1. GCP-GRM
September 21-25, Hyderabad
Rice Challenge Initiative
&
Cross cutting issues
derived from parallel Rice sessions

2. Improving rice productivity
in lowland ecosystems
of Burkina Faso, Mali and Nigeria
through
Marker Assisted Recurrent Selection
for drought tolerance
and yield potential
NCRI
Rice Challenge Initiative

3. Objectives
• Develop drought tolerant rice cultivars, with
medium to high yields in normal years for the
rainfed lowland ecosystems of Sub-Saharan
Africa
• Build capacity for rice breeding and introduce
new tools and new breeding approaches in
the breeding programs of the target NARS
and AfricaRice

4. WP1- Consolidating the knowledge base
• Characterization of rainfed lowland environment
• Designing Ideotype for TPE
WP2- Phenotyping
• Drought tolerance
• MARS populations,
• Genetic stocks
developed during GCP
phase 1
• Yield & other traits under
various levels of
environment control
WP3- Breeding
• Developing breeding
populations
• Genotyping MARS
populations
• QTL analysis
• Building ideo-genotype
WP4- Capacity &
Community building
• Developing the rice
drought breeding
community of
practice for West
Africa
• Capacity building
(PhD student and
short training on
specific topics)
WP5- Project and information management
• Data management : drought tolerance, yield & other traits
• Information management
Project organisation

5. Project target areas
Sudano-Guinean savannah
Of
Mali, Burkina Faso & Nigeria
Badeggi

6. Sudanean and
Guinean savannah
Inventory of rainfed
lowlands
Regional map of
drought profile (TPE)
Selection of
representative sites
IVC-DB on RLLs
Satellite images
Farmers survey
SARRAH model
adapted to RLL rice
New water balance
model for RLLs
Field experiments
contrasting cultivars
Crop growth
model SARRAH
SARRAH model
validated
Ideotypes fitting
to TPE
Agro-meteo DB
Simulation
Target traits for
breeding for DT
Consolidating the knowledge on rainfed lowlands (RLLs)
Classification
(Physical data)

7. - Identified/selection of experimental sites
- Installation of weather stations
- Analysis of soil hydraulic characteristics
- Establishment of Irrigation scheme & list
of equipments need
- Wells digging & reservoir installation
- Installation of water pipelines, ....
WP2-1: development of phenotyping facilities for field
evaluation of yield potential and drought tolerance
Longorola station
(Mali)
Bonfora station
(Burkina)
Badeggi station
(Nigeria)

8. A pilot study for the feasibility of a rainout shelter was done at
AfricaRice
WP2-2: Facility for evaluation of drought tolerance
under controlled conditions
• Installation of rain out
shelter almost achieved
• Blank test of the facility
and of secondary traits
measurement
is expected to start in early
October

9. WP2-3: Methodological pre-studies for
phenotyping for drought tolerance
• Adjustment of field drought intensity (Ibadan)
– Three intensities tested, in a trial using parental
lines of MARS populations
– Mild stress lead to 46% yield reduction
– Varieties x stress intensity Interaction
• Adjustment of methods for indirect
measurement of drought tolerance
– Cotonou, rainout shelter: under achievement
– Montpellier, PhenoArch: “Queue” for access to
this precision phenotyping facility

10. - Weather & soil water
- Yield components
- Traits for indirect selection
- Morphogenetic responses
- Canopy Temp / transpiration
- Fluorometric diagnosis
Drought tolerance
(rainout shelter )
220 F3:5 lines
+
10 check varieties
Yield potential
(Rainfed lowland , WS)
- Weather & soil water status
- Yield and yield components
- Other traits of interest
- Plant architecture & phenology
- Leaf rolling and senescence
- diseases, grain quality, …
WP2.4: phenotyping
Drought tolerance
(Field, dry season)
- Weather, soil water status
-Yield & yield components
- 6 experimental sites
Elite donor A x Elite donor B
SSD
Bulk
.
.
F3
.
F3:5

11. WP2.4:phenotyping
• Ongoing : first MARS pop. for yield potential ongoing
– Plant material: 220 F3:5 lines of the IR64 x B6144
– Sites and ecology
• Burkina (Banfora): valley fringe and Valley Bottom
• Mali (Longorola) : valley fringe
• Nigeria (Badeggi): valley fringe & Irrigated
• Nigeria (Ibadan): valley fringe & Irrigated
– Experimental design and field management
• Alpha lattice design with two replications with a plot size of 3m x
3 rows
• A complete protocol was written, translated and shared with
partners
– Filed book for data collection
• Crop: plant height, days to flowering, lodging , yield
• Environment: weather and soil water status
• Expected for early 2012 : drought tolerance
– Field trials : 6 sites,
– Rainout shelter trial: AfricaRice

12. • Selection of parents
– Six local/regional elite lines
proposed by project partners
– One “mega variety” (IR64), used as
common parent
• F3 populations evaluated for
general adaptability in 2010 WS
– One F3 pop. by each NARS partner
– Three F3 pop. by Africa Rice
• F3:4 populations seed increased
in dry season (Ibadan)
• One population selected to
undergo phenotyping
• Leaves of F3:4 lines collected for
genotyping
WP3-1: Development of MARS populations

13. IR64 x B6144
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12
IR64 x WAB638-1
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12
IR64 x Kogoni91-1
WP3-1: SNPs polymorphism survey
on MARS populations parental lines
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5
Heterogeneous coverage

14. WP4: Rice drought molecular biology and
breeding community of practice for West Africa
• Participation to workshops
- GCP-IBP, Data analysis, Spain
- Management of agricultural research
stations
- GCP-IBP, Data Management, Ibadan,
- GCP-IBP, QTL detection & breeding
strategy course, Wageningen
• Training organized at AfricaRice for 3
technicians (Nigeria, Mali & Burkina)
– Labs techniques applications to plant
breeding,
– hybridization and field data recording
• Drought phenotyping workshop
• Recruitment of PhD student
• Information & technology exchange
between and within NARS

15. WP5: Project and information management
• Data management
– Establishment of nomenclature and standards for
germplasm and traits
– Entering germplasm list (parental lines, F1, F2 &
F3) in the data base
– Field books created and transmitted to partners
for data recording
• Information management
– http://www.africarice.org/rice-challenge/

16. Cross cutting issues and links with
other projects
derived from parallel Rice sessions

17. Data management and data sharing
• Dada management
– Rice_CI is pioneering the development of a “local” (Africa) rice
database, under IPB format, compatible with IRIS developed,
implemented and curetted by IRRI.
– Rice_CI will help NARS partners to develop their own “local” database,
compatible with the one of AfaricaRice.
– Field book and hand-held should include possibility of hand writing
• Data sharing
– developing local database for major players and Communities of
practices
– Mekong region, India, African NARS for projects outside Rice_CI
• Ontology tools
– Some 220 traits are already documented by IRRI team
– System ready for receiving new traits
– It is time to test the system with users : Rice_CI, other volunteers

18. New genetic stocks, MAGICs
• Asia: Combodia (CARDI), Indonesia (CRR-Java) Vistnam (CRRI), Philippines (PhilRice)
• Africa: Senegal (AfricaRice), Tanzania (Dakawa Research Centre)
• Open for new volunteer partners

19. • Rice NAM population
– IR64 as common parent
– 20 indica & japonica donors
• Current status
– 10 crosses: F7-RIL
– 10+ crosses: F4-RIL
• Issues : population of about 4000
lines
– How to phenotype?
• GRiSP phenotyping platforms &
network
• Extraction of representative panel
– How to genotype?
• Low density sequence based
genotyping
• Genotype inference
– How to connect with breeding
activities?
• One by one phenotyping
New genetic stock, NAM

20. • Several association panels available
– sativa panel (Cornell Univ.)
• 413 accessions
• 44000 SNP available & soon 1M_SNP
– Group specific panels (Cirad, IRRI,...)
• 200-250 accessions for each panel (indica,
temp. japonica, trop. japonica, Aus)
• Large amount of phenotypic data , including
drought tolerance, accumulate
• Waiting for the 1M_SNP chip
• Issues
– Complementarily between association
panels and other genetic stocks
– How to connect with breeding activity ?
New genetic stocks, association panels

21. Phenotyping
• Phenotyping root system
– Several phenotyping methodologies now available for rice
– Still some need for confirming relationship with field
behaviour & with yield advantage under drought
– Infrared thermography a synthetic measurement of root
development and water-uptake ?
– Euroot: “delineate a root system ideotype in terms of
architecture, H20, N & P uptake and signalling processes,
including beneficial interactions with micro-organisms”
• Drought phenotyping facilities: several facilities
(including rainout shelters) developed or under
development in Asia (India, Mekong region) and Africa
• Time for harmonising drought phenotyping protocols

22. Breeding for drought tolerance
• QTLs with large effects
– Effect of QTLs, first detected in Vandana x Way Rarem,
confirmed
– QTLs transferred in other elite background
– Issue
• Evaluation in Africa
• Integration into the MARS process of Rice_CI
• MARS
– IRRI team has developed 2 MARS populations
– First QTL analysis & recombination cycle in 2011 WS
– Issue : sharing the experience with Rice_Ci partners

23. GIS for identification of drought prone area
• Mekong region experience
– 7 sites identified in each of the 3 countries
– 10 lines evaluated across the 7x3 sites
• GIS for establishing drought profile
– Mekong region experience
– International databases on drought profiles
– Issue: how to take advantage of existing
experiences to accelerate the implementation of
WP1 in Rice_CI

24. Communities of practice
• What would motivate you to be active
contributing member of your CoP?
– Knowledge sharing
– Same problem and sense of urgency to make impact
– Helping the community
• What might motivate others to become actively
involved?
– Getting assistance
• What will be the important component of your
CoP?
– Having a leader
– Giving & sharing things

25. • Mekong region CoP success –story
– Catalyser: leadership & Rockefeller Foundation financial
support
– Driving force: molecular breeding
– Asset: sharing the same culture and the “love” of rice !
• IRRI-India experience
– Catalyser : IRRI leadership
– Driving force : development of drought tolerant rice varieties
• Africa Cop
– Expression of interest
– But barriers: language (French/English), access to web
– Driving force: to be identified
Communities of practice