This document describes a phenotyping experiment using infrared thermography to evaluate canopy temperature as a trait for drought tolerance in rainfed lowland rice. The objectives were to develop drought tolerant cultivars for target environments in West Africa through a multi-partner project. Canopy temperature indicates leaf cooling capacity and drought stress. The experiment tested 250 varieties in Colombia, measuring canopy temperature, soil moisture, and weather data. Results showed soil heterogeneity and diversity in transpiration between varieties. Association studies aim to identify quantitative trait loci correlated with canopy temperature and drought tolerance. Ongoing phenotyping across multiple countries will enable further association analyses.

1. Canopy temperature as field phenotyping
trait for rainfed-lowland rice breeding
program for drought tolerance
A. Audebert

2. RCI Project
• Objectives : to develop drought-tolerant cultivars with high yield potential
in normal years and good yield under drought and other major stresses for
each target environment.
• Sponsor : Generation Challenge Programme (GCP)
• Target countries : Burkina, Nigeria and Mali
• Target environment : Rainfed lowland ecosystem
• Duration : 4 years
• Partners : CIRAD, IRD, IRRI, INERA, IER, NCRI, CIAT and AfricaRice

3. Field phenotyping for drought tolerance
• Based on Infra-red thermography.
– Canopy temperature give an indication of the leaf surface cooling capacity by
transpiration along environmental conditions
– Could be use as a trait for phenotyping
• (indirect evaluation of drought)
– This trait depending of
• Environmental conditions
– Air temperature
– Wind speed
– Solar radiation
– Evaporative demand (VPD)
• Sol water conditions
– Humidity / available
• Plant characteristics
– Surface of canopy
– Plant Architecture
– Water status management

4. Difficulties to solve
• Environmental conditions highly variable
• Quick plant reaction
– Wind
– Radiation
• Low equipment (1 camera and 1 technician)
• Impossible to have one unique picture for the whole experiment
– Helicopter, plane
– Drone
• Optimum 3-4 lines per image
– 500 lines -> 160 pictures
– 1 image per 30 sec
– Tc canopy temperature
• Time for measurement
– About 3 hours
– Environmental stability
How to control the environment variability and compare results ?

5. Normalizing canopy temperatures
• Quantifying the water stress with standardizing canopy temperature by
evaporative demand (CWSI)
– Ta (Air temperature)
– VPD (Vapor pressure deficit)
– CWSI (Crop water stress index)
CWSI
(Ts Ta ) (Ts Ta ) min
(Ts Ta ) max (Ts Ta ) min
• Need simultaneously measurement of the evaporative demand
– Weather station
– Psychrometer measurement
• Humid and dry temperature

6. Phenotyping experiment
•
•
Dry season 2012-2013
Field experiment
– Villavicencio station “Santa Rosa “(Colombia)
• 250 varieties tested with 2 reps
– 230 Mars lines (IR64 * B6144-F-MR-6-0-0)
– 10 controls repeated twice
• 3 row of 3 m long
•
Stress period 3 weeks (5/01-25/01/2013)
•
Design
•
• Reproductive stage
–
–
–
–
Alpha lattice 8 sub-Blocs with 2 replications
2 treatments
Complete randomization
5 control varieties repeated
Measurements
– Canopy temperature (IR thermography camera)
– Soil humidity with Aqua Pro system
– Microclimatic data with Davis weather station

7. Methods
• Soil humidity
– 60 AquaPro tubes,
• Distributed in the field
• Weather data
– Davis station (Vantage Pro 2)
• 1 minute delay
• Canopy temperature
– NEC TH9100 M
•
•
•
Human height
500 pictures
Image analysis with Image processor

8. Field experiment results
Soil heterogeneity
Soil desiccation
35
16
30
Top-soil humidity (%)
14
25
12
20
10
8
15
6
10
4
07/01
14/01
21/01
28/01
Date
04/02
11/02
5
0
0
5
10
Experimental design to control the soil heterogeneity
15
20

9. Phenotyping Results
16
15
12
10
8
5
4
0
Frequency (%)
20
20
Frequency (%)
25
0
-4
-3
-2
-1
0
1
2
3
Tc-Ta (°C)
4
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
CWSI
Better lines with low temperature
E207, E153, E14, E110, E31, E16, E79, E167, E59, E242, E130, E217, E139, E239, E220, E30, E163, E57, E231, E127

10. Perspectives : Association studies
• Qtls
Using a mixed model with correction
for structure and kinship, the
association study detected some
markers
• Based on ajusted values
• Software Tassel or other
• Determination of LOD
• Qtls determination (P-Value)
• MARS

11. Conclusions
• High-throughput phenotyping with thermographic camera on field condition
is possible
– Could be improved by using drone
• The use of the CWSI allows to compare cultivars between them during the
phenotyping time
• Good diversity is observed for transpiration
• QTls could be determine with association studies
RCI project
• Phenotyping is on going
– 3 countries (PhD students)
• Association study will be done further with SNPs

12. Thank you