Remote Sensing in Plant Breeding

(Field-based Phenomics)
Novi Tri Astutiningsih

Outline
Introduction
Why using remote sensing platform for plant
breeding?

Data and methods used

What type of platforms used?
What type of parameters measured?

Results and conclusions

Introduction
Current plant breeding purpose mainly
focused on the development of high yielding
and stress resisting cultivars or lines
Reduces in cost and time for genomics
processes

How to predict crop performance as a

function of genetic architecture?

http://www.plant-phenotyping-network.eu/

(von Mogel, 2012)

Phytomorph project at the University of WisconsinMadison:

robotic camera that photographs growing seedlings and roots at
regular intervals, with micron-level precision

LemnaTec (Germany):
phenotyping individual plants in large, robotic greenhouses
using photography, fluorescence imaging, 3D image analysis

Current phenotyping limitation:

mainly performed in a controlled-environment system (e.g.
greenhouse or plant growth chamber)
limited space and soil volume, and atmospheric differences

High-throughput field-based
phenotyping (FBP)
Simultaneous proximal sensing for spectral
reflectance, canopy temperature, and plant
architecture
Larger samples/scales
Multiple environments
Throughout crop life cycle
Characterize multiple traits in a single pass

Remote sensing platform

*Using sensing platform commonly applied for remote sensing of vegetation

1. Static and within-field platforms

2. Aircraft
3. Satellites

Static and within-field platforms

Monitoring plant status for either a single leaf (or plant) or the
entire field plots
Proximal (close-range) sensing
Is often the only approach that can provide adequate resolution for
phenotyping studies
Higher resolution sensing pixel-to-pixel analyses
Provide multiple view-angles, control illumination and regulate the distance
from the target to the sensors
Reduce background signal and atmospheric correction
Permit positioning of sensors or sources of illumination at the base or side of
the canopy, allowing measurement of transmittance rather than reflectance

Using hand-held instrument or vehicle-mounted instruments

(e.g. high-clearance tractors, crane-like vehicles, cable robots)

At the USDA Arid-Land Agricultural Research Center in Maricopa, AZ

Measuring:
- Canopy height
- Canopy temperature
- Spectral reflectance (three bandwidths)

(White et al., 2012)

Ag Eyes (AgIIS, Agricultural Irrigation Imaging System) at the Maricopa Agricultural Center

AgIIS rail

AgIIS cart, arm, and sensor

(Haberland et al., 2010)

Prototype of RoboCrane (Large-area Overhead Manipulator for Access of Fields, LOMAF)

at The National Institute of Standards and Technology (NIST)

(White and Bostelman, 2011)

Aircraft
Versatile
Adjusted height
Specific area, particular angle

May be not reproducible

Not universally available and
certain permissions have to be
acquired
Not a very stable platform
Operational skills

E.g. UAVs (unmanned aerial vehicles), balloons, light planes,

helicopters, aerostats, model aircrafts, phenocopters

Phenocopter (a remote controlled gas-powered model helicopter) at CSIRO

Measure:
- Plant height
- Canopy cover
- Lodging
- temperature throughout a day

(von Mogel, 2013)

(Garcia-Ruiz et al., 2013)

Being developed at the Department of Biological Systems

Engineering (WSU) for plant phenotyping purpose

Comparison of five vehicle options for field-based phenomics

(White et al., 2012)

Satellites
Current satellite platforms provide various sensor instruments
for vegetation monitoring. Several satellite platforms that are
commonly used in remote sensing of vegetation
Terra (using MODIS)
Landsat 7 (using EMT+)
NOAA (using AVHRR).

To maintain its performance, each satellite is supported with

ground validation to constantly monitoring the operation of
each instrument.

(Xie et al., 2008)

(Jones and Vaughan, 2010)

(Jones and Vaughan, 2010)

(Jones and Vaughan, 2010)

Parameters measured
1.
2.
3.
4.

Thermography (digital, infrared, NIR)

Chlorophyll fluorescence analysis
Reflectance Spectroscopy
Digital growth analysis

Thermography
Non-destructive measurement of
plant performance using its canopy
temperature
Hand-held thermometers or infrared
camera are time consuming
Infrared sensors mounted on
vehicles on or above the
experimental plots can be used to
remotely sense canopy
temperatures. (Berger et al., 2010;
Furbank and Tester, 2011)

(Furbank and Tester, 2011)

Jones, H. G., Serraj, R., Loveys, B. R., Xiong, L., Wheaton, A., and Price, A.
H. (2009). Thermal infrared imaging of crop canopies for the remote
diagnosis and quantification of plant responses to water stress in the
field. Functional Plant Biology 36, 978-989.

(Jones et al., 2009)

(Jones et al., 2009)

(Jones et al., 2009)

Prashar, A., Yildiz, J., McNicol, J. W., Bryan, G. J., and Jones, H. G. (2013).
Infra-red Thermography for High Throughput Field Phenotyping in
Solanum tuberosum. PLoS ONE 8, e65816.

(Prashar et al., 2013)

(Prashar et al., 2013)

Chlorophyll fluorescence analysis

Measuring plant photosynthesis performance by identifying the
photochemical efficiency
Using a fluorimeter
dark-adapted Fv/Fm
electron transport rate (ETR)
non-photochemical quenching (NPQ)

As a complimentary (Berger et al.,

2010)
Fluorescence imaging to determine
plant growth using projected leaf area

higher sensitivity but challenging

(Campbell et al. 3003)

Protocol for chlorophyll fluorescence analysis using pulse

modulated technique (Baker and Rosenqvist, 2004)

Parameter
Fo

Definition
Initial fluorescence

Fm

Maximum
fluorescence

Fv

Variable
fluorescence (=FmFo)
Maximum quantum
yield of PSII

Fv/Fm

Fv/Fo

Tfm
Area

PI
RC/ABS

(1-Vj)/Vj

Performance Index
Concentration of
active PSII reaction
centers per photon
flux absorbed by the
antenna pigments

Description
initial emission of the
oxidized electron acceptors of
PSII after illumination
maximum chlorophyll
fluorescence value obtained
after electron acceptors in
PSII is fully reduced by
photochemistry
indicates fluorescence
emission during the excitation
of chlorophyll molecules
indicates efficiency of PSII to
do photochemistry

indicates the efficiency of

oxygen evolving complex in
PSII
indicate the time at which Fm
was reached
proportional to the pool size
of the electron acceptors on
PS II
indicate sample vitality
quantify the energy for
absorption by PSII

indicate the force related to

the dark reaction

Reference
(Baker and
Rosenqvist, 2004)
(Baker and
Rosenqvist, 2004)

(Baker and
Rosenqvist, 2004)
(Maxwell and
Johnson, 2000; Baker
and Rosenqvist,
2004)
(Skrska and Szwarc,
2007)
(Strasser et al., 2004)
(Strasser et al., 2004)

(Strasser et al., 2004)

(Strasser et al., 2004)

(Strasser et al., 2004)

Reflectance spectroscopy
Measurement of leaf spectroscopy using radiometric or imaging sensors
Leaf absorption and reflectance features of different solar radiation
wavelength allows the development of several indices to measure leaf or
tissue component and their correlation with plant photosynthesis activity
or plant biomass; such as
NDVI (normalized difference vegetation index)
PRI (photosynthetic reflective index)

Environmental variability (e.g. solar angle and cloud cover) created

difficulties to interpreting and qualifying hyperspectral reflectance
spectroscopy data and has not commonly been used in plant phenotyping
(Furbank, 2009; Peuelas and Filella, 1998)

Multi-spectral imagery

Thermal (IR) imagery

(Prashar et al., 2013)

Hyper-spectral imagery

NIR imagery

(von Mogel, 2013)

(White et al., 2012)

Examples of possible locations of sensors or cameras (S) and high-intensity illumination

(HIL) suspended above or below the crop canopy to measure transmittance and thus infer
light interception or canopy architecture at specific wavelengths

(Peuelas and Filella, 1998)

Examples of proximal sensing methods that show promise for field-based phenomics

(White et al., 2012)

Digital growth analysis

Using multiple viewing angle analysis of projected leaf area or biomass
Currently used in in situ phenotyping under controlled environments
Examining digital plant growth in a period of plant development that
allows accurate assessment of plant stress response mechanisms.
Using visual score from visible digital imaging, it is also possible to obtain
information related to plant size and color for plant senescence or toxicity
quantification (Furbank and Tester, 2011)

(Furbank and Tester, 2011)

An integrated FBP platform

1.
2.
3.
4.
5.
6.

Instruments for acquiring raw data

Systems for integrating instruments
Vehicles for positioning instruments
High-throughput analysis of plant samples
Management of data flow and analysis
Integrated management of FBP
The system needs to be rapid, flexible and reliable
(White et al., 2012)

Integrated management of FBP

Standard operating procedures are needed to ensure
reliable performance throughout an experiment,
including crop management, instrument calibration,
data transfer and initial analysis, and vehicle
maintenance
Field management to minimize or control within-field
sources of variation (e.g. soil characterization, soil
nutrient content, weather station, irrigation)

(White et al., 2012)

(Montes et al., 2007)

Examples of possible paths of data analysis

Challenges
Highly integrative approaches cannot rely on
individual/small group researchers
Recently established national and international collaborations
Desired phenotype are combination of multiple traits
Large volumes of data
Develop protocols for testing instruments
Better algorithms for analyzing proximal sensing data
Patents??
Future sophisticated instruments (e.g. Kinect technology)

Conclusion
FBP appears capable of attaining the requisite
high levels of throughput needed as
phenotyping tools.
FBP requires integrative, interdisciplinary
teamwork and thorough attention at all stages
field preparation and experimental design
processing and analysis of data
direct application toward finding solutions to
major problems currently limiting crop production

Future possibilities
The platform can also be used for site-specific
crop management
However, it would be hard to implement in
the developing countries (smallholder type
farming system) easier approaches are
preferable (e.g Leaf Color Chart for rice)

Current phenomics centers

High Resolution Plant Phenomics Centre (CSIRO, Australia)

(http://www.csiro.au/Outcomes/Food-and-Agriculture/HRPPC.aspx)
Australian Plant Phenomics Facility (APPF) (www.plantphenomics.org.au)
National Plant Phenomics Centre (Aberystwyth University, UK)
(www.phenomics.org.uk)
PhenoFab the Plant Phenomics Service Center (LemnaTec, Germany)
(http://www.lemnatec.com/news/phenofab-plant-phenomics-service-center)
International Plant Phenomics Network (IPPN) (http://www.plantphenotyping.org/)
Jlich Plant Phenotyping Centre (Germany) (http://www.fz-juelich.de/ibg/ibg2/EN/organisation/JPPC/JPPC_node.html)
European Plant Phenotyping Network (EPPN) (http://www.plant-phenotypingnetwork.eu/)

Further Readings
Part One of Field Phenomics: Developing and Using a Sensor Array
http://www.extension.org/pages/68269/part-one-of-field-phenomics:-developing-and-using-asensor-array#.Uo73Z8TB3X7
Part Two of Field Phenomics: Data Analysis
http://www.extension.org/pages/68270/part-two-of-field-phenomics:-dataanalysis#.Uo73acTB3X7

References
Berger, B., Parent, B., and Tester, M. (2010). High-throughput shoot imaging to study drought responses. Journal of
Experimental Botany.
Furbank, R. T. (2009). Plant phenomics: from gene to form and function. Functional Plant Biology 36, vvi.
Furbank, R. T., and Tester, M. (2011). Phenomics technologies to relieve the phenotyping bottleneck. Trends in Plant
Science 16, 635-644.
Garcia-Ruiz, F., Sankaran, S., Maja, J. M., Lee, W. S., Rasmussen, J., and Ehsani, R. (2013). Comparison of two aerial
imaging platforms for identification of Huanglongbing-infected citrus trees. Computers and Electronics in
Agriculture 91, 106-115.
Jones, H. G., Serraj, R., Loveys, B. R., Xiong, L., Wheaton, A., and Price, A. H. (2009). Thermal infrared imaging of crop
canopies for the remote diagnosis and quantification of plant responses to water stress in the field. Functional
Plant Biology 36, 978-989.
Jones, H. G., and Vaughan, R. A. (2010). "Remote sensing of vegetation: principles, techniques, and applications,"
Oxford University Press.
Peuelas, J., and Filella, I. (1998). Visible and near-infrared reflectance techniques for diagnosing plant physiological
status. Trends in Plant Science 3, 151-156.
Prashar, A., Yildiz, J., McNicol, J. W., Bryan, G. J., and Jones, H. G. (2013). Infra-red Thermography for High Throughput
Field Phenotyping in Solanum tuberosum. PLoS ONE 8, e65816.
von Mogel, K. H. (2013). Taking the Phenomics Revolution into the Field. CSA News 58, 4-10.
White, J. W., Andrade-Sanchez, P., Gore, M. A., Bronson, K. F., Coffelt, T. A., Conley, M. M., Feldmann, K. A., French, A.
N., Heun, J. T., Hunsaker, D. J., Jenks, M. A., Kimball, B. A., Roth, R. L., Strand, R. J., Thorp, K. R., Wall, G. W., and
Wang, G. (2012). Field-based phenomics for plant genetics research. Field Crops Research 133, 101-112.
Xie, Y., Sha, Z., and Yu, M. (2008). Remote sensing imagery in vegetation mapping: a review. Journal of Plant Ecology 1,
9-23.

Questions?

http://www.plant-phenotyping-network.eu/

electron acceptors in the

PSII saturated (fully
reduced / closed) due
to the continuously
electron transport

proportional to the
pool size of the
electron acceptors
(Qa) on PS II

= Fm-Fo
fluorescence
emission during the
excitation of
chlorophyll molecules

Fv/Fo
oxygen evolving
efficiency
electron acceptors
are fully oxidized (or
in an open state)
and ready to receive
electrons

Fv/Fm
Performance Index (PI)
indicator of sample vitality
(samples internal force to resist
constraints from outside

efficiency of PSII to do
photochemistry or to convert
absorbed light into chemical
energy