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« 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

AgroEcology RU’s groups: EcolDur

Ecology of communities and durability of agricultural systems

GEAPSI

Genetic environmental determinisms of plant adaptation to innovative cropping systems

IPM

Mechanisms and management of plantmicro organisms interactions,

 Various thematics/research objects C. Salon

PAG XiX, San Diego, 2/15


Example : case studies of legume plants Phenotyping pods and seeds

Phenotyping plant architecture, flowering, senescence, …

[NO3-]

Seeds : Number, size and shape

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

• Mutants (Tilling..) • RILs • Ecotypes collections P. sativum

M. truncatula CONTROLED

Fluorescence:

GFP

 In vitro kinetic development

ENVIRONMENTAL CONDITIONS

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

C. Salon

PAG XiX, San Diego, 3/15


Measuring « manually » phenotypes (1/2) Analytical approaches + model: leaf area is a relevant phenotypic target for detecting any contrasted N nutrition among various genotypes.

Efficience biologique 3,5

SURFACE FOLIAIRE PROJETEE

BIOMASSE TOTALE

3,0 2,5 2,0 1,5 1,0 0

Efficience de conversion de N en surface projetée

10

20

30

40

Coefficients d’ajustement

PAR (mol m-2 jour-1)

Camera

4500

1,5

4

3750

3

(

1,0

3000 2

2250

0,5

1

1500 0

10

20

30

[NO3-]

40

PAR (mol m-2 jour-1)

0

0,0 0

10

20

30

40

PAR (mol m-2 jour-1)

0

10

20

30

40

PAR (mol m-2 jour-1)

Date de début de fixation de N2 1200

QUANTITE TOTALE D’AZOTE

BIOMASSE SOUTERRAINE

800 400 0 0

2

4

6

8

[NO3-] (mM)

0,3

Prélèvement de N spécifique AVANT la date de début de fixation de N2

10

0,4

Prélèvement de N spécifique APRES la date de début de fixation de N2

0,3

0,2

0,2

0,1

0,1

0,0

0,0

0

2

4

6

8

10

0

Thèse Delphine Moreau – 13 avril 2007 [NO3-] (mM)

Model

2

4

6

8

10

[NO3-] (mM)

Genotypes of Medicago RIL ranked for ability to uptake N!

Dynamic Leaf area measurement

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.

C. Salon

PAG XiX, San Diego, 4/15


Measuring « manually » phenotypes (2/2) Nodule number and size, isotopic flux measurements to understand adaptative strategy of plants to N deficiency.

KNO3 0.5 mM

0,18

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

0,16

14 days after inoculation

Manual root scan

Root Dry Weight (g root/plant)

-N

0,14 0,12 0,10 0,08 0,06 0,04 20

30

40

50

60

70

Surface area 0,020

Nodules Dry Weight (g)

NH4NO3 10 mM

y = 0.0106 ln(x) + 0.0369, R² = 0.78

0,018 0,016 0,014 0,012 0,010 0,008 0,006 0,004 0,04 0,06 0,08 0,10 0,12 0,14 0,16 0,18 Roots Dry Weight (g)

Real number of nodules

1000

y = 1.1645 x - 9.45, R² = 0.90

800 600 400

Morphometry versus functional strategy identifcation

200 0 0

200

400

600

800

Number of nodules counted on the scan

Split roots

Nodules number and size, appearance 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.

C. Salon

PAG XiX, San Diego, 5/15


Pheno and Geno … mix Need to identify genes for key agronomic traits : Available : - large genetic variability - numbers of « omic’s »

plant/organ phenotype?

Combine high throughput phenotyping and genotyping rates! C. Salon

PAG XiX, San Diego, 6/15


Pheno and Geno … mix Need to identify genes for key agronomic traits : Available : - large genetic variability - numbers of « omic’s »

plant/organ phenotype?

Combine high throughput phenotyping and genotyping rates! C. Salon

PAG XiX, San Diego, 7/15


PPHD’s Objectives High throughput innovative technics of morphometry for: • characterizing a large number of biological units, their interactions…

•…under different environmental conditions…

[Co2]

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

C. Salon

PAG XiX, San Diego, 8/15


PPHD S2 Building (700m2)

What’s in the phenotyping platform? Greenhouses

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

Growth chambers

(100m², 8 units)

Capacity of up to 2500 plants C. Salon

PAG XiX, San Diego, 9/15


PPHD

What’s in the phenotyping platform?

Scan 3D system

« HTS » System

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

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

Rhizotrons

(300, conveyed, RGB, NIR, UV.

InoviaFlow.

1800,0

Database

mean area colour classified cm²

1600,0 1400,0 1200,0 1000,0 800,0 600,0 400,0 200,0 0,0 Plant 1

C. Salon

Plant 2

Plant 3

Plant 4

Plant 5

Plant 6

PAG XiX, San Diego, 10/15


Food for thoughts We also need: - validation in the field to tackle G *E *M interactions

- to combine approaches Phenotyping Approach

+

Analytical approach

+

Modelisation

CO2

Efficience biologique 3,5

SURFACE FOLIAIRE PROJETEE

BIOMASSE TOTALE

3,0 2,5 2,0 1,5 1,0 0

Efficience de conversion de N en surface projetée

10

20

30

40

Coefficients d’ajustement

PAR (mol m-2 jour-1)

4500

1,5

4

3750

3

(

1,0

3000 2

2250 1500

CO2

N2

0,5

1

0

10

20

30

[NO3-]

40

PAR (mol m-2 jour-1)

0

0,0 0

10

20

30

40

PAR (mol m-2 jour-1)

0

10

20

30

40

PAR (mol m-2 jour-1)

Date de début de fixation de N2 1200

QUANTITE TOTALE D’AZOTE

BIOMASSE SOUTERRAINE

800 400

N

0 0

Identifying differences among genotypes

C. Salon

4

6

8

10

0,4

Prélèvement de N spécifique APRES la date de début de fixation de N2

0,3

0,2

0,2

0,1

0,1

0,0

0,0

0

NO3-

2

[NO3-] (mM)

0,3

Prélèvement de N spécifique AVANT la date de début de fixation de N2

2

4

6

8

Thèse Delphine Moreau – 13 avril 2007 [NO3-] (mM)

10

0

2

4

6

8

10

[NO3-] (mM)

Interpreting the detected difference

PAG XiX, San Diego, 11/15


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

C. Salon

PAG XiX, San Diego, 12/15


Conclusion A large variety of partners Partenariat Etat, Europe

Partenariat Territorial Europe

Institutionnel

ANR, Ministères,….

Socio-économique

Fédération de recherche

UMR Agroécologie

Partenariat économique et développement

Partenariat R&D CRT Agro Env

Synerjinov

PIAE

C. Salon

PAG XiX, San Diego, 13/15


Conclusion Part of a consortium of French Phenotyping platforms

“TOO GAYTHER WEEZE PPHD !”

C. Salon

PAG XiX, San Diego, 14/15


Conclusion Open to other collaborations‌

Thanks four your attention C. Salon

PAG XiX, San Diego, 15/15


A Platform For High Throughput Phenotyping of Plant/Plant And Plant/Microorganisms Interactions  

Plant Phenomics Plant Phenotyping at PAG