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Christophe SALON 1,2 Christian JEUDY 1 1 UMR Legumes Genetics and Ecophysiology (LEG), INRA 17 rue Sully, BP86510 Dijon Cedex, France 2 Experimental Unit Greenhouse and Phenotyping platform, INRA, 17 rue Sully, BP86510 Dijon Cedex, France
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Christophe SALON1,2
Christian JEUDY1
Céline BERNARD2
1UMR Legumes Genetics and Ecophysiology (LEG), INRA
17 rue Sully, BP86510 Dijon Cedex, France
2Experimental Unit Greenhouse and Phenotyping platform,
INRA, 17 rue Sully, BP86510 Dijon Cedex, France
Towards innovative cropping systems :
High Throughput Phenotyping of plant
biotic interactions.
Goals
PPHD Dijon, Phenodays, Slide 2/18
Large Research Unit « Agroecology »
Research units gathered around knowledge for conception & evaluation of the performance of innovative cropping systems
EcolDur
Ecology of communities and
durability of agricultural
systems
GEAPSI
Genetic environmental
determinisms of plant adaptation to
innovative cropping systems
IPM
Mechanisms management of plant-micro
organisms interactions,
MERS
Microbiological and
environmental sanitary risks
Various thematics
Goals
Legumes, Legumes/Cereals Associations
Legumes, Weeds, Cereals, Brassica
Legumes, Arabidopsis, Wine, Tobacco, Tomato
Listeria and root tissues
GEAPSI EcolDur IPM MERS
A variety of research objects
Large Research Unit « Agroecology »
PPHD Dijon, Phenodays, Slide 3/18
Available:
- large genetic var.
- « omic’s »
Goals
Pheno and Geno … mix
Automated plateforms!
Combine similar phenotyping and genotypage rates
Filling the gap
PPHD Dijon, Phenodays, Slide 4/18
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
PPHD Dijon, Phenodays, Slide 5/18
Germination date % viable seeds, dormancy…
Gardarin et al. (2011),Ecol. Modelling 222: 626-636 Gardarin et al. (2010), Weed Res. 50: 91-101
Gardarin et al. (2010),Seed Sci. Res.20: 243-256 Sester et al. (2007) Ecol. Modelling 204: 47-58 Sester et al. (2006) Eur. J. Agron. 24: 19-25
“Dynamic” analysis of weed germination under various environmental conditions
Model parameters
Establishing traits/functional relations
0
0.2
0.4
0.6
0.8
1
0 10 20 30 40 50 60 70 80
Cu
mu
late
d p
rop
ort
ion
of g
erm
ina
ted
se
ed
s
Days since water addition
3°C
6°C
20°C
0
0.2
0.4
0.6
0.8
1
0 50 100 150 200 250 300
Pro
po
rtio
n o
f g
erm
ina
ted
se
ed
s
Cumulated degree-days (°C) since water addition
0
-0.05
-0.95
Soil water
Measuring « manually » phenotypes (1/3)
PPHD Dijon, Phenodays, Slide 6/18
Measuring « manually » phenotypes (2/3)
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!
PPHD Dijon, Phenodays, Slide 7/18
Roots Dry Weight (g)
0,04 0,06 0,08 0,10 0,12 0,14 0,16 0,18
No
du
les D
ry W
eig
ht
(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
Rea
l n
um
ber
of
no
du
les
0
200
400
600
800
1000
Surface area
20 30 40 50 60 70
Ro
ot
Dry
Weig
ht
(g r
oo
t/p
lan
t)
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
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 (3/3)
PPHD Dijon, Phenodays, Slide 8/18
[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)
PPHD Dijon, Phenodays, Slide 9/18
Nb Units
Unit Surface (m2)
Total surface
(m2) Greenhouses 16 19 304 988 m2 4 21 84 3 40 120 1 84 84 1 100 100 1 128 128 1 168 168
Climatic chambers 4 9 36
75 m2 5 6 30 3 3 9
Infrastructures and equipments: S1 Greenhouses and
climatic chambers
27 greenhouse units (total surface = 1000 m2) 12 climatic chambers (total surface = 75m2)
Organisation
PPHD Dijon, Phenodays, Slide 10/18
PPHD : S2 building, greenhouses, climatic
chambers (1/3)
A building,
Lemnatec© Phenotyping equipments
greenhouses (240+110m2),
And climatic chambers (80m2)
Organisation
PPHD Dijon, Phenodays, Slide 11/18
« Scan 3D » system
«Large» biological units
… and rhizotrons (1000)
InoviaFlow.
Cameras: RVB Fluo NIR
Organisation PPHD : S2 building, greenhouses, climatic
chambers (2/3)
PPHD Dijon, Phenodays, Slide 12/18
« HTS » system
«Small» biological units : petri dishes, seeds, plantlets
Cameras:
RVB
Fluo
NIR
Organisation PPHD : S2 building, greenhouses, climatic
chambers (3/3)
PPHD Dijon, Phenodays, Slide 13/18
European Funds (30%)
INRA (31%)
Burgundy Region(31%)
French Minister (8%)
2011/2012
«Investments of future»
Phénome (2800 K€)
Budget
PPHD Dijon, Phenodays, Slide 15/18
Local : Agrosup (partership for image analysis, data mining)
Vitagora
National: Réseau EFOR (partage pour plantes modèle)
« Investissement d’avenir » : Phenome
LETI network
International EU FP7 European Plant Phenomic Network (EPPN)
EU FP7 ABSTRESS project (WP leader, 450K€)
Positioning
PPHD Dijon, Phenodays, Slide 16/18
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
Do not forget:
- to validate in the field to tackle G *E *M interactions
Identifying differences
among genotypes
Interpreting the
detected difference
Food for thoughts
+ +
- to combine approaches
PPHD Dijon, Phenodays, Slide 17/18
Food for thoughts
Thanks for your attention….
PPHD Dijon, Phendays, The end