GRM 2013: Drought phenotyping and modeling across crops -- V Vadez
1. GCP-ARM – Lisbon 27-30 Sept 2013
Objective 5: Cross-crop issues
Drought phenotyping
and modeling across crops
ICRISAT – CIAT – ISRA – Univ North Carolina
2. Water uptake / Root
Water use / WUE
Reproduction and partitioning
Modeling
Sub-Activity5:Training
Trait value
predicted
Refined protocols
More tools
Better pheno-
typing data
Phenotyping of cell-based processes – toward gene discovery
Purpose: Looking at similar traits across species
3. Lysimetric system: in
CIAT and ICRISAT-Niger
Total water extracted
Kinetics of water extraction
Root length density at different depth
Relationships RLD vs Water extraction
To measure:
Lysimetric assessments
4. Root length density and water extraction
Drought root length density (cm cm-3)
0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75
Droughtwaterextraction(kgplant-1)
5.5
6.0
6.5
7.0
7.5
8.0
8.5
BRB 191
PAN 127
SUG 131
VAX 1
BAT 477
DOR 364
CAL 143
VAX 3
RCW
SEA 5
SEA 15
SER 16
SEQ 1003
SEQ 11CAL 96
SAB 259
RAA 21
ICA Quimbaya
SER 8
Mean: 0.56
LSD0.05: 0.13
SEC 16
Mean: 6.84
LSD0.05: 1.53
r = 0.08
No relation between water extraction (WS)
and root length / RLD
Beans Chickpea
5. Post-rainy season Rainy season
0
2
4
6
8
10
12
14
16
0 1000 2000 3000 4000 5000 6000 7000
Podyield(gplant-1)
Total water extracted (g plant-1)
0
1
2
3
4
5
6
7
8
9
10
0 1000 2000 3000 4000 5000 6000 7000
Podyield(gkg-1)
Total water extracted (g plant-1)
No relationship between total water
extracted and grain yield
0
2
4
6
8
10
12
14
0 1000 2000 3000 4000 5000 6000 7000
Podyield(gplant-1)
Total water extracted (g plant-1)
Cowpea
Peanut
0.0
1.0
2.0
3.0
4.0
5.0
6.0
7.0
0 1000 2000 3000 4000 5000 6000 7000
Podyield(gplant-1)
Total water extracted (g plant-1)
Bean
Peanut
Rainy seasonRainy season
Pod yield and water extraction
6. Water extraction pattern (WS)
Zaman-Allah, Jenkinson, Vadez 2011 JXB
0
1
2
3
4
5
6
7
8
9
10
21 28 35 42 49 56 63 70 77 84 91 98
CumulatedWaterUsed
(kgpl-1)
Days after sowing
Flowering
8 Sensitive lines
12 Tolerant lines
Tolerant: less WU at vegetative stage,
more for reproduction & grain filling
7. Zaman-Allah, Jenkinson, Vadez 2011 JXB
0
1
2
3
4
5
6
7
8
9
10
21 28 35 42 49 56 63 70 77 84 91 98
Waterused(kgpl-1)
Days after sowing
Sensitive
Tolerant
Tolerant: EUW = 27 kg grain mm-1
Grain yield and post-anthesis water use
Chickpea
8. Cowpea
Similar results in cowpea and chickpea
Grain yield and post-anthesis water use
Water use
PhD Thesis Omar Halilou
9. Seed yield relates to higher pre-flowering water use
Nitrogen issue?? (Sinclair & Vadez 2013 Crop&Pasture Science)
Pre-anthesis
Beans
Grain yield and pre- / post-anthesis water use
10. 0.0
2.0
4.0
6.0
8.0
WW-HN WW-LN WS-HN WS-LN
Yield(g/plant)WS
0.0
2.0
4.0
6.0
8.0
WW-HN WW-LN WS-HN WS-LN
Yield(g/plant)WS
0
2
4
6
8
10
12
14
16
HN-WW LN-WW HN-WS LN-WS
Yield(gplant-1)WS
Cowpea
Bean
Effect of high N (HN) or low N (LN) treatments under water
stress (WS) and irrigation (WW)
Peanut
Among the three legumes,
peanut is least sensitive to
low N
Low N is more a problem
than drought for bean
12. Leafarea
Thermal time
A – Fast early LA
B – Slow early LA
C – Fast early LA / small max LA
D – Slow early LA / small max LA
Canopy development dynamics
Water use
difference
13. Field trial
0 5 10 15 20 25
0
1000
2000
3000
4000
5000
6000
A = 2,91
Fleur 11
WW condition
R² = 0,999
Nodes number
Leafarea(cm²)
Field trial
0 5 10 15 20 25
0
1000
2000
3000
4000
5000
6000
A = 2,63
ICG 1834
WW condition
R²= 0.91
Nodes number
Leafarea(cm²)
PhD training of Oumaru Halilou - Niger
Large variation available
Peanut
Coefficients relating leaf area to node number
14. y = 23.302e0.2562x
R² = 0.9367
0
2000
4000
6000
8000
10000
12000
0 5 10 15 20 25
Leafareaoffiveplants
(cm2)
Node number on main stem
y = 11.995e0.31x
R² = 0.9607
0
2000
4000
6000
8000
10000
12000
0 5 10 15 20 25
Node number on main stem
Coefficients relating leaf area to node number
MSc training of Ruth Wangari - Kenya
Chickpea
15. Rainy season
(VPD<2kPa)R² = 0.03
0
1
2
3
4
5
6
7
8
9
10
0.0 1.0 2.0 3.0
R² = 0.65
0
4
8
12
16
0.0 1.0 2.0 3.0
Post Rainy Season
(VPD>2kPa)
TE variation and link to yield depends on season
Transpiration efficiency – Peanut
and relationship to yield
Podyield(gplant-1)
250% range
60% range
19. R² = 0.64
-40
-30
-20
-10
0
10
20
30
40
50
0.000 0.010 0.020 0.030 0.040 0.050 0.060
Residualtranspiration
Transpiration rate under high VPD
What drives transpiration in that population??
Leaf area
(69%)
Conductance at high VPD
(64% of residual)
Get QTL for both these traits
PhD training of Nouhoun Belko – Burkina Faso
R² = 0.69
0
50
100
150
200
250
0 200 400 600 800 1000 1200
Totaltranspiration
(gplant-1)
Leaf area (cm2 plant-1)
20. QTLs from ICI Mapping – Drought
tolerance traits
VuLG1 VuLG2 VuLG3 VuLG4 VuLG5 VuLG6 VuLG7 VuLG8 VuLG9 VuLG10 VuLG11
Plant transp., leaf area, stem DW, leaf DW
12-18% phenotypic variance
(High allele from CB46)
Canopy conductance
12-16% phenotypic variance
(High allele from IT93K-503-1)
SLA, 20%
phenotypic
variance
(High allele from
CB46)
SLA, 14%
phenotypic
variance
(High allele from
IT93K-503-1)
From Phil Roberts/Tim Close and team
21. QTLs from ICI Mapping – Drought
tolerance traits
From Phil Roberts/Tim Close and team
Select RILs having different “dosage” of these QTLs
and test them across contrasting drought scenarios
TraitName
Chromo
some
Position
(cM)
Flanking
markers LOD PVE(%)
Additive
effect
Positive
allele
Plt DW 2 4 1_0113 - 1_0021 3.1 15.5 0.3 CB46
SLA 2 31 1_1139 - 1_1061 3.6 14.4 -11.5 IT93K-503-1
LA 2 85 1_0834 - 1_0297 4.0 18.5 57.0 CB46
Leaf DW 2 85 1_0834 - 1_0297 2.8 13.4 0.2 CB46
Plant transp Total 6h 2 85 1_0834 - 1_0297 2.9 13.1 8.9 CB46
Conductance High VPD 5 19 1_0806 - 1_0557 3.2 16.3 0.0 IT93K-503-1
Conductance Low VPD 5 20 1_0806 - 1_0557 2.8 13.3 0.0 IT93K-503-1
Conductance Low VPD 5 23 1_0806 - 1_0557 3.3 14.0 0.0 IT93K-503-1
Conductance Low VPD 7 13 1_0279 - 1_1482 3.6 15.0 0.0 IT93K-503-1
SLA 9 25 1_0051 - 1_0048 4.9 19.7 13.5 CB46
Conductance high VPD 9 52 1_0425 - 1_1337 2.6 11.5 0.0 IT93K-503-1
22. Vapor Pressure Deficit (VPD, in kPa)
Transpirationrate(gcm-2h-1)
0.0 2.0 4.0
0.0
1.0
A – Insensitive to VPD – High rate at low VPD
B – Sensitive to VPD – High rate at low VPD
C – Sensitive to VPD – Low rate at low VPD
D – Insensitive to VPD – Low rate at low/high VPD
Main types of Tr response to VPD
Water use
difference
24. Marksim weather can be used to test trait effects
Can we use data from weather generator??
25. -77 0 +9
Pod yield differences between rainfed and irrigated conditions
• Drought affected countries for peanut: Senegal, Mali,
Niger, Burkina + Few spots in Ivory Coast
• Genotypes developed for WCA region can’t be the same
for the entire region
26. -33 0 +1
15-30% yield decrease, especially at high latitudes
% yield decrease for not having
transpiration sensitive to high VPD:
27. -26 0
20% yield decrease almost everywhere
% yield decrease for having
shorter crop duration genotype
29. Training on drought phenotyping
Long term training
Few of the trainees:
Ruth Wangari (Chickpea RIL)
Abalo Hodo TOSSIM (Groundnut CSSL)
Omar Halilou (Groundnut) – Crop modeling
Nouhoun Belko (Cowpea) – Trait mapping – Crop
modeling
Jaumer Ricaurte (Bean) – Trait mapping – Crop
modeling
Training
30. In Summary / “products”:
An approach to drought
QTL for several water use traits in different crops
Generation of scenarios / probability maps in the
“production stage” for peanut, chickpea, soybean.
Trainees (Oumaru, Belko, Ruth, Jaumer, …) on both eco-
physiology of drought adaptation and modeling
Editor's Notes
The overall structure of the project: Three aspects of plant adaptation to drought are looked at.Modelling is the “integrater” of these different components
Experiments have continued in Year 3 at ICRISAT-Niamey, ICRISAT-Patancheru, and CIAT
Last year we tested bean genotypes under a factorial of water regimes (WW and WS) and of nitrogen treatments (high N and low N), and found that bean suffered the effect of low N more than it suffered drought.This year, we tested the same thing in cowpea.Cowpea also suffers the effect of low N conditions, although less than beanThen cowpea suffers further the effect of water stress when grown in low N conditions
In previous presentations we have shown that the leaf area vary between genotypes and could impact the overall plant water budget, leading to possible effect on plant adaptation to drought.Leaf area development can be predicted from exponential functions of the number of nodes on the main stemThe graph shows variations in the coefficients, indicating that leaf area develops larger/quicker in certain genotypes.We can then use these coeficients to test possible effects of changing such coefficient on yield
We also measured these exponential function coefficients in different chickpea genotypes.Here also we have quite a large range of genetic variationThe graph gives an example of two contrasting genotypes
Segregation in a RIL population of cowpea for plant transpiration and conductivity
As expected, the leaf area explains about 2/3 of the variations in total transpiration. The residual transpiration variation (not explained by the leaf area), is then explained by the conductance under high VPDNext step is then to map QTL for these 2 traits
QTL analysis was done by Phil Roberts and Tim Close’s team at UC Riverside6 very interesting QTL were identified for either leaf area or leaf conductanceVery exciting is the fact that these QTLs are contributed by different parents
Alleles contributing to either higher leaf area come mostly from CB46Alleles contributing to either higher leaf conductancecome mostly from IT93K-503-1Since transpiration is contributed both by LA and conductance, it should be possible to select extreme “water use phenotypes” by choosing those either excluding, or including, all the alleles contributing to higher water use (eg LA alleles from CB46 and Leaf conductance alleles from IT93K-503-1).
The graph indicates the percentage decrease in yield due to drought (ratio of rainfed yield/irrigated yield)The blue strip in the northern part (plus a spot in Ivory Coast) is really where efforts on drought need to be made.It means also that the genotypes that are developed for that region can’t be the same everywhere
The top graph shows the effect on yield (%) in case the standard genotype does not have the capacity to restrict transpiration when the VPD is high.The bottom graph explore the validity of the statement that we need to breed short duration peanut. Here we modeled the effect of reducing the peanut crop cycle by about 10 days. Clearly, reducing the crop cycle by about 10 days leads to yield reduction of about 20%, even in the driest places.
The top graph shows the effect on yield (%) in case the standard genotype does not have the capacity to restrict transpiration when the VPD is high.The bottom graph explore the validity of the statement that we need to breed short duration peanut. Here we modeled the effect of reducing the peanut crop cycle by about 10 days. Clearly, reducing the crop cycle by about 10 days leads to yield reduction of about 20%, even in the driest places.