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Root phenotyping
at Jülich Plant Phenotyping Centre (JPPC)
new routes to explore non-invasively
the hidden half of plants
Kerstin A. Nagel - 17/02/2014
Phenotyping the hidden half of plants – Why?
• Root system architecture can strongly affect yield
• Sustainable plant production requires root systems
optimised for growing conditions in the field
• Many of the traits required in future crops are tightly
linked to root properties:
- abiotic/biotic stress tolerance
- water and nutrient use efficiency
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- yield...
 However, root phenotyping is a challenging task,
mainly because of the hidden nature of this plant organ
Non-invasive phenotyping of roots
• Allows repetitive analysis of the same plant or plant organ
• This enables finding phenotypic differences that occur:
- transiently
- at certain developmental stages
- under certain environmental conditions
• Combined with robotic systems – enables high-throughput screening
of large numbers of genotypes
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• Overcome the phenotyping bottleneck
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Non-invasive technologies are key to quantify
plant structure and function
Fiorani et al. 2012, Current Opinion Biotechnology
Imaging plant function and structure is more than ‘taken pictures‘
Interpretation of images
requires knowledge of
•
•
•
•
sensor physics
sensor calibration
image analysis
plant traits
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Aim: measuring
quantitatively traits
Requirements for high throughput phenotyping
Automation of:
• quantitative image analysis
• plant cultivation (sowing – harvest)
• environmental monitoring
• data storage
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• quality monitoring
Development of root phenotyping facilities at JPPC
• reproducibly quantification of growth and architecture of roots
• elucidating dynamic establishment of roots in space and time
• interaction of root responses with aboveground plant part
• from artificial growth media to soil
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• from controlled conditions to field environment
Root phenotyping in artificial growth media
Throughput: 300 plants – 15 min
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Concept: plant-to-sensor
Nagel et al. 2009, Functional Plant Biology
Image analysis - quantify root system architecture
A
B
C
D
• Image preprocessing
• Identification of local root
elements
• Concatenating local root
elements by following roots
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• Crossings and branching
Mühlich et al. 2008, LNCS
Nagel et al. 2009, Functional Plant Biology
Root traits
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Global root traits
• total root length
• spatial distribution of roots
- root length density
- rooting depth
- root system width
- area covered by roots
Root traits derived from individual roots
• root length
• number of roots
• root diameter
• branching angle
Static root traits – measured at single time point
Dynamic root traits – related to dynamic changes
Nagel et al. 2009, Functional Plant Biology
Nagel et al. 2012, Functional Plant Biology
Vertical temperature gradients
for more realistic representation of field heterogeneity
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Biomass (g)
10
15
20
20-10
Root temperature treatment (°C)
Nagel et al. 2009, Functional Plant Biology
Füllner et al. 2012, Plant, Cell and Environment
Branching angle of laterals is temperature dependent
Branching angle (°)
10°C
15°C
20°C
20-10°C
75
70
65
60
55
50
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45
40
4
6
8
10
12
14
Time after sowing (d)
.
Nagel et al. 2009, Functional Plant Biology
Root phenotyping of soil grown plants
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GROWSCREEN-Rhizo
Throughput: 60-240 plants – 60 min
Concept: sensor-to-plant / plant-to-sensor
Nagel et al. 2012, Functional Plant Biology
Simultaneous phenotyping of root and shoot traits
Shoot traits
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Root traits
Projected shoot area correlates with shoot biomass
Shoot biomass (g)
20
R² = 0.9505
15
10
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5
0
0
100
200
300
400
500
600
Projected shoot area - 2D images (cm²)
Nagel et al. 2012, Functional Plant Biology
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Some parts of the root system are hidden in the soil
Visible portion of a root system depends on
the inclination angle of rhizotrons
40
vi
ro sib Ra
ot le tio
le vs
ng . t
th ota
(% l
)
30
20
10
0
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0°
25°
α
43°
β
Nagel et al. 2012,
Functional Plant Biology
Visible portion seems to depend on root diameter
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Plant species
Arabidopsis
Visible portion of
root system
Arabidopsis
77%
Rapeseed
42%
Barley
33%
Wheat
33%
Rice
32%
Brachypodium
24%
Maize
17%
Maize
Nagel et al. 2012, Functional Plant Biology
Visible root length correlates with total root length
Visible root length (cm)
900
800
700
600
500
400
300
Barley
R² = 0.91
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200
100
0
0
500
1000
1500
2000
2500
3000
Total root length (cm)
Nagel et al. 2012, Functional Plant Biology
Visible root length correlates with root biomass
Visible root length (cm)
900
800
700
600
500
400
300
Barley
R² = 0.92
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200
100
0
0
20
40
60
80
100
120
Root biomass (mg)
Nagel et al. 2012, Functional Plant Biology
Mechanical impedance affects root system architecture
Root system length (cm)
Depth (cm)
500
0
Low compaction
Moderate compaction
400
20
300
40
200
60
100
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0
80
6
8
10
12
14
16
18
Time after sowing (d)
20
0.0
0.1
0.2
0.3
0.4
0.5
Root length density (cm cm-2)
Nagel et al. 2012, Functional Plant Biology
Barley roots respond to localized soil compaction
Lateral root development
low/low
high/high
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Split-root
low/low
high/high
low/high
Split-root
On ‘low compacted side‘ of split root system
• roots grow deeper and
• lateral roots emerged earlier
Time after transplanting (d)
Pfeifer et al. 2014,
Functional Plant Biology
low
high
Root phenotyping non-invasively
• Screening for phenotypic plasticity
• Selection of root system architecture ideotypes for improved resource
use efficiency
• Identification of candidate genotypes with improved plant productivity
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• Development of new phenotyping concepts for crop breeding