a Boost for Genomics in the 21st Century

Transcription

High-throughput Plant
Phenotyping –
a Boost for Genomics in
the 21st Century
Dr. Jörg Vandenhirtz · CMO LemnaTec
Head of Research and Development
[email protected]
LemnaTec
 founded May 1998 in Aachen, Germany
 interdisciplinary team (biology, physics, engineering)
 12 years of experience with image based biological
measurement
 in-house development of image processing software
 in-house development of hardware
 development of comprehensive and integrated solutions
 compliance with international standards
Speaker: Dr. Joerg Vandenhirtz – CMO
Date:
10/24/2011
Slide 2
The human eye
How many legs does this elephant have?
The human eye
Count the number of black dots…
The human eye
The circles in the centers…
…are exactly the same size
The human eye
Accelerating plant phenomics
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
opening new prospects
high-throughput screens
multiple camera units
non-destructive measurement
quantitative analysis
monitor growth dynamics
stress assessment
link to genomics
Date:
10/24/2011
Slide 7
Hardware
3D
scanalyzer
accelerating plant phenomics
Hardware scanalyzer3D
Finding the needle in the haystack
Modern breeding or GMO methods are able to produce THOUSANDS of new varieties per week
The LemnaTec
Scanalyzer System
discovers THE ONE
which is relevant…
+3%
For example, THE plant with 3% increase in value is worth
$50m if it obtains 10% market penetration and released 2 years earlier
Automatic screening 10x more efficient than human screening
Date:
10/24/2011
Slide 10
scanalyzer3D multiple imaging
3D imaging of full plants
1.
3.
2.
1.
2.
3.
4.
top View
side View
side View 90°
more views
optional
Date:
10/24/2011
Slide 11
scanalyzer3D scanning modes
Scanning in different
wavelength and modes
1. RGB visible light
2. NIR near infrared light
3. FLUOR fluorescent light
4. IR infrared light
2.
3.
4.
5.
5. ROOT NIR / RGB
1.
Date:
10/24/2011
Slide 12
scanalyzer3D VIS imaging – shape
1.
Scanning – visible light
High-resolution colour images for comprehensive
morphological and growth phenotyping
Date:
10/24/2011
Slide 13
scanalyzer3D VIS imaging – colour
1.
Plant colour classification – Key to plant health,
stress, nutrients and senescence
Date:
10/24/2011
Slide 14
scanalyzer3D VIS imaging – architecture
1.
Plant skeleton analysis – key to growth dynamics,
morphology and architecture
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separation of stem and leaves
information about nodes, length of leaves
morphology
plant growth phases
Date:
10/24/2011
Slide 15
scanalyzer3D VIS imaging – architecture
1.
Phenotyping of growth under field-density growth conditions
2.
Phenotyping based on complex
morphological criteria like:
4,50
4,00
bending index
3,50
medium heigt, wide,
kinked leaves
3,00
high,straight upright
2,50
2,00
compact straight,
intermediate height
1,50
compact curved
1,00
0,50
0,00
0,00
1,00
2,00
3,00
4,00
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structure orientation,
momentum of inertia,
height,
width,
roundness,
compactness.
axis momentum ratio
Date:
10/24/2011
Slide 16
scanalyzer3D NIR imaging – shoot
2.
0h
100%
4h
% NIR absorption class
90%
80%
70%
60%
50%
40%
30%
20%
10%
8h
16 h
0%
0
1
2
3
4
5
6
7
8 9 10 11 12 13 14 15 16
hours
• wheat dried down over 16 h at elevated temperature
• LemnaTec NIR imaging and analysis can cover the
whole water dynamics of the drying for wheat
• LemnaTec NIR cameras are suitable for detection of
fine cereals structures of fully grown wheat
Date:
10/24/2011
Slide 17
scanalyzer3D flourescence imaging
3.
Scanning – flourescent light
blue light (< 500 nm) visualises any related fluorescence
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chlorophyll (cont., flash)
green fluo. Protein (GFP)
phenolics
autofluorescence
custom solutions
Date:
10/24/2011
Slide 18
scanalyzer3D IR imaging
4.
Scanning – infrared light
Quantify temperature differences
(e. g. within leaves and between plants)
Date:
10/24/2011
Slide 19
scanalyzer3D IR imaging
4.
Scanning – infrared light
Quantify temperature differences
(e. g. within leaves and between plants)
Date:
10/24/2011
Slide 20
scanalyzer3D RGB imaging – root
Static root density profiles – growth pattern
Bangui
Sweet Corn
Prelude
Bangui
Date:
10/24/2011
Slide 21
scanalyzer3D RGB imaging – root
Dynamic root growth - pattern
Day 0
12
25
35
60
100
image and
data show
the
development
of roots of
one plant in
time.
Date:
10/24/2011
Slide 22
scanalyzer3D NIR imaging – root
5.
Scanning – near infrared light for roots
spatial distribution of water content in soil
0h 2h 4h 6h 8h
Date:
10/24/2011
Slide 23
scanalyzer3D NIR imaging – root
Corn plant previously shown was grown in a
transparent 8 cm polyacryl column
Results of NIR monitoring allow measurement of
spatial distribution water content in soil
total development
of drying over time
area classification pixel
1500
1000
2h 4h
6h 8h
0h
A01
B01
C01
D01
E01
F01
G01
H01
I01
J01
K01
L01
2000
0h
drying dynamics based on soil layer
500
0
0h 2h 4h 6h 8h
8h
A01
B01
C01
D01
E01
F01
G01
H01
I01
J01
K01
L01
0
25 50 75 100 125 150 175
area classified pixels
0
25 50 75 100 125 150 175
area classified pixels
Date:
10/24/2011
Slide 24
Hardware Future Developments?
Non invasive imaging of plants and plant roots in substrate with Nuclear Magnetic
Resonant Imaging (NMRI) and (Sub) Terahertz Imaging (THz)
Dr. Axel Jung
Ricarda van der Heijden
Beta Klinik Bonn
Dr. Karsten Specht
Prof. Dr. Martin Koch
University of Bergen
IHF TU Braunschweig
Dr. Jörg Vandenhirtz
Matthias Eberius
Dirk Vandenhirtz
LemnaTec
Goal of this joint study:
Can Nuclear Magnetic Resonant Imaging (NMRI) or (Sub) Terahertz Imaging (Thz) be used for obtaining
non invasive and valuable information about plant roots in substrate?
• 3D root morphologie
• 3D root dynamics
• 3D root activity (water distribution)
• etc...
Used Plants:
Corn Plants in transparent pots:
movingfield
linking greenhouse to field
Siemens MAGNETOM Espree 1.5T
NMR settings:
B
TE
TR
FoV
ST
Price: 1.5 Mio Euro
=
=
=
=
=
1.5 T
12 ms
5.0 s
250 x 250
1 mm
First Results of Dr. Axel Jung, Beta-Klinik, Bonn
First Results of Dr. Axel Jung, Beta-Klinik, Bonn
Problems:
• artefacts (debris) in substrate hide roots (H2O + Fe)
• low contrast between roots and background
• correct setting of NMR has to be researched
-> Contact to Dr. Karsten Specht
Department of Biological and Medical Psychology
University of Bergen, Norway
Research on NMRI
Dr. Specht tried NMRI of his office Plant...
First Results of Dr. Karsten Specht, Uni Bergen:
First Results of Dr. Karsten Specht, Uni Bergen:
Complementary option for non invasive and penetrating plant
sensors:
Visible
Radiowaves
10
7
“THz”
Microwaves
10
8
10
9
10
10
10
11
10
Infrared
12
10
13
10
Ultraviolet
14
10
15
10
16
X-Ray
10
17
Frequency (Hz)
THz radation can be considered as high-frequency microwaves
or very long waved light.
Prof. Dr. Martin Koch
Institut für Hochfrequenztechnik
TU Braunschweig
water concentration
First THz image of a leaf with high resolution
Fresh leaf
48 hours after cut
B.B. Hu und M.C. Nuss, Opt. Lett. 20, 1716 (1995)
Bell Labs
Lucent Technologies
First Results of Prof. Dr. Martin Koch, Braunschweig:
…and measuring the
transmission of the
sub THz signal
THz
detector
THz
transmitter
moving a coffee plant
between a sub THz
transmitter and detector…
The lift and rotating devices of the LemnaTec Phenotyping Platform are
already integrated for 3D THz scans in cylindrical coordinates:
THz
z
f
detector
transmitter
Combining 3D THz transmission measurements with visible 3D RGB image
data of the LemnaTec Phenotyping Platform
Conclusions:
NMRI
THz
hardware
standard of the shelf technology
to be developed
software
to be developed
to be developed
throughput
ca. 20 min. per plant
ca. 2 min. per plant
resolution
ca. 1 mm
ca. 1 cm
high B-Field
none
price
ca. 1.5 Mio. Euro
ca. 150,000 Euro
target
roots and shoots
shoots (roots?)
hazards
Software Future Developments?
EuroStar Project PhenoFab
January 2009 – January 2011
Project sum ca. 1.000.000 Euro
Development of a software interface between the output
database format of DNA sequencers (e.g. La Roche) and the
output database format of the image processing of the
LemnaTec High Throughput Phenotyping Platform for
multidimensional correlation analysis between the 2 datasets
Software Future Developments?
Genomics
Plant
CORRELATION ???
Phenomics
Contractracted
Phenotyping
Research
Date:
10/24/2011
Slide 40
References
Most Global Players in Breeding and GMO are already using the
LemnaTec Technology:
• BASF
• Pioneer Dupont
• Bayer CropScience
• Monsanto
• Syngenta
• Dow Agro
• Keygene
• IPK
• CSIRO
• ACPFG
• etc.
Thank you for
your attention!
Visit our website www.lemnatec.com
Time for your
questions
Visit our website www.lemnatec.com

a Boost for Genomics in the 21st Century

Transcription

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