« PPHD » : A Platform For High Throughput Phenotyping of Plant/Plant and Plant/Microorganisms Interactions.

Christophe SALON

Christian JEUDY

Céline BERNARD

and Richard THOMPSON, Vivienne GIANINAZZI-PEARSON? Xavier REBOUD, Philippe LEMANCEAU, Jacques CANEILL

UMR AgroEcology, National Institute of Agronomical Research (INRA),

17 rue Sully, BP 86510, 21065 Dijon Cedex, France

Large Research Unit « Agroecology » Research units gathered around knowledge for conception &

evaluation of the performance of innovative cropping systems

Various thematics/research objects

AgroEcology RU’s groups:

Ecology of communities and

durability of agricultural

systems

EcolDur

Genetic environmental

determinisms of plant adaptation to

innovative cropping systems

GEAPSI

Mechanisms and management of plant-

micro organisms interactions,

IPM

PAG XiX, San Diego, 2/15 C. Salon

Phenotyping plant architecture, flowering, senescence, …

Phenotyping pods and seeds

Fluorescence: GFP

Seeds : Number, size and shape

Kroj et al. Development (2003) 130, 6065-6073

• Mutants (Tilling..)

• RILs

• Ecotypes collections

CONTROLED

CONDITIONS

[NO3 - ] [NO3 - ] [NO3 - ]

ENVIRONMENTAL

In vitro kinetic development P. sativum M. truncatula

Phenotyping roots and interactions with micro organisms (nodules, µR), …

Example : case studies of legume plants

PAG XiX, San Diego, 3/15 C. Salon

Measuring « manually » phenotypes (1/2)

Camera

Model

Moreau et aL. (2006), Plant, Cell and Envir., 29:1087-1098. Moreau et aL. (2007), Plant, Cell and Envir., 30:213-224. Moreau et al. (2008), J. Exp. Bot., 59:3509–3522.

Thèse Delphine Moreau – 13 avril 2007

QUANTITE

TOTALE D’AZOTE

SURFACE FOLIAIRE

PROJETEE

BIOMASSE

SOUTERRAINE

BIOMASSE

TOTALE

Coefficients

d’ajustement

Efficience biologique

Date de début de fixation de N2

1,0

1,5

2,0

2,5

3,0

3,5

0 10 20 30 40

PAR (mol m-2 jour-1)

0

1

2

3

4

0 10 20 30 40

0,0

0,5

1,0

1,5

0 10 20 30 40

(

1500

2250

3000

3750

4500

0 10 20 30 40

0,0

0,1

0,2

0,3

0 2 4 6 8 10

0,0

0,1

0,2

0,3

0,4

0 2 4 6 8 10

PAR (mol m-2 jour-1)PAR (mol m-2 jour-1)PAR (mol m-2 jour-1)

[NO3-] (mM)

[NO3-] (mM) [NO3

-] (mM)

0

400

800

1200

0 2 4 6 8 10

Efficience de conversion de N

en surface projetée

Prélèvement de N

spécifique AVANT

la date de début de

fixation de N2

Prélèvement de N

spécifique APRES

la date de début de

fixation de N2

[NO3-][NO3-]

Dynamic Leaf area measurement

Analytical approaches + model: leaf area is a relevant phenotypic target for detecting any contrasted N nutrition among various genotypes.

Genotypes of Medicago RIL

ranked for ability to uptake N!

PAG XiX, San Diego, 4/15 C. Salon

Roots Dry Weight (g)

0,04 0,06 0,08 0,10 0,12 0,14 0,16 0,18

No

du

les

Dry

We

igh

t (g

)

0,004

0,006

0,008

0,010

0,012

0,014

0,016

0,018

0,020

Number of nodules counted on the scan

0 200 400 600 800

Re

al n

um

be

r o

f n

od

ule

s

0

200

400

600

800

1000

Surface area

20 30 40 50 60 70

Ro

ot

Dry

We

igh

t(g

ro

ot/

pla

nt)

0,04

0,06

0,08

0,10

0,12

0,14

0,16

0,18

y = 0.0106 ln(x) + 0.0369, R² = 0.78

y = 0,000041x2 - 0,001530x + 0,087432, R² = 0,839

y = 1.1645 x - 9.45, R² = 0.90

Nodules number and size, appearance

NH4NO3

10 mM -N KNO3

0.5 mM

14 days after inoculation

Split roots

Manual root scan

Ruffel et al. (2008), Plant Physiol. 146: 2020-2035. Salon et al. (2009), CRAS, 332 :1022-1033. Jeudy et al. (2010), New Phytol, New Phytol., 185:817-828. Bertin et al. (2010) J. Exp. Bot., 61: 955 - 967.

Nodule number and size, isotopic flux measurements to understand adaptative strategy of plants to N deficiency.

Morphometry versus

functional strategy

identifcation

Measuring « manually » phenotypes (2/2)

PAG XiX, San Diego, 5/15 C. Salon

Available :

- large genetic variability

- numbers of « omic’s »

Pheno and Geno … mix Need to identify genes for key agronomic traits :

Combine high throughput phenotyping and genotyping rates!

plant/organ phenotype?

PAG XiX, San Diego, 6/15 C. Salon

Available :

- large genetic variability

- numbers of « omic’s »

Pheno and Geno … mix Need to identify genes for key agronomic traits :

Combine high throughput phenotyping and genotyping rates!

plant/organ phenotype?

PAG XiX, San Diego, 7/15 C. Salon

[Co2] •…under different environmental conditions…

PPHD’s Objectives

High throughput innovative technics of

morphometry for:

• characterizing a large number of biological units, their interactions…

… at various organizational levels (plant/plant, plant /organ)

PAG XiX, San Diego, 8/15 C. Salon

What’s in the phenotyping platform?

S2 Building (700m2)

Growth

chambers (100m², 8 units)

Greenhouses

(240 m²automated, 120 m² reg., 10 units)

Capacity of up to 2500 plants

PPHD

PAG XiX, San Diego, 9/15 C. Salon

Fix cam (in pot, trays), plants conveyed, RGB, NIR, UV

0,0

200,0

400,0

600,0

800,0

1000,0

1200,0

1400,0

1600,0

1800,0

Plant 1 Plant 2 Plant 3 Plant 4 Plant 5 Plant 6

mea

n ar

ea c

olou

r cla

ssifi

ed c

m²

Database

What’s in the phenotyping platform?

Scan 3D system

Mobile cam for small biological units, RGB, NIR, UV.

« HTS » System

PPHD

Rhizotrons (300, conveyed, RGB,

NIR, UV. InoviaFlow.

PAG XiX, San Diego, 10/15 C. Salon

NO3-NO3-

N2

CO2

CO2

N

Thèse Delphine Moreau – 13 avril 2007

QUANTITE

TOTALE D’AZOTE

SURFACE FOLIAIRE

PROJETEE

BIOMASSE

SOUTERRAINE

BIOMASSE

TOTALE

Coefficients

d’ajustement

Efficience biologique

Date de début de fixation de N2

1,0

1,5

2,0

2,5

3,0

3,5

0 10 20 30 40

PAR (mol m-2 jour-1)

0

1

2

3

4

0 10 20 30 40

0,0

0,5

1,0

1,5

0 10 20 30 40

(

1500

2250

3000

3750

4500

0 10 20 30 40

0,0

0,1

0,2

0,3

0 2 4 6 8 10

0,0

0,1

0,2

0,3

0,4

0 2 4 6 8 10

PAR (mol m-2 jour-1)PAR (mol m-2 jour-1)PAR (mol m-2 jour-1)

[NO3-] (mM)

[NO3-] (mM) [NO3

-] (mM)

0

400

800

1200

0 2 4 6 8 10

Efficience de conversion de N

en surface projetée

Prélèvement de N

spécifique AVANT

la date de début de

fixation de N2

Prélèvement de N

spécifique APRES

la date de début de

fixation de N2

[NO3-][NO3-]

Analytical

approach

Modelisation Phenotyping

Approach

We also need:

- validation in the field to tackle G *E *M interactions

Identifying differences

among genotypes

Interpreting the

detected difference

Food for thoughts

+ +

- to combine approaches

PAG XiX, San Diego, 11/15 C. Salon

Conclusion Opening Oct 2011 A major resource for identifying determinants of plant adaptation.

PAG XiX, San Diego, 12/15 C. Salon

Conclusion

UMR Agroécologie

ANR, Ministères,….Institutionnel

Partenariat Etat, Europe Partenariat Territorial

Europe

Fédération

de recherche

Socio-économique

SynerjinovCRT Agro Env

PIAE

Partenariat R&DPartenariat économique et développement

A large variety of partners

PAG XiX, San Diego, 13/15 C. Salon

Conclusion

“TOO

GAYTHER

WEEZE

PPHD !”

Part of a consortium of French Phenotyping platforms

PAG XiX, San Diego, 14/15 C. Salon

Conclusion

Thanks four your attention

Open to other collaborations…

PAG XiX, San Diego, 15/15 C. Salon