HAL Id: hal-02739422
https://hal.inrae.fr/hal-02739422
Submitted on 2 Jun 2020
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High througput phenotyping of interactions between plants and microorganisms, associated devices.
Phenotyping Platform for Plant and Plant Micro organisms Interactions (4PMI, INRA Dijon)
Christophe Salon
To cite this version:
Christophe Salon. High througput phenotyping of interactions between plants and microorganisms, associated devices. Phenotyping Platform for Plant and Plant Micro organisms Interactions (4PMI, INRA Dijon). Scientific Workshop on the effects of biotic and abiotic stresses in legumes: the AB- STRESS and BIOTECSOJASUR projects, Mar 2016, Balcarce, Argentina. �hal-02739422�
Christophe Salon
UMR 1347AgroSup/INRA/uB, 17 rue Sully BP 86510 21065 Dijon France
High trougput phenotyping of interactions between plants and microorganisms, associated devices
Phenotyping Platform for Plant and Plant Micro organisms Interactions
(4PMI, INRA Dijon)
Maize Wheat Pea
Achievements: Shoot phenotyping
Calibration, image analysis
“Manual” image
4PMI image
0 2 4 6 8 10 12
0 0,02 0,04 0,06 0,08 0,1 0,12 0,14
Shoot Fresh weight
Projected area (cm²)
Shoot fresh weitgh (g)
“Manual” weight
0 10 20 30 40 50
0 2 4 6 8 10 12
Projected area (cm²)
Mesured Leaf area (cm²)
Shoot leaf area
Choice of best image acquisition model !
Mean of 3 lateral views
Achievements: Shoot phenotyping
0 2 4 6 8 10 12
Projected area from images
Days since sowing
Projected area (cm²) 0
2 4 6 8 10
12Plant Height from image
Days since sowing
Height (cm)
0 2 4 6 8 10 12
Shoot Dry Weight
Days since sowing
Shoot dry weight (g)
Wheat
Shoot/root phenotyping: dynamic simulation
Calibration, image analysis
4PMI image
EPPN Project, Josh Klein AARO Volcani Israel
Prototyping approach: Partnership with SMEs (Inoviaflow and Shakti):
- very innovative rhizotrons (European patent) called RhizotubeHD,
- associated imaging cabins (Rhizocab and Rhizocab-HT) and software,
- irrigating, potting depotting tools.
Standalone: RhizoCab
Conveyors
EU Patent INRA InoviaFlow, World licence distributions ongoing (INRA-Inoviaflow)
RhizoCab
RhizoCab
Segmentation software
Irrigation arm
Ok for small amount of nutritive solutions Drainage hole
RhizoTubes
Shell
High throughput:
100ds/day 15s/RT
Medium resolution (42 µm) Low throughput:
50 RT/day, 45s/RT
Very high resolution (7 µm)
RhizoCab HT development
0 2 4 6 8 10 12
Shoots over root biomass ratio
Biomasse (g/plante)
0 2 4 6 8 10 12
Mean Nodule weigth
Biomasse (g/plante)
BOM: RhizoTubes vs Pots ?
Similar plant compartments and nodule traits
0 2 4 6 8 10 12 0
2 4 6 8 10 12
Number
BOM: RhizoTubes vs Pots ?
Pot RhizoTube
Same length upper
0 2 4 6 8 10 12
0 10 20 30 40 50 60 70
Number
0 2 4 6 8 10 12
0 5 10 15 20 25 30 354045
Length (cm)
0 2 4 6 8 10 12
0 2 4 6 8 10 12 14 16 18
Distance from stem base (cm)
Length (cm)
1st order lateral roots2nd order lateral roots
* * * * * * * * * * *
*
* * * * * * * *
* * * * *
* * * * * Same number and distribution of roots on 2nd order laterals
… but pot vs RhizoTube depth !
BOM: RhizoTubes vs Pots ?
Pot
0 2 4 6 8 10 12
0 0,5 1 1,5 2 2,5 3 3,5
Nb nodules on main root
0 2 4 6 8 10 12
0 20 40 60 80 100 120 140
Distance from stem base (cm)
Nb nodules lateral roots
RhizoTube
Same nodule profile distribution, shifted
0 5
Date de la mesure
Longueur en cm
0 1
Date de la mesure
Nombre de nodules
0 10
Date de la mesure
Nombre de latérales
0 5
Date de la mesure
Longueur en cm
0 1
Date de la mesure
Nombre de nodules
0 10
Date de la mesure
Nombre de latérales
0
Date de la mesure
Longueur en cm
0 10
Date de la mesure
Nombre de latérales
0 1
Date de la mesure
Nombre de nodules
0
Date de la mesure
Longueur en cm
0 10
Date de la mesure
Nombre de latérales
0
Date de la mesure
Nombre de nodules
0
Date de la mesure
Longueur en cm
0
Date de la mesure
Nombre de latérales
0
Date de la mesure
Nombre de nodules
Length main root
Number of nodule
Number of laterals
Date
Date
Date
NumberNumberLength (cm)
Focus on image Nodules: Number, projected surface, position, color
PhD Simeng Han (unpublished)
Phenotypic traits: examples
Hybrid spaces (color + texture)
(Cointault et al, 2008) Nodules: Number, projected surface, position, color
PhD Simeng Han (unpublished)
Phenotypic traits: examples
Image with nodules
Nodules: Number, projected surface, position, color
PhD Simeng Han (unpublished)
Phenotypic traits: examples
Original image + superimposed nodules
Nodules: Number, projected surface, position, color
PhD Simeng Han (unpublished)
Phenotypic traits: examples
Nodules automatically detected
95% detection efficiency
Nodules: Number, projected surface, position, color
PhD Simeng Han (unpublished)
Phenotypic traits: examples
0 2 4 6 8 10 12
0 2 4 6 8 10 12
0 2 4 6 8 10 12
R2=0,95
Biomasse (g/plant)Rhizotron
Hydroponique et substrat
Pea core collection
CAMEOR L1073
KAYANNE AMINO
PI186093
ISARD CUZCO LIVIOLETTA
Nodules: Number, projected surface, position, color
PhD Simeng Han (unpublished)
Phenotypic traits: examples
Pois Féverolle Lupin Haricot
Vesce Commune Colza Vulpie Maïs
Some root example
17?8
10 cm
Maïs
1 cm
Maïs
100 microns
Maïs
50 microns
Maïs
10 microns
Maïs
17?8
10 cm
Maïs
zoom
Root tips
Hyphae
Root phenotyping: High resolution
Down to 7 microns
Nodules
