Plant Phenotyping, a new scientific discipline to quantify plant traits

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Plant Phenotyping , A new scientific discipline to quantify plant traits_Anke Schickling_Siagro2014_Embrapa Instrumentação

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Plant Phenotyping, a new scientific discipline to quantify plant traits

  1. 1. Mitglied der Helmholtz-Gemeinschaft Institute of Bio- und Geosciences IBG-2: Plant Sciences Plant Phenotyping -a new scientific discipline to quantify plant traits- Anke Schickling a.schickling@fz-juelich.de November 18, 2014
  2. 2. Forschungszentrum Jülich
  3. 3. Forschungszentrum Jülich Budget: 380 Mio. € Third party funding: 95 Mio. € (16 Mio. Industry) Employees: 4.300 Scientists: 1.500 + 900 guest scientists per year 8.500 patents
  4. 4. Forschungszentrum Jülich IBG-2 Plant Sciences www.fz-juelich.de/ibg/ibg-2 150 Employees ● 45 Scientists ● 25 PhD students • Bioeconomy • Plant Phenotyping • Adaptation to Climate Change • Sustainable Bioproduction • From basic research to application
  5. 5. Campus Klein-Altendorf (University of Bonn) • Long-term cooperation with University of Bonn ensures access to agricultural experimental field station • 250 ha fields plus greenhouse facilities
  6. 6. Mitglied der Helmholtz-Gemeinschaft Phenotyping: Why? Emerging discipline & Scientific challenge
  7. 7. environment Plant performance and plant production genes Phenotype is determined by gene x environment interaction Phenotype
  8. 8. Example for phenotypic plasticity a: medium light, moderate water b: low light, moderate water c: medium light, well watered d: low light, well watered
  9. 9. Example for phentypic plasticity e: different soils
  10. 10. Example for phentypic plasticity f: phentypic plasticity of different genotypes
  11. 11. Example for phentypic plasticity a: medium light, moderate water b: low light, moderate water c: medium light, well watered d: low light, well watered e: different soils f: different genotypes Complex interactions of various environmental factors and genetic plasticity requires large numbers of measurements to understand gene x environment interaction  Automisation of measurements
  12. 12. Phenotyping: Quantification of plant traits in space and time (including environmental and genetic constraints) Plant Production momentary traits Precision farming Breeding Seasonal and spatial development of traits Guided breeding
  13. 13. Studying genotype x environment interactions: from vision to practice
  14. 14. Quantitative measurement of shoot traits Parameters Method Resolution Pros Cons Shoot biomass, seedling vigor, color, shape RGB Whole organs or Rapid measurements, descriptors, root architecture, seed morphology organ parts; affordable solutions and surface features, leaf disease assessments minutes/days Limited physiological information PSII status, disease severity Fluorescence Whole shoot/ leaf tissue; minutes /days Probe of PSII photochemistry in vivo Only for rosettes; pre-acclimation conditions Surface temperature Thermal Whole shoot, or leaf tissue; time series minutes/days Rapid, potential information about leaf and canopy transpiration Sound bio-physical interpretation required Water content, seed composition NIR, multispectral Time series or single time point analyses of shoots and canopies; single seeds Estimates of biomass composition by chemometric methods Extensive calibration required Biomass, leaf and canopy water status, disease severity, pigment composition NIR, multi-hyperspectralt hermal Vegetation cycles outdoor/indoor Large amount of information Cost; illumination conditions; large image datasets; complex data interpretation Shoot structure , leaf angles distribution, canopy structure Stereo camera systems Whole shoots time series at various resolutions High 3D accuracy; shoot and canopy models Complex data reconstruction
  15. 15. Mitglied der Helmholtz-Gemeinschaft Automated measurements for fast screening: Example 1: Automated mapping of rosette fluorescence from A. thaliana to better understand adaptation of light reactions of photosynthesis
  16. 16. Automation of fluorescence imaging technique Jansen et al. (2009) Functional Plant Biology, 36, 902–914
  17. 17. Automation of fluorescence imaging technique Automation for fast measurement of large numbers of phenotypic data Jansen et al. (2009) Functional Plant Biology, 36, 902–914 Extraction of quantitative plant traits: ‘not only colorful pictures’
  18. 18. Automation of fluorescence imaging technique Three advantages of quantitative phenotyping  Extraction of quantitative traits  Temporal and spatial dynamics  Large number of standardized measurements Rascher et al. (2011) Functional Plant Biology, 38, 968–983
  19. 19. Automation of fluorescence imaging technique
  20. 20. Mitglied der Helmholtz-Gemeinschaft Automated measurements for fast screening: Example 2: Measuring the roots
  21. 21. Phenotyping of roots and shoots Shoot traits Root traits
  22. 22. GROWSCREEN-RHIZO: a new automated system for 2D imaging of roots and shoots Nagel et al. Funct Plant Biol (2012)
  23. 23. Measuring the roots
  24. 24. Mitglied der Helmholtz-Gemeinschaft Bringing Phenotyping to the Field Plant Phenotyping where it really matters – field / production conditions
  25. 25. Field Phenotyping at Campus Klein- Altendorf (University of Bonn)  Long-term cooperation with University of Bonn ensures access to agricultural experimental field station  250 ha fields plus greenhouse facilities
  26. 26. Mini plots for greenhouse and field • Large (1 x 0.8 x 0.6 m), mobile pots to cultivate crops under controlled and field conditions • Greenhouse and outdoor area • Automated sensor positioning system • RGB-camera, thermography camera, NIR-camera and laser scanner
  27. 27. FieldLift: mobile plattform to lift people and sensors • Mobile platform with integrated environmental monitoring module • Span 8 m – height 1 to 12 m • Autonomous electrical power supply
  28. 28. Mitglied der Helmholtz-Gemeinschaft Field Phenotyping: 3-D canopy reconstruction to better understand the influence of species and nitrogen availability on leaf display
  29. 29. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure
  30. 30. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure
  31. 31. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure  Zenith and azimuth of leaves can be quantified.  Method is parameterized and established for Arabidopsis, sugar beet, barley and apple trees Biskup et al. (2007) Plant, Cell & Environ. 30, 1299-1308 Rascher et al. (2010) Photosynthesis Research 105, 15-25 Müller-Linow & Rascher (to be submitted) BMC
  32. 32. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure  4 varieties of sugar beet show different leaf orientation  No nitrogen effect on leaf display
  33. 33. Mitglied der Helmholtz-Gemeinschaft Field Phenotyping: from airborne platforms
  34. 34. Flying platforms Zeppelin • Payload up to 5 kg • long flying time • RGB-camera, thermography camera, stereo camera setup and hyperspectral camera • Sensitive to wind Octocopter • Payload up to 1 kg • 20 min flying time • RGB-camera, thermography camera, and high-performance spectrometer • Highly flexible
  35. 35. Field: Phenotyping from flying platforms Octocopter • Payload up to 1 kg; 20 minutes flying time • Different sensors: RGB-camera, thermography camera, and high-performance spectrometer Burkart et al. (2013) IEEE – Sensors, Sensors-8468-2013.
  36. 36. Time series from experimental plots recorded in one vegetation period 16 m
  37. 37. Optical remote sensing of plants and vegetation Absorption, transmission and reflection of photons is primarily determined by plant pigments and constituents
  38. 38. Field: Phenotyping from flying platforms  HyPlant: a novel high performance spectrometer to measure sun-induced chlorophyll fluorescence First flight campaign of HyPlant in September 2012. Flight data after 3 years of development
  39. 39. Field: Phenotyping from flying platforms Flight of HyPlant in June 2014: Different barley varieties in the same environmental conditions
  40. 40. Field phenotyping within LABEX-GIB LABEX contract signed October 2012 Topics • Bioeconomy • Adaptation to Climate Change • Integrated Systems of Bioproduction • Sustainable use of resources in agro-systems • Phenotyping • Bioinformatics Specific projects • Field Phenotyping including campaign activities – a large international airborne campaign 2015/2016 • Development of IPPN with Brazil as partner
  41. 41. Mitglied der Helmholtz-Gemeinschaft Thank you for your attention!

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