« 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