High Resolution
Plant Phenomics Centre
http://www.plantphenomics.org.au/hrppc
High Resolution Plant Phenomics Centre
From growth cabinet to the field
‘Deep phenotyping’ technology
- development, validation and deployment
Model Plant Module (HTP)
Crop Plant Shoot Module (MTP)
Crop Plant Root Module (MTP)
Crop Plant Field Module (HTP)
 1500 m2 lab space and ‘research hotel’
 Imaging modules interfaced with 245 m2 greenhouse,
260 m2 growth cabinets
 Large field site with distributed sensor networks
portable ‘phenomobile’ and 15m imaging tower
Measuring systems and traits to be
measured – model plants to crops
Key technologies
–Colour images
Plant area, volume, mass, structure,
phenology
Senescence, relative chlorophyll content,
pathogenic lesions
Seed yield, agronomic traits
–Near IR imaging
Tissue water content
Soil water content
–Far IR imaging
Canopy / leaf temperature / water use /
salt tolerance
–Chl Fluorescence imaging
Physiological state of photosynthetic
machinery
–Hyperspectral imaging
Carbohydrates, pigments and protein
–Carbon isotope ratio
Transpiration efficiency,
photosynthetic pathway (TDL/MS)
–FTIR Imaging Spectroscopy
Cellular localisation of metabolites
(sugars, protein, aromatics)
Model plant module
Fluorogro-scan
TrayScan
• Growth and morphology
• Photosynthetic performance (Chl
Fluor) under defined environmental
conditions
RGB / FIR in-Cabinet
•IR screening for leaf temperature
• Automated destructive sampling
for metabolites, protein, DNA and
RNA, delta13C
Target plants : Arabidopsis, Tobacco, Brachypodium
and seedling screens
Data Analysis: non-destructive
Growth Analysis and morphological
clustering
• Leaf area / growth analysis
(eg heterosis and drought
stress)
• Photosynthetic mutants
• Lesions / pathogen attack
• Architecture / morphology
• Morphological clustering
• Interfaced to PODD
phenotypic dBase
Conveyor Tray Scan: 3000 plants per day
Phenome / Genome
Database at last!
Isolating Photosynthetic
and Photorespiratory Mutants
Fv/Fm
NPQ
Badger et al., 2009
In Cabinet HTP FIR Tray Screens
30cm X 25cm trays
Defined grids and automatic
regions of interest defined
Brachypodium distachyon as a model for wheat and
biofuel feedstocks (USDA / DOE)
• Small cereal (can be grown in trays of
20, as for Arabidopsis, 10cm high at
maturity)
• 6-8 week lifecycle
• Small sequenced genome (50Mb)
• High synteny with wheat
• Phenotyping 2000 genome wide KO’s
and 100 accessions for growth,
biomass and yield, photosynthesis,
abiotic stress tolerance and lignin /
cell wall properties
• Mapping traits to genomic regions
and genes
• Cloning homologues in wheat and C4
grasses
Crop Shoot Module :Growth imaging, 3D
reconstruction and overlay of signals in controlled
environments
• Whole of lifecycle photosynthesis and
growth
• Dynamic growth and carbon allocation
to plants organs
• Transpiration and water use
• Hyperspectral detection of leaf protein
and CHO
Max NPQ=1.25
Max ETR=0.2
Full 3-D Models with mesh overlay
Plant Scan and Imaging Arch
HRPPC, ADFA and CMIS collaboration
Digital estimation of biomass validated for a
range of species
•Wheat
•Rice
•Barley
•Cotton
•Chickpea
•Cowpea
•Flaveria
•Arabidopsis
1000
900
y = 31.553x + 32.357
2
R = 0.9865
Plant Area (Pixels)
800
700
600
500
400
300
200
100
3-D Volume and In silico Dissection
0
0
5
10
15
20
Leaf Area (cm-2)
25
30
Automated analysis protocol for IR thermography
Array multiplication (element by
element) to separate background
Use threshold limit
toleaves
set binary
from
and to apportion
mask
temperature data to leaf area
297.84oK
297.84oK
Thermograph: matrix of
temperature [640x480]
(8-bit false colour image for
visualisation)
Automatic threshold detection (Otsu
method, 1979)
100 mM
296.91ooK
296.91 K
control
∆ = 0.93oC
Temperature data averaged for
each plant and saved in EXCEL
spreadsheet
Crop Plant Root Module : NIR imaging of soil /roots
Mean pixel value
250
100mm diameter
45mm diameter
200
150
R2 = 0.9932
100
R2 = 0.9943
Results of NIR
monitoring allow
measurement of spatial
distribution water
content in soil
We have shown it can be
made quantitative
0h 2h 4h 6h 8h
50
0
0.00
0.02
0.04
0.06
0.08
0.10
0.12
Gravimetric water content (g/g)
0.14
Ground-based : Phenomobile, Imaging tower
and Distributed Sensors
Gives 1m2 area coverage at 2M boom height
• Variable span buggy 3M boom
• IR Camera + Hyperspec Radiometer /
camera
•Stereo camera / Lidar
• 2cm Hi Res GPS registers all data
•Porometer / SPAD Licor 6400
•Fits on a trailer
What Next ? : Cropatron
The Challenges at HRPPC
• Variety of non-commercial imaging systems and sensors
• Need to link experiments across platforms
• Metadata may have genotype, experimental and growth
conditions plus GIS data
• Users must be able to retrieve calculated and raw data
• Requirements to preserve large data sets for later reanalysis
or for “probity” in publication
• Long term desire to link to public databases