Rice: Phenotyping for drought traits

Amelia Henry

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

1. Ensure uniformity

in stress treatment

and characterize the

drought stress

2. Phenotyping

High throughput methods →detailed

methods

Sequence for drought phenotyping

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

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

Characterization of drought at partner sites

Rajshahi, Bangladesh

• tensiometers

• soil analysis

• water retention curves

Large-scale phenotyping of breeding lines

Traits

1. Yield

• Plant height

• Time to flowering

• Shoot biomass/ harvest index

Aus lines 2010DS and 2011DS

220+ lines

Stress and control

• Early vigor

• Canopy temp

• NDVI

• Yield

• shoot and root biomass

Phenotyping of association panels

Greenhouse lysimeter facility

Capacity:

1200 cylinders

Throughput:

250 plants / day

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)

If some genotypes show better water uptake when the soil is dry, we look

for root-related mechanisms

Canopy temperature

Root sampling in the field

Throughput: roots from about 100 soil cores sampled, washed, and

scanned within 2 weeks

Detailed measurements

Leaf gas exchange

Leaf water potential

Root hydraulic conductance

Microscopy

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 8

3376-

B-B

-130-

3

IR74

371-

54-1

-1

IR 8

3377-

B-B

-48-3

IR 8

3380-

B-B

-124-

3

IR 8

3387-

B-B

-110-

1

IR 8

3383-

B-B

-141-

2

IR 8

3388-

B-B

-108-

3

IR 8

3387-

B-B

-27-4

IR 8

3383-

B-B

-141-

4IR

64

IR74

371-

70-1

-1

Can

op

y T

em

p (

C)

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

Un

pla

nte

d

Ch

eck

Re

fere

nce

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

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

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

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

RL

D (

cm

cm

-3)

30-45 cm

45-60 cm

+ QTL - QTL + QTL - QTL

Root function for water uptake: hydraulic conductance

IR64

IR77

298-

14-1

-2-1

0 (+

)

IR77

298-

14-1

-2-1

3 (-)

IR77

298-

5-6-

18 (+

)

IR77

298-

5-6-

11 (-

)

log S

ap

flu

x a

t 5

00

kP

a (

m3 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

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

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

Acknowledgements:

IRRI Drought Physiology Group

Generation Challenge Program

Gates Foundation (STRASA project)

Ken McNally

Arvind Kumar