Crop Canopy Sensors for High
Throughput Phenomic Systems
Dr. Mike Schlemmer, Agronomist/Wheat Trial Manager
Bayer Field Phenomics Program
Scope
• Exploit the potential of phenomics to provide
novel insights in plant response to genetic and
environmental variation.
Intent
• Integrate phenomics with genomic marker
assisted selection to create a more efficient
marker based selection process.
High Throughput Phenomic Sensor Suite
Testing: Initial Phase
Genotype x Nitrogen x Plant Density
Data Collection
26 Apr
6 May
3 Jun
14 May
16 Jul
Yield Results
•
•
Yield Response plateaus, 40-60 lbs
N ac-1.
Yield Response plateaus, 0.8-1.2 M
plants ac-1.
Rapid Field Phenomic Sensor Suite
Optical Sensor
Companion Sensor
Upwelling PAR
IRT
Crop Circle DAS43X
2 Chan Voltage Input/
Humidity/Temp
Downwelling
PAR
Pulse Counter
Rapid Field Phenomic Sensor Suite
Measured Variables
3-second Running Average
Reflectance from 3 bands, 10nm FWHM (Red, Red Edge(RE), NIR)
•
Select Optical Indices - Canopy Chlorophyll Index(RE), NDVI.
6
5
CI red-edge
•
•
Canopy Chl Content.
•
Green Leaf LAI.
•
Canopy Height (via optical methods and ultra-sonic).
4
3
2
1
0
1
459 917 1375 1833 2291 2749 3207 3665 4123 4581 5039 5497 5955 6413
Number of Readings
•
Downwelling PAR, Upwelling PAR = Fractional PAR (fPAR).
•
Relative Humidity.
•
Ambient Temperature, Canopy Temperature = Temperature Departure (DT).
3000
y = 773.74x - 198.3
r2 = 0.8702
Canopy Chl Content, mg m-2
2500
2000
1500
1000
500
0
0
0.5
1
1.5
2
Chl Index Red Edge (CIRE)
2.5
3
3.5
4
Data Collection Rate: 5Hz
What spectral regions are most sensitive to
Chlorophyll Content. Green and Red Edge
Coefficient of determination for the
relationship between reflectance and chl
content for each wavelength.
• The peaks at 555 nm and 715 nm
indicate these regions to be maximally
sensitive to chl content.
• Those peaks show a strong linear
relationship to chl content where the
blue and red absorbance regions do
not.
Green-Refl.
Near IR-Refl.
Blue/Red Absorb.
Chlorophyll
Palisade Cells
Upper and Lower
Epidermis
Spongy mesophyll
Stoma
Air
space
60
0.7
50
0.6
yNIR = 0.0019x + 52.433
R2 = 0.0149
Blue
Green
Red
Red Edge
NIR
0.5
Reflectance, %
Coefficient of Determination, r
2
40
0.4
0.3
yRE = -0.0267x + 42.563
R2 = 0.7628
30
yGRN = -0.0233x + 30.76
20
R2 = 0.7473
0.2
10
0.1
0
400
450
500
550
600
650
Wavelength, nm
700
750
800
850
900
0
100
200
yBlue = -0.0035x + 12.985
yRed = -0.0041x + 13.134
R2 = 0.2827
R2 = 0.2472
300
400
Leaf Chl Content, mg m-2
500
600
700
Canopy Chl Content as a function of the Red
Edge Chl Index.
•
•
•
Canopy Chl at the time of
flowering may reach a
response plateau near 100
lbs N ac-1.
Yield Response plateaus
near 40-60 lbs N ac-1.
N Partitioning /
Translocation? Grain
Protein Content?
Fractionally Absorbed PAR (fAPAR).
•
•
fAPAR was derived by calculating the ratio of
upwelling to downwelling PAR, both measured at
the height of the sensor.
Provides an indication as to the efficiency of
Photosynthesis and Net Primary Production.
Leaf Area Index as a function of NDVI
•
•
Relationship between the NDVI function and leaf
area index is not linear but reaches it’s limit more
gradually at higher LAI’s.
Green LAI is an exponential function of NDVI
linearly related to measured LAI.
Canopy Height
•
•
Plant height was determined by
subtracting calculated sensor to
target distance from measured
sensor height.
Sensor to target distance was
calculated using square root of
inverse NIR irradiance.
Holland et al., IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens. (JSTARS) , V5, N6, 2012
Canopy Temperature Departure
•
•
Delta Temperature was calculated by subtracting IRT measured
canopy temperature from measured ambient temperature.
Aerial IR cameras were used to acquire late season imagery.
Stay green and late season varieties are clearly identifiable.
Opportunities with Phenomic Sensor Systems
in Precision Agriculture and Plant Breeding:
• Develop Phenomic markers to compliment Genomic markers that assist with
efficient breeder selections.
Variety Plant Density
BL110002
800
NE06545
1200
Overland
800
Robidoux
1000
Wesley
1200
N
40
60
40
40
40
Average Yld
+
0
-
chl
0
0
0
+
fPAR
0
+
+
0
LAI
+
+
Height
0
+
+
Delta T
0
0
0
+
• Utilize Greenhouse Lemnatec system to incorporate phenomic data into
decision support system. Move this concept to the field scale.
• Future advances in high speed data capture, transfer, and analysis should
enable on-the-go image based phenomic systems, providing more
morphological information.
• UAV’s should be exploited to deliver both image and spectral sensor based
systems to the field.
Parallel Phenomic Research within Bayer
• Image Recognition Approach (Field and Greenhouse).
• Lemnatec Greenhouse Activities.
Additional Information
Sampling Date GDD:
26 Apr 12 – 835.7
6 May 12 – 944.3
14 May 12 – 1068.7
3 Jun 12 – 1441.9