grm 2011: rice research initiative progress report

GCP-GRM

September 21-25, Hyderabad

Rice Challenge Initiative &

Cross cutting issues derived from parallel Rice sessions

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

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

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

Project target areas Sudano-Guinean savannah

Of Mali, Burkina Faso & Nigeria

Badeggi

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)

- 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)

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

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

- 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

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

• 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

IR64 x B6144

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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

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

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/

http://www.africarice.org/rice-challenge/



Cross cutting issues and links with other projects

derived from parallel Rice sessions

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

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

• 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

• 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

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

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

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

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

• 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

grm 2011: rice research initiative progress report

Technology

africa rice f3

drought tolerance field

rice breeding

ascommon parent f3 populations

water pipelines

phenotyping ongoing

valley fringe nigeria

dry season weather