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

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Non-invasive measurements of plant traits at the J端lich 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

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

IMAGING AND ROBOTICS Automation and Integration Quantitative Image Analysis

DATA MANAGEMENT Environment Data Base Plant Information System

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

Fiorani et al. 2012

Root structure and function - integration across scales Root architecture agar / soil

Root tip agar

Root function pot

Plant size Resolution

Quantification of root architecture in agar

throughput: 300 plants – 12 min Arabidopsis Small seedlings Nagel et al. 2009

• 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

Pot size matters - barley root mass distribution in a pot Root mass distribution

Root mass %

inner half (50% of volume) outer part (20% of volume)

Root mass (%)

60

40

20

Mean ÂąSD, n = 6

0 24

26

28

30

32

34

36

38

Time (days after sowing)

Poorter et al. 2012

40

42

44

46

MRI-PET combining structure and functuion MRI

11CO 2

Magnetic Resonance Imaging

1.5T

4.7T

CYPRES Cyclotron for Plant Research

PET Positron Emission Tomograph

MRI-PET insight into carbon flow MRI

Coregistration

Jahnke et al. 2009

PET

Shoot structure and function - integration across scales

Leaf and plant

Greenhouse and field

Growth and chlorophyll fluoroescence of Arabidopsis

APT (cm²)

Projected Leaf Area (cm²) 40 35 30 25 20 15 10 5

minimal nutrient soil normal nutrient soil

15 20 25 30 35 40 45 50 55 Time (d a.s.)

Quantum Yield Quantum yield

0.8

0.7

0.6 0.5 0.4 0.3 15 20 25 30 35 40 45 50 55 Time (d a.s.)

Jansen et al. 2009

SCREEN House phenotyping of plants with different size and structure

• Biomass (image based) • Biomass (micro wave based) • Geometric parameters • Transpiration

Automated field positioning systeme 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

Plückers et al. 2012

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

F Fm'

-1

0.8

(A) PAM: y=2.236x+0.024 R²=0.993 LIFT: y=1.373x-0.021 R²=0.947

0.6 0.4 PAM (X. strumarium) LIFT (H. annuus) LIFT (Ph. vulgaris) LIFT (Citrus spec.)

0.2 0.0 0.0

0.1

0.2

0.3

0.4

0.5

150

(B)

-2

-1

ETRPAM & ETRLIFT [µmol m- s ]

ETRA / PPFD

100

50

0 0

50

100 -2

150 -1

ETRA [µmol m s ]

Pieruschka et al. 2010

LIFT based maps of diurnal dynamics of photosynthetic efficiency in a tree canopy 0.10 – 0.90 W

20:00

E

6:00

8:00

10:00

12:00

14:00

16:00

18:00

22:00

6:00

8:00

10:00

12:00

14:00

16:00

Nichols et al. 2012

Sun-induced fluorescence Solar and earth atmosphere is a spectrally selective filter Two oxygen bands are at the spectral region for fluorescence retrieval https://sites.google.com/site/jamestuttlekeane/astronomy/physics

Sun-induced fluorescence retrieval concept Fluorescence retrieval according to the Fraunhofer Line Depth (FLD) method

slope: reflectance intercept: fluorescence

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

Stereo plus multispectral reflectance imaging: quantification of canopy structure and function Deapth (disparity) map

Leaf orientation

NDVI

PRI

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

Collaboration is key to respond to a growing plant phenotyping demand USERS

Phenotyping community

RESEARCHERS

DEVELOPERS

26

Phenotyping – a networking approach Phenotyping projects coordinated by JPPC

EPPN is the first integrated FP 7 EU

Research Infrastructure project in Plant Sciences 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 ₏

Grant Agreement No. 284443.

The EPPN consortium consists of 14 Partners

Transnational Access 23 facilities across Europe open for access: free of charge

simple selection procedure

FZJ

IPK

HMGU

INRA

UNOTT

HAS

ABER

1. Screen Chamber

5. APPP

7. ExpoScreen

9. Phenopsis

13. MicroCT

18. RSDS

20. FTIR/NMR

2. Screen House

6. MP

8. SunScreen

10. Phenodyn

14. Root Trace

19. SSDS

21. IPC

3. ScreenRoot LP

11. PPHD

4. Screen Root SP

12. Diaphen

15. Screen Glasshouse

22. Micro Raman

16. Vertical Confocal

23. TGA-py GC/MS

17. Screen Field

Resources: www.plant-phenotyping-network.eu

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

JPPC in the national and international framework

Root resource use efficiency in cereals

Transnational access

Worldwide network

PREBREED YIELD Nested association mapping in canola

Sensor technology for crop breeding and management

Building a national plant phenotyping platform

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