 2014 New Phytologist (arXiv)

Statisticians: M. Vignes (INRA Toulouse) and Pierre Geurts and V-A Huynh-Thu (U. Liege)

Evolutionary Biologists: N. Kane (UC Boulder and L. Rieseberg UBC Vancouver)

Genetics: P. Vincourt, S. Muños, B. Mangin

Bioinformatics: J. Gouzy, S. Carrère

Sunflower biotech and breeders: Biogemma, RAGT 2N, Soltis, Syngenta

G. Marchand