High ResolutionPlant Phenomics Centre

http://www.plantphenomics.org.au/hrppc

High Resolution Plant Phenomics CentreFrom 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

–Colour imagesPlant area, volume, mass, structure, phenology Senescence, relative chlorophyll content, pathogenic lesionsSeed yield, agronomic traits

–Near IR imagingTissue water contentSoil water content

–Far IR imagingCanopy / leaf temperature / water use / salt tolerance

–Chl Fluorescence imagingPhysiological 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)

Key technologies

Model plant module

• Growth and morphology• Photosynthetic performance (Chl Fluor) under defined environmental conditions

Fluorogro-scan TrayScan RGB / FIR in-Cabinet

•IR screening for leaf temperature• Automated destructive sampling for metabolites, protein, DNA and RNA, delta13C

Target plants : Arabidopsis, Tobacco, Brachypodiumand 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 traysDefined grids and automaticregions 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 ETR=0.2

Max NPQ=1.25

Full 3-D Models with mesh overlay

Plant Scan and Imaging Arch

HRPPC, ADFA and CMIS collaboration

y = 31.553x + 32.357R2 = 0.9865

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Leaf Area (cm-2)

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Digital estimation of biomass validated for a range of species

•Wheat•Rice•Barley•Cotton•Chickpea•Cowpea•Flaveria•Arabidopsis

3-D Volume and In silico Dissection

Array multiplication (element by element) to separate background from leaves and to apportion temperature data to leaf area

control

297.84oK 296.91oK

∆ = 0.93oC

100 mM

297.84oK 296.91oK

Temperature data averaged for each plant and saved in EXCEL spreadsheet

Automated analysis protocol for IR thermography

Thermograph: matrix of temperature [640x480](8-bit false colour image for visualisation)

Automatic threshold detection (Otsu method, 1979)

Use threshold limit to set binary mask

Crop Plant Root Module : NIR imaging of soil /roots

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

R2 = 0.9943

R2 = 0.9932

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Gravimetric water content (g/g)

Mea

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45mm diameter

Ground-based : Phenomobile, Imaging tower and Distributed Sensors

• 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

Gives 1m2 area coverage at 2M boom height

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