This document summarizes rice drought phenotyping methods used at IRRI. Uniform drought stress treatment is ensured using level fields separated from flooded fields. Stress is characterized using soil moisture sensors. Large-scale phenotyping of breeding lines focuses on yield and related traits. High throughput methods like NDVI and canopy temperature are followed by more detailed physiological measurements. Analysis of drought QTL lines found smaller root and xylem vessels in positive QTL lines, reducing cavitation under stress.

1. Rice: Phenotyping for drought traits
Amelia Henry

2. Rice Drought Phenotyping objectives:
1. Large-scale screening of breeding lines
2. Characterization of diversity panels for association
mapping
3. Dissection of drought tolerance mechanisms in major
drought QTL lines

3. 1. Ensure uniformity
in stress treatment
and characterize the
drought stress
2. Phenotyping
High throughput methods →detailed
methods
Sequence for drought phenotyping

4. Uniform drought stress treatment:
• use level fields
•separate the drought stress from flooded fields
•avoid areas of high soil variability
Soil mapping based on apparent electrical conductivity

5. Characterizing the severity of the drought stress
Volumetric soil water content
with depth
tensiometers
water table tubes (piezometers)
• rainfall
• water table depth
• soil moisture status

6. Characterization of drought at partner sites
Rajshahi, Bangladesh
• tensiometers
• soil analysis
• water retention curves

7. Large-scale phenotyping of breeding lines
Traits
1. Yield
• Plant height
• Time to flowering
• Shoot biomass/ harvest index

8. Aus lines 2010DS and 2011DS
220+ lines
Stress and control
• Early vigor
• Canopy temp
• NDVI
• Yield
• shoot and root biomass
Phenotyping of association panels

9. Greenhouse lysimeter facility
Capacity:
1200 cylinders
Throughput:
250 plants / day

10. Canopy reflectance
Normalized Difference Vegetation Index
NDVI = (NIR_reflected -Red_reflected)
(NIR_reflected + Red_reflected)
Soil-Adjusted Vegetation Index
SAVI = 1.5 * (NIR_reflected - Red_reflected)
(NIR_reflected + Red_reflected * 0.5)

11. If some genotypes show better water uptake when the soil is dry, we look
for root-related mechanisms
Canopy temperature

12. Root sampling in the field
Throughput: roots from about 100 soil cores sampled, washed, and
scanned within 2 weeks

13. Detailed measurements
Leaf gas exchange
Leaf water potential
Root hydraulic conductance
Microscopy

14. Screening of advanced breeding lines by India Drought Breeding Network
Hazaribag April 26 2011 2:45 PM
22.5
22.7
22.9
23.1
23.3
23.5
23.7
IR
83376-B-B-130-3
IR74371-54-1-1
IR
83377-B-B-48-3
IR
83380-B-B-124-3
IR
83387-B-B-110-1
IR
83383-B-B-141-2
IR
83388-B-B-108-3
IR
83387-B-B-27-4
IR
83383-B-B-141-4
IR64
IR74371-70-1-1
CanopyTemp(C)

18. IRT.
Canopy Temperature
Sonic sensor
Plant Height
Crop Circle Multispectral Sensor
Biomass, Development, Nutrient, Stress Response
NDVI, PRI, RI, TCARI, OSAVI, WDVI...
24 m boom
RTK GPS Auto Steer
+/- 2 cm accuracy
CR1000 data logger & AM16 multiplexor
Sensor control and data processing
PAR/Pyranometer T/RH
Ambient Monitoring
Fixed IRT
Plant Ref
Unplanted
Check
Reference
Crop Circle– 3 band multispectral sensor with dedicated logger
Plant IRT and sonic Ht data processing on CS logger
Ambient PAR, SW, T/RH, and soil T on CS logger
Reference plots to monitor temporal variability
Check plots to monitor spatial variability
Unplanted plots to monitor soil background
8 – 16 plot system
Example 1 m wide plots
linearconical
Sensor Measurement
Field of View
SpectraIIRT/sonic
Ambient
PAR, SW, and T/RH Sensor
IRT
Soil Ref
On our wish list:
Mobile field-based
phenotyping
platform

19. Dissection of drought tolerance mechanisms in major drought
QTL lines: Aday Sel x IR64 NILs
+QTL
14-1-2-10
-QTL
14-1-2-13

20. IR64
-QTL
14-1-2-13
+QTL
14-1-2-10
Aday Sel NIL pairs show large differences in canopy temp under severe drought
+QTL
5-6-18
-QTL
5-6-11
Aday Sel

21. Aday Sel NIL pairs did not show large differences in root length density at depth
Expt 4s Aday Sel ROS
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
IR 64 IR77298-14-1-2-
10
IR77298-14-1-2-
13
IR 77298-5-6-18 IR77298-5-6-11
RLD(cmcm-3
)
30-45 cm
45-60 cm
+ QTL - QTL + QTL - QTL

22. Root function for water uptake: hydraulic conductance
IR
64
IR
77298-14-1-2-10
(+)IR
77298-14-1-2-13
(-)IR
77298-5-6-18
(+)IR
77298-5-6-11
(-)
logSapfluxat500kPa(m
3
s
-1
)
1e-12
1e-11
1e-10
1e-9
well-watered control
dry-down from field capacity
dry-down from 75% field capacity
Lower Lpr in + QTL lines
from Aday Sel x IR64

23. 14-1-2-10 (+ QTL) 14-1-2-13 (- QTL)
+ QTL lines had smaller root and xylem vessel diameters
Hypothesis: smaller xylem vessel diameters in +QTL lines result in decreased
xylem cavitation under severe stress

24. Summary for rice drought phenotyping:
1. Use a uniform field and characterize the type of drought stress
2. Phenotyping for drought breeding: focus on yield
3. Phenotyping for physiology: start at high throughput (NDVI and
canopy temp)
 More detailed methods

25. Acknowledgements:
IRRI Drought Physiology Group
Generation Challenge Program
Gates Foundation (STRASA project)
Ken McNally
Arvind Kumar