The document summarizes research on plant phenotyping conducted at the Forschungszentrum Jülich. It describes phenotyping as quantifying plant traits in space and time, including effects of environment and genetics. Methods discussed include automated measurements of shoots and roots, field phenotyping using mini-plots and aerial sensors, and 3D reconstruction of canopies. Examples demonstrate quantifying photosynthesis and measuring various plant traits from airborne platforms to better understand crop responses and gene-environment interactions.

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. Forschungszentrum Jülich

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. 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. 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. Mitglied der Helmholtz-Gemeinschaft
Phenotyping:
Why?
Emerging discipline &
Scientific challenge

7. environment
Plant performance and
plant production
genes
Phenotype is determined by
gene x environment interaction
Phenotype

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. Example for phentypic plasticity
e: different soils

10. Example for phentypic plasticity
f: phentypic plasticity of different genotypes

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. 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. Studying genotype x environment
interactions: from vision to practice

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. 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. Automation of fluorescence imaging
technique
Jansen et al. (2009) Functional Plant
Biology, 36, 902–914

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. 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. Automation of fluorescence imaging
technique

20. Mitglied der Helmholtz-Gemeinschaft
Automated measurements
for fast screening:
Example 2: Measuring the roots

21. Phenotyping of roots and shoots
Shoot traits
Root traits

22. GROWSCREEN-RHIZO: a new automated
system for 2D imaging of roots and shoots
Nagel et al. Funct Plant Biol (2012)

23. Measuring the roots

24. Mitglied der Helmholtz-Gemeinschaft
Bringing Phenotyping to the
Field
Plant Phenotyping where it really matters –
field / production conditions

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. 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. 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. Mitglied der Helmholtz-Gemeinschaft
Field Phenotyping:
3-D canopy reconstruction to better understand
the influence of species and nitrogen availability
on leaf display

29. 3-D Canopy structure: Stereo Imaging allows the
quantification of canopy structure

30. 3-D Canopy structure: Stereo Imaging allows the
quantification of canopy structure

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. 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. Mitglied der Helmholtz-Gemeinschaft
Field Phenotyping:
from airborne platforms

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. 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. Time series from experimental plots
recorded in one vegetation period
16 m

38. Optical remote sensing of plants and
vegetation
Absorption, transmission
and reflection of photons is
primarily determined by
plant pigments and
constituents

39. 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

40. Field: Phenotyping from flying platforms
Flight of HyPlant in June 2014:
Different barley varieties in the same
environmental conditions

41. 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

42. Mitglied der Helmholtz-Gemeinschaft
Thank you for your attention!