High Resolution Plant Phenomics Centre plantphenomics.au/hrppc

1. High Resolution Plant Phenomics Centre http://www.plantphenomics.org.au/hrppc

2. 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

3. 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)

4. Model plant module Fluorogro-scan TrayScan RGB / FIR in-Cabinet • Growth and morphology • Photosynthetic performance (Chl Fluor) under defined environmental conditions • IR screening for leaf temperature • Automated destructive sampling for metabolites, protein, DNA and RNA, delta13C Target plants : Arabidopsis, Tobacco, Brachypodium and seedling screens

5. 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!

6. Isolating Photosynthetic and Photorespiratory Mutants Fv/Fm NPQ Badger et al., 2009

7. In Cabinet HTP FIR Tray Screens 30cm X 25cm trays Defined grids and automatic regions of interest defined

8. 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

9. 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

10. Full 3-D Models with mesh overlay Plant Scan and Imaging Arch HRPPC, ADFA and CMIS collaboration

11. 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

12. Array multiplication (element by element) to separate background from leaves and to apportion temperature data to leaf area Use threshold limit to set binary mask 296.91oK 297.84oK 296.91oK 297.84oK Thermograph: matrix of temperature [640x480] (8-bit false colour image for visualisation) control 100 mM ∆ = 0.93oC Automatic threshold detection (Otsu method, 1979) Temperature data averaged for each plant and saved in EXCEL spreadsheet Automated analysis protocol for IR thermography

13. 250 100mm diameter 45mm diameter 200 Mean pixel value 150 R 2 = 0.9932 100 R 2 = 0.9943 50 0 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 Gravimetric water content (g/g) 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

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

15. What Next ? : Cropatron

16. 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