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CIAT Agrobiodiversity Teams Driving discovery, development and delivery for an Eco-Efficient Agriculture Annual Program Review 2011 Nairobi, Kenya 10 May 2011. Joe Tohme. Agrobiodiversity Teams. Research Advances on genetic resources GRiSP : a successful start

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Joe tohme

CIAT Agrobiodiversity Teams

Driving discovery, development and delivery for an Eco-Efficient Agriculture

Annual Program Review 2011

Nairobi, Kenya10 May2011

Joe Tohme

Agrobiodiversity teams
Agrobiodiversity Teams

  • Research Advances on genetic resources

  • GRiSP: a successful start

  • Research Areas of Emphasis in rice and biotechnology

  • Challenges and outlook for 2012

Joe tohme

Putative common bean domestication (2000 ybp)

Putative lima bean domestication, gene pool MI (1300 ybp)

Putative lima bean domestication, gene pool AI (5600 ybp)

Common bean domestication (4000 ybp)

cpDNA gene pools

Wild MI

Domesticated MI

Wild AI

Domesticated AI

Research Highlight: Genetic Resources

New Insights on Origins of Lima bean

Towards a better definition of the conservation targets

Crop Science 50 (5): 1773-1787 [2010]

Joe tohme

Acquisition of relevant bean germplasm by comparing potential distribution as revealed by herbarium studies with accessions existing ex situ

Explorations in western Mexico are likely to be relevant and rewarding

Collaboration between GRU, DAPA and the Global Crop Trust

Gap analysis published in PLoSONE 5 (10): 1-18 [2010]

Joe tohme
Continuous improvement of seed production, distribution and conservation:Flowering and seed setting of Phaseoluscostaricensis

Flowering and seed setting of Phaseoluscostaricensisin Tenerife, at 2400 masl, high up above Palmira in the Central Cordillera

All attempts to multiply this species before, in Palmira or in Popayan, have failed, while the GRU got success from the first planting

Joe tohme
GRU Continuous improvement of seed production, distribution and conservation:Diseasesindexingstatus theManihotcollectionat CIAT

Outcome: Different materials of Manihot distributed to date: 6,110 (or 91%)

Grisp a successful start
GRiSP: A Successful Start

  • Well integrated workplan between IRRI, AfricaRice, CIAT, IRD, CIRAD and JIRCAS

  • WebEx PMT conference call every 3 weeks

  • A major collaboration with the Beijing Genomics Institute (BGI) established

  • Workshops and Grants initiated

Grisp new initiatives
GRiSP New Initiatives

  • GRiSP

    • New Partnerships for Global Networking

    • New Frontiers Research 2011 for discovery/basic research

    • PhD Scholarships

Joe tohme

IRG Traditional Germplasm

100,000 cultivated accessions

GRiSP-Beijing Genomics Institute (BGI) Collaboration

Unique major sequencing effort in plants

Sequencing 10,000 accessions fully funded by BGI

BGI de novo sequencing

200 @ 50X depth

1000 @ 10-20X depth

rest @ 5-10X depth

Iterative sampling

Start @

5X depth

10,000 GeneBank accessions1

Cultivated + close wild relatives

1Include publicly accessible germplasmfrom IRRI, AfricaRice, CIAT and regional collections

10,000 genomes

April 2011

Sept 2012

May 2011

>3000 DNA to BGI

Sept 2011

Sequence data from BGI

Nov 2011

Bioinformatics(prelimin analysis)

March 2012?

Sequence data

July 2012


Second batch of DNA (>5,000) to BGI

Grisp evaluation decision tree
GRiSP evaluation decision tree

Is the activity research or delivery?

Regular reviews



Impact pathway analysis

Is the theory of change clear?




Are the milestones being met?

Has the research been reoriented?

Targeted review




Progress monitoring

Is the research product yet trialable?



Is it established that the product meets user demands?

Product evaluation



Average treatment effect assessment

Is the contribution to on farm performance known?



Is the research product widely/rapidly adopted?

Adoption constraint analysis



Aggregate adoption analysis

Is the adoption documented?



Ex post impact assessment

Joe tohme

GRiSP: Towards a global phenotypingstrategy

  • Association genetics using common core collections and special genetic stocks

    • Phenotype a common set of 2000 lines that are finely genotyped (1 SNP/500bp)

    • Functional inference with specialized genetic populations

    • Use breeding materials and transgenes to validate gene function prediction

  • Validate relationship between phenotypes determined by HTP and conventional methods

    • Identify HTP phenotyping applicable to breeding; establish genetic correlation, proxy for agronomic traits

    • Genetic stocks to determine the “ground truth” of HTP phenotyping

  • 3. Establish phenotyping hubs with general and specialized phenotyping capabilities and functions

    • Hubs for a broad set of phenotypes

    • Hubs for transgenic materials (could be 2-3 sites)

    • Centers and labs for evaluating conditional traits (e.g. stress tolerance) that require specialised methods

Grisp 2011 calendar
GRiSP 2011 Calendar

  • May: allocate GRiSP scholarships; call for new frontiers research proposals

  • June: final budget allocation for 2011

  • June 6-9: Africa mechanization workshop, Senegal (AfricaRice)

  • Aug 15-18: W-C Asia workshop, Iran (IRRI)

  • Aug 22-26: Yield potential workshop and annual review LA, Cali (CIAT)

  • Sep 12-15: Annual review Africa, Cotonou (AfricaRice)

  • Sep 19-23: Annual review Asia & GRiSP Annual Science Forum, Los Baños (IRRI)

  • Oct 10: GRiSP annual report and business plan for next year completed for approval by BOT & OC (virtual)

  • Oct 15: submit GRiSP annual report and budget proposal to Consortium

  • Nov 15: Expected FC approval of 2012 budget proposal

  • Dec 15: annual staff evaluation finished, budget for next year allocated to research teams

Joe tohme

CIAT strength globally Product development

High productivity rice genotypes for irrigated and upland systems


CIAT rice program contributed at least 60% of the 400 varieties released by national programs in Latin America

The Rice team is currently working on a second genetics revolution using biotechnology

Joe tohme

Phenotyping globally

Genetics CIAT/IRD


Molecular biology

The team





Genetic transformation

J. Rane


drought tolerance

G. Mosquera



Katherine Loaiza

Amylose, Milling quality, Nutrient content

Breeding CIAT/FLAR

Breeding –CIAT/Cirad

M. Lorieux

iBridges, NAMs, CSSLs,T-DNA/Tos17 mutants

M. Lorieux

Drought tolerance

Panicle architecture

Yield components

M. Lorieux


M. Lorieux

Grain aroma

S Ayling

Sequence analysis,

SNP identification

M. Ishitani

Abiotic stresses

G. Mosquera

Identification of pathogen population

B. Dedicova


Transgenic Events

Abiotic stresses;

C. Martinez

E. Torres

Inter-generic crosses


E. Torres

Yield potential

Stay green

C. Martinez

E. Torres


C. Martinez

E. Torres

Zn and Fe enrichment

Milling and cooking quality

C. Grenier

Synthetic populations with large genetic base

C. Grenier

WUE, NUE, tolerance to drought, acid soils and Al toxicity

Where yield increase will come from in latin america
Where yield increase will come from in Latin America? globally

CIAT Strategies

  • An agronomical revolution

  • Define breeding objectives in the context of Eco-Efficient Agriculture and climate changes

  • Target specific traits breeding

    • Quality- nutrition / biofortification

    • Blast, sheath blight, virus resistance

    • Cold tolerance, stay green, large panicle …

  • Exploring natural genetic variation from wild species

  • Marker assisted selection for accelerating breeding (SNP)

  • Transgenics for water and nitrogen use efficiency

  • Hybrids (initiated in 2010)

Rice priority traits multi institutional approaches
Rice Priority Traits globally Multi-institutional Approaches

Abiotic, Biotic, Quality and Yield

Joe tohme

The globally O. sativa x O. glaberrima sterility barrierhampers the use of interspecific lines in breeding

Sterility loci

  • O. sativa x O. glaberrimaBC3 lines are fertile, but produce sterile hybrids with O.sativa

  • Phenomenon also found in NERICAs

  • Hampers full use of CSSLs for breeding

Opening the african rice diversity to breeders
Opening globally the African rice diversity to breeders

  • Africa rice (O. glaberrima) has many useful genes (Nematodes, Striga, blast, viruses, drought, NUE, etc.)

  • The Asian x African rice reproductive barrier hampers full use of Africa rice diversity in breeding programs

  •  Need for interspecific bridges = iBridges

  • We mapped the main sterility gene, S1

  • We use the S1 markers to derive iBridges

  • iBridges = lines with 20-25% of O. glaberrima genes

  • iBridges x O. sativa hybrids are fertile  direct use in breeding schemes

  • From 25 donor accessions  broad access to the diversity available in the African species



























CG14 38E01













A CIAT – IRD project supported by Generation, with many partners (AfricaRice – PhilRice - NARs from Asia, Africa and Latin America)

Joe tohme
Upland Drought Evaluation at CIAT globally Palmira (Rainout shelter) and Santa Rosa (natural condition)Transgenic and Non transgenic

Transgenic CIAT-JIRCAS

  • Promoter-gene combination

    • 4 promoters + 13 genes

  • Transgenic events

    • Curinga, Japonica upland

    • NERICA, Upland from JIRCAS

    • IR64, Indica lowland from IRRI

  • Growth stages

    • Reproductive, Vegetative, Seedling

  • Automation/IR & Visible Images

    • 500 images/40 minutes

At Palmira

Non transgenic




Non transgenic CIAT-CIRAD

  • 400 lines(4 population of 100 S1 lines) + 6 checks

At Santa Rosa (Dry season)

Abiotic, Biotic, Quality and Yield

Joe tohme

CIAT Research on Nitrogen Use Efficiency (NUE) globally

  • Genetic Improvement for NUE

  • Transgenic approach

  • Non-transgenic approach

  • Precise phenotyping for trait discovery

Unique position for transgenic research

  • Water Management

  • Reduce production cost

  • Improve fertilizer use

  • Reduce CH4 emission

  • Gas Emission Analysis

  • Impact assessment

  • Translation to CO2 credit

A new research model for eco-efficient agriculture

Ample experience in farmer’s field in Latin America

Nue field preparation over 3 years
NUE Field Preparation over 3 years globally

Creation of N use efficiency platform

  • N omission plots

    • By growing successive crops of Maize without N fertilizer over 2 years

    • N level brought down by 50%

    • 50% reduction in grain yield of popular variety Fedearroz-50

  • Evaluation of candidate genotypes

    • Local check and transgenic events that were proved to be superior in pot experiment

    • CSSL lines available at CIAT

Nitrogen use efficiency testing at ciat

Lowland Rice NUE evaluation globally

1.5 ha of area- expandable based on necessity

N-omission plots

(> 200 lines, 4 Reps)

50% and 100%N Treatments

Screening protocols to differentiate tolerant and intolerant lines

Nitrogen Use Efficiency testing at CIAT

  • Traits

  • N uptake

  • N utilization

  • Leaf chlorosis

  • Biomass

  • Yield and yield components

Abiotic, Biotic, Quality and Yield

Nue field testing methods
NUE Field Testing Methods globally

  • Field design

    • Randomized block design for each of the 3 treatments

      • No N; 50% N(75kg/ha) 100%N(150Kg/ha)

    • Each N treatment as a separate growth environment for GXE interaction

  • Fertilizer application

    • 3 splits

      • At the time of transplanting(40%) along with P2O5 and K2O, Zn

      • 30 days after sowing/ 2 days after transplanting

      • 54 days after sowing

      • 64 days after sowing

    • Dry surface of the soil after regulating irrigation and draining down excess surface water

    • Known amount of Urea was dissolved in measured quantity of water and spread in between rows by using spray pump without nozzle

Joe tohme

JICA/JSPS Program globally

Posting of S & T Researchers (2011-2012)

“Development of NUE technology to reduce greenhouse gas effect in agriculture system”

Impact Assessment Precise Phenotyping

Gas emission analysis Imaging analysis

Dr. Takahiro Koide Drs. Kenji Omasa, Yutaka Urano, Fumiki Hosoi

N20, CO2, methane to measure Automatic measurement of fluorescence,

environmental impact canopy team to select best performer

Joe tohme

Gas Emission Analysis for globally

Impact Assessment

  • Participated Institutes in Colombia

  • Fedearroz

  • Cenicaña

  • Local University

  • Dr. Takahiro Koide, JICA Expert

  • Measurement of N20, CO2, methane in paddy fields at CIAT

Joe tohme

Gas emission chamber in the field at CIAT in 2011 globally

Whole plants covered

Able to catch ebullition

  • CO2 budget

  • GHG emission via vascular system

Rice hybrid breeding at ciat
Rice Hybrid Breeding at CIAT globally

Hybrid rice technology is a new approach to contribute to increase rice productivity in Latin America

Currently the CIAT Rice Program is working in hybrid rice using two strategies:

Conventional trough the Hybrid Rice Development Consortium (HRDC) with IRRI and GRiSP. to produce highly heterotic hybrids. new parental lines CMS and TGMS and transferring alogamy traits from wild species

New male sterility system working with Yale University and University of Rhode Island to understand and monoecius traits present in a rice related genus

Conventional hybrid breeding
Conventional Hybrid Breeding globally


To develop experimental hybrids with high heterosis resistance to diseases and good grain quality for the tropical conditions in LAC;

To develop new CMS pairs using the system WA (wild abortive) with good combinatory ability and adaptation to the tropics in LAC;

To develop new TGMS (Termosensitive male sterility) lines with good combinatory ability and adaptation to the tropics in LAC;

To develop new restores for the CMS system;

To establish pilot test of seed production under field conditions using direct seeding

Joe tohme

Conventional Hybrid Breeding globally

Some results

A CMS pairs with excellent outcrossing capacity, high milling yield (total and whole grain), high amilose content, tolerance to the RHBV and tolerance to Tagosodeoryzicoulous have been identified

19 hybrids were identified in preliminary testing with good potential to be tested in advanced yield trials

A total of 16 lines are under conversion to produce new AB pairs with CIAT material

In 2010, a total of 384 new testcrosses in field conditions were produced, these are under preliminary testing now

Currently three CMS pairs are under multiplication with the objective of increasing the amount of seed to establish experimental plots of seed production

A new system for rice hybrid hybrid technologies for cosexual cereals
A new system for rice hybrid? globally Hybrid Technologies for Cosexual Cereals


Breeding → mapping & wide crosses

Genetic → SD orthologs

Molecular → synthetic lethality

Yale, U. Rhode Island, CIAT. BREAD-NSF

A new system for rice hybrid hybrid technologies for cosexual cereals1
A new system for rice hybrid? globally Hybrid Technologies for Cosexual Cereals

Results from the inter genus crosses

The Luziola genus and the Zizaniaare the two monoecius genus in the Oryzaetribe.

Our objective was to produce a mapping populations between Oryzaand Luziola

Using conventional hand pollination procedures and embryo rescue, we were able obtain F1 hybrids. These produced panicles with perfect florets and secondary panicles with female florets

Because of complete sterility, a procedure to produce callus and plantlets was establish

Currently we are working to produce allopolyoid plants

Joe tohme

Operational Challenges globally

  • Staffing

    • Virology position advertised

    • Programs leaderships over stretched due to the CRP

    • Staff retention of newly recruited staff a major concern (Issues: spouse employment and offers from top institutions in the US and UK)

  • Mega Programs (CRP)

    • Big transaction cost – affecting fund raising

    • Legumes CRP requires further work

Joe tohme

Research Challenges globally

  • How the new sequencing tools will change breeding/transgenicstrategies to develop better – superior genotypes?

    • How can we bridge the gap between sequences data generation and analysis?

    • What kind of phenotyping platforms we need to put in place?

    • How will information be managed and distributed?

Joe tohme

Areas for globally Emphasis in 2012

  • Calibration of the breeding objectives in context of climate change

  • Evaluate how the sequencing data will change breeding – transgenicsstrategies

  • Biotechnology- Genetic Resources Platforms: Completion of Phase I (Strengthening CIAT internal capacities) and starting Phase II of linking with LAC institutions