crop canopy sensors for high throughput phenomic systems
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Crop Canopy Sensors for High Throughput Phenomic SystemsDr. 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
6 May
14 May
3 Jun
16 Jul
26 Apr
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
2 Chan Voltage Input/Pulse Counter Downwelling PAR
Humidity/Temp
Crop Circle DAS43X
Rapid Field Phenomic Sensor SuiteMeasured Variables
• Reflectance from 3 bands, 10nm FWHM (Red, Red Edge(RE), NIR)
• Select Optical Indices - Canopy Chlorophyll Index(RE), NDVI.
• Canopy Chl Content.
• Green Leaf LAI.
• Canopy Height (via optical methods and ultra-sonic).
• Downwelling PAR, Upwelling PAR = Fractional PAR (fPAR).
• Relative Humidity.
• Ambient Temperature, Canopy Temperature = Temperature Departure (DT).
3-second Running Average
0
1
2
3
4
5
6
1 459 917 1375 1833 2291 2749 3207 3665 4123 4581 5039 5497 5955 6413
Number of Readings
CI re
d-ed
ge
y = 773.74x - 198.3r2 = 0.8702
0
500
1000
1500
2000
2500
3000
0 0.5 1 1.5 2 2.5 3 3.5 4
Chl Index Red Edge (CIRE)
Can
opy
Chl
Con
tent
, mg
m-2
Data Collection Rate: 5Hz
yRed = -0.0041x + 13.134R2 = 0.2472
yBlue = -0.0035x + 12.985R2 = 0.2827
yGRN = -0.0233x + 30.76R2 = 0.7473
yRE = -0.0267x + 42.563R2 = 0.7628
yNIR = 0.0019x + 52.433R2 = 0.0149
0
10
20
30
40
50
60
100 200 300 400 500 600 700
Leaf Chl Content, mg m-2
Ref
lect
ance
, %
BlueGreenRedRed EdgeNIR
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
400 450 500 550 600 650 700 750 800 850 900
Wavelength, nm
Coe
ffici
ent o
f Det
erm
inat
ion,
r2
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.
Blue/Red - Absorb.
Upper and Lower Epidermis
Spongy mesophyll
Green-Refl.Near IR-Refl.
Air space
Stoma
Palisade Cells Chlorophyll
What spectral regions are most sensitive to Chlorophyll Content. Green and Red Edge
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.
• Develop Phenomic markers to compliment Genomic markers that assist with efficient breeder selections.
• 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.
Opportunities with Phenomic Sensor Systems in Precision Agriculture and Plant Breeding:
Variety Plant Density N Average Yld chl fPAR LAI Height Delta TBL110002 800 40 - 0 0 - 0 0NE06545 1200 60 + - - - + -Overland 800 40 0 0 + + - 0Robidoux 1000 40 - 0 + - - 0
Wesley 1200 40 - + 0 + + +
•Image Recognition Approach (Field and Greenhouse).
•Lemnatec Greenhouse Activities.
Parallel Phenomic Research within Bayer
Additional Information
Sampling Date GDD:26 Apr 12 – 835.76 May 12 – 944.3
14 May 12 – 1068.73 Jun 12 – 1441.9
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