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Plant Phenomics at PAG 2011
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Evaluation of Next Generation Phenotyping:
The Australian Plant Phenomics Facility
Geoff Fincher, Mark Tester, Bob Furbank,
Murray Badger
PAG 2011 LemnaTec Workshop San Diego; 18 January 2011
Abiotic Stress Tolerance in Australian Cereals
• Drought
• Salinity
• Frost
• Hostile soils
– nutrients at toxic levels
– nutrients at deficient levels.
The key research strategies to enhanced drought and salinity tolerance
Reverse genetics Nominate candidate genes from -omics approaches, bioinformatics; measure effects of
altering levels and patterns of expression in crop and model plants Forward genetics Discover and exploit natural variation • germplasm collections, mapping populations, association panels, mutant populations,
breeding populations • positional cloning of responsible alleles • introgression into commercial lines Useful approach for complex, multi-genic traits (drought, salinity tolerance)
Phenotyping – overcoming
the bottleneck
Genotyping is relatively fast; genome sequencing advancing!
Phenotyping is still time consuming and labor intensive
Technological advances essential for high throughput phenotyping – robotics, non-destructive image analysis, powerful computers
Australian Plant Phenomics
Facility – two nodes
The Plant Accelerator™
Adelaide
Mark Tester and Geoff Fincher
High Resolution Plant Phenomics Centre
Canberra
Bob Furbank and Murray Badger
$21 m
$32 m
Australian Plant Phenomics Facility
(Commissioned January 2010)
High Resolution Plant Phenomics Centre
(Canberra): Phenotyping technology
• Infra-red imaging of transpiration
• Hyperspectral imaging of C, N, phenolics
• FTIR imaging at cellular level
• Chlorophyll fluorescence imaging of photosynthesis
• Hyperspectral sensing of stress tolerance
• Validation and deployment.
High Resolution Plant Phenomics Centre
Australian Plant Phenomics
Facility – two nodes
The Plant Accelerator™
Adelaide
Mark Tester and Geoff Fincher
High Resolution Plant Phenomics Centre
Canberra
Bob Furbank and Murray Badger
$21 m
$32 m
Australian Plant Phenomics Facility
The Plant Accelerator
4,485 m2 building, 2,340 m2 of greenhouses, 250 m2 for growth chambers
4 x 140 m2 fully automated ‘Smart-houses’
Plants delivered on 1.2 km of conveyors to four sets of cameras
High capacity image capture and analysis equipment
50% containment/quarantine - 50% standard glasshouse; 2x imaging stations in each
handle >100,000 plants annually in a range of conditions, automated watering
variable room/compartment sizes and independent environmental control for each room
water purification and re-cycling system.
LemnaTec System
Image capture
Side View Side View 90° Top view
Bettina Berger Barley cv. Sahara
Image analysis data match with
measured phenotypic data in wheat
Rajendran et al. (2009) Plant Cell Environ 32, 237-249
• The projected shoot
area of the RBG
image gives a good
correlation with
shoot biomass
• Tested for various
plant species
– wheat, barley
– rice
– cotton
– Arabidopsis …
y = 154154x + 19065
R² = 0.9205
0
50000
100000
150000
200000
250000
300000
0 0,5 1 1,5
Pro
jecte
d s
ho
ot
are
a [
pix
el]
Dry weight [g]
Measuring techniques
relevant for drought and
salinity research
Colour imaging – biomass, structure, phenology
– leaf health (chlorosis, necrosis)
Near infrared imaging – tissue water content
– soil water content
Far infrared imaging – canopy/leaf temperature
Fluorescence imaging – physiological state of photosynthetic machinery
Automated weighing and watering – water usage, imposing drought/salinity conditions
Colour classified image
Line Green area Necrotic area % Necrosis
Sahara 30739 4232 12%
Clipper 11640 15321 57%
Treated with 100 mM GeO2, 8 d
Julie Hayes, Margie Pallotta and Tim Sutton, ACPFG
Use of colour information e.g. Ge/B toxicity screen in barley
Original image
Germanium can alleviate B toxicity: same transporter?
B toxicity - leaf symptom score Ge toxicity - leaf symptoms
Jefferies et al. 1999. TAG 98, 1293-1303 Hayes et al., unpubl., using LemnaTec
QTL for Ge tolerance identified using colour imaging overlaps QTL for B tolerance
Barley Chromosome 2H
Clipper Vlamingh
Object properties
• minimum enclosing
rectangle
• minimum enclosing
circle
• convex hull
• compactness
e.g. wilting:
- Alters rectangle
parameters
- Increases area below
top of pot
- Increases the
rotational moment
System can quantify
morphometric parameters
Measured shoot dry weight [g]
Pre
dic
ted s
hoot
dry
weig
ht
[g]
Golzarian et al. (2010) Plant Methods, submitted
Estimation of shoot biomass
Improved estimate of biomass
when age of the plant is
taken into account
Y = a0 + a1×(G+B+Y)+
a2×(G+B+Y)×H
(H = number of days after seed
preparation date)
(Correction for leaf colour did
not greatly improve weight
estimates)
(Cross validation run 10x)
Osmotic tolerance in wheat
Mapping population of Berkut x Krichauff – Berkut – CIMMYT
– Krichauff – Australian cultivar
– Berkut higher overall tolerance despite higher tissue [Na+]
Parents – Berkut – 0.65
– Krichauff – 0.33
Range of progeny – 0.13 to 0.96
Mapped significant (21%) QTL to chromosome 1D
(day-1)
Berkut
Krichauff
Karthika Rajendran
QTL mapping of osmotic tolerance
Significant QTL on chromosome 1D
QTL1D.9 explains 21% of phenotypic variation in the population
Favourable allele comes from Berkut
Chromosome 1D
Karthika Rajendran
Data acquisition
Data management
Image analysis
Statistical analyses
Modeling and biological interpretation
aligning phenomics data with genomics data
ontologies development.
Offsite back-up
UniSA and ACPFG established a Chair and Assoc Prof in Plant Phenomics and Bioinformatics ($1.5m)
LemnaTec Data System
FLUO
1392 x 1040
RGB
2056 x 2454
IR
320 x 256 320 x 256
NIR
Snapshot
Smarthouse database
Imaging configurations
Conveyor tasks
Watering tasks
Smarthouse operations
Around 30MB per snapshot – 72 GB per day, 0.5 TB per week
Analysis results
The Plant Accelerator™ team to date
Mark Tester
Geoff Fincher
Helli Meinecke – business manager
Bettina Berger – postdoctoral scientist
James Eddes, Bogdan Masznicz, Jianfeng Li – computer programmers
Robin Hosking – horticulturalist
Richard Norrish – electrical engineer
Lidia Mischis, A.N. Other – technicians
Karthika Rajendran – PhD student
Brett Harris – Honours student
Desmond Lun, Irene Hudson, Mahmood Golzarian
– UniSA /ACPFG maths, stats
Anton van den Hengel – UA computer vision
+ three programmers in UQ to construct the database repository
www.plantaccelerator.org.au www.plantphenomics.org.au
Acknowledgement of funding
Adelaide Canberra
NCRIS $10 m NCRIS $5.24 m
NCRIS - ALA $0.25 m NCRIS - ALA
$0.25 m
Federal government (stimulus package)
$5 m Federal government
$5 m
South Australian government
$10 m ACT government $1.1 m
University of Adelaide $5.9 m CSIRO $5.8 m
Interest (est.) $0.41 m ANU $3.5 m
Total $31.56 m Total $20.89 m
Evaluation of Next Generation Phenotyping:
The Australian Plant Phenomics Facility
Geoff Fincher, Mark Tester, Bob Furbank,
Murray Badger
PAG 2011 LemnaTec Workshop San Diego; 18 January 2011