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Non-invasive measurements of plant traits at the Jülich Plant Phenotyping Centre

Roland Pieruschka, Kerstin A. Nagel, Siegfried Jahnke, Uwe Rascher, Fabio Fiorani, Ulrich Schurr

Why phenotyping?

Keeping the pace with genomics

Evaluation of key traits for target environment

Resistance to abiotic and biotic factors

Identification of genomics regions related to performance

Identify genes involved in physiological processes

Monitoring and quality control

Plant phenotyping science requires integrated solutions

IMAGING AND ROBOTICS Automation and Integration Quantitative Image Analysis

SPECIALIZED PLANT GROWTH FACILITIES UV-transparent greenhouse Automated growth chambers Field positioning systems

DATA MANAGEMENT Environment Data Base Plant Information System

Non-invasive technologies are key to quantify plant structure and function

Fiorani et al. 2012

Plant size

Root tip

agar

Root architecture agar / soil

Resolution

Root function

pot

Root structure and function - integration across scales

throughput: 300 plants – 12 min

Quantification of root architecture in agar

Nagel et al. 2009

Arabidopsis Small seedlings

• Nutrients (N, P) • Temperature • Osmotic

GROWSCREEN-RHIZO - automated system for 2D imaging of roots and shoots

40 cm

60 cm

Nagel et al. 2012

Visible root length correlates with global root parameters

Nagel et al. 2012

Correlation with average root diameter?

Plant species Ratio visible / total

root length

Arabidopsis 77%

Rapeseed 42%

Barley 33%

Wheat 33%

Rice 32%

Brachypodium 24%

Maize 17%

Nagel et al. 2012

Root mass distribution

Time (days after sowing)

24 26 28 30 32 34 36 38 40 42 44 46

Ro

ot

ma

ss (

%)

0

20

40

60

inner half (50% of volume)

outer part (20% of volume)

Mean ±SD, n = 6

Pot size matters - barley root mass distribution in a pot

Poorter et al. 2012

Root mass %

4.7T

11CO2

CYPRES Cyclotron for Plant Research

1.5T

MRI Magnetic Resonance Imaging

PET Positron Emission Tomograph

MRI-PET combining structure and functuion

Jahnke et al. 2009

MRI PET Coregistration

MRI-PET insight into carbon flow

Shoot structure and function - integration across scales

Leaf and plant Greenhouse and field

Growth and chlorophyll fluoroescence of Arabidopsis

Jansen et al. 2009

Time (d a.s.)

15 20 25 30 35 40 45 50 55

Qu

an

tum

yie

ld

0.30.40.50.6

0.7

0.8

Time (d a.s.)

15 20 25 30 35 40 45 50 55

AP

T (

cm

²)

5

10

15

20

25

30

35

40

minimal nutrient soil

normal nutrient soil

Projected Leaf Area (cm²)

Quantum Yield

• Biomass (image based)

• Biomass (micro wave based)

• Geometric parameters

• Transpiration

SCREEN House phenotyping of plants with different size and structure

Automated field positioning systeme

Plückers et al. 2012

FieldScreen (developed at FZJ IBG-2 in 2009)

• an outdoor field system for automated and

repeated optical measurements over canopies

• the system consists of a large 4 meter high

computer-programmable x-y-moving stage

equipped with diverse sensors

Remote measurement from a distance up to 50 m Laser Induced Fluorescence Transient (LIFT) approach

ETRA / PPFD

0.0 0.1 0.2 0.3 0.4 0.5

F F

m'-1

0.0

0.2

0.4

0.6

0.8

PAM (X. strumarium)

LIFT (H. annuus)

LIFT (Ph. vulgaris)

LIFT (Citrus spec.)

PAM: y=2.236x+0.024

R²=0.993

LIFT: y=1.373x-0.021

R²=0.947

(A)

ETRA [µmol m-2

s-1

]

0 50 100 150

ET

RP

AM &

ET

RLIF

T [µ

mol m

--2 s

-1]

0

50

100

150 (B)

Pieruschka et al. 2010

W E

6:00 8:00 10:00 12:00 14:00 16:00 18:00

20:00 22:00 6:00 8:00 10:00 12:00 14:00 16:00

0.10 – 0.90

LIFT based maps of diurnal dynamics of photosynthetic

efficiency in a tree canopy

Nichols et al. 2012

Solar and earth atmosphere is a spectrally selective filter

Two oxygen bands are at the spectral region for fluorescence retrieval

Sun-induced fluorescence

https://sites.google.com/site/jamestuttlekeane/astronomy/physics

Sun-induced fluorescence retrieval concept

slope:

reflectance

intercept:

fluorescence

Fluorescence retrieval according to the Fraunhofer Line Depth (FLD) method

Rascher & Damm 2010, Meroni et al. 2009

Sun-induced fluorecence can be mapped in the field giving new insight into canopy energy conversion

Rascher et al. 2009

Imaging spectroscopy in the field

Specific wavebands are characteristic

for plant constituents

Non-invasive monitoring of seasonal

and variety specific traits

Rascher & Damm 2010, Fiorani et al. 2012, Jansen et al. in press

Deapth (disparity) map

Leaf orientation

NDVI PRI

Stereo plus multispectral reflectance imaging: quantification of canopy structure and function

Fiorani et al. 2012

1. Phenotyping requires systematic approaches

2. Phenotyping ‘chains’ to bridge between lab and field

3. Relevant environmental conditions are crucial

4. Multi-mode - multi-scale - multi-disciplinary

26

Phenotyping

community

USERS

DEVELOPERS RESEARCHERS

Collaboration is key to respond to a growing plant phenotyping demand

Phenotyping – a networking approach

Phenotyping projects coordinated by JPPC

Goals:

Create a European integrated network

Provide Tansnational Access for the user community

Develop novel instrumentation for non-invasive methods

Establish definition of standards

Duration: January 2012 – December 2015

Budget: 5 500 000 €

EPPN is the first integrated FP 7 EU

Research Infrastructure project

in Plant Sciences

Grant Agreement No. 284443.

The EPPN consortium consists of 14 Partners

FZJ IPK HMGU INRA UNOTT HAS ABER

Transnational Access

23 facilities across Europe open for access:

free of charge

simple selection procedure

1. Screen Chamber

2. Screen House

3. ScreenRoot LP

4. Screen Root SP

5. APPP

6. MP

7. ExpoScreen

8. SunScreen

9. Phenopsis

10. Phenodyn

11. PPHD

12. Diaphen

13. MicroCT

14. Root Trace

15. Screen Glasshouse

16. Vertical Confocal

17. Screen Field

18. RSDS

19. SSDS

20. FTIR/NMR

21. IPC

22. Micro Raman

23. TGA-py GC/MS

Transnational Access call is permanently open

for 23 facilities across Europe

Several workshops and summer schools

will be organized

Standards and protocols will be accessible

Contact information

Resources: www.plant-phenotyping-network.eu

JPPC in the national and international framework

Transnational access Root resource use efficiency in cereals

PREBREED YIELD Sensor technology for crop breeding and management

Nested association mapping in canola

Building a national plant phenotyping platform

Worldwide network

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